question

2D DIGE

answer

Difference gel electrophresis
Samples are dyed different colours, mixed, and separated by 2D gel electrophoresis. Determines relative abundance in each sample, and identifies protein with significant differences.

question

2D gel electrophoresis

answer

Proteins are separated in one direction based on charge, and the second based on size. A tube with a pH gradient; proteins are focused to their isoelectric point, and the tube is placed on top of an SDS-PAGE gel, and proteins are separated by size. Proteins are stained with dyes and quantified.

question

3T3 cells

answer

An immortalized, but not transformed mouse cell line. Indefinite life span, but will not form tumours in animals.

question

3T3 transformation assay

answer

Isolate DNA from cancer cells, fragment DNA into small pieces. Transfect DNA into 3T3 cells, each cell takes up a different fragment. Grow cells and identify foci, groups of cells growing in clumps. Isolate the human DNA fragment, with human repetitive DNA.
1. Transfection of human bladder carcinoma DNA identified as a sequence that was identical to H-ras oncogene from Harvey rat sarcoma virus.
2. Transfection of DAN from normal human cells transformed by treatment with a chemical carinogen identified as a sequence related to the Ki-ras oncogene from Kirsten rat sarcoma retrovirus.

question

19S cap

answer

A component of a proteasome. Controls entrance of unfolded ubiquinated proteins into the interior of the proteasome.

question

20S core particle

answer

A component of a proteasome. Four rings, each with seven subunits. Consists of ? subunits and ? subunits.

question

454 technology

answer

A form of next generation sequencing. Reads are about 300 - 500 nucleotides, but one sequencing reaction can produce millions of reads. Reads one gigabase (1/3 of the human genome) in a single day. It is much cheaper than Sanger sequencing: $0.02/1000 bases.
1. Generation of a single-stranded template DNA libary. DNA is fragmented and denatured, and adaptors are added to each end
2. EMulsion-based clonal amplification of the library. Each DNA fragment is bound to a bead, encapsulated in emulsion. DNA is amplified by PCR within the micelle, beads are then loaded into a picotiter plate
3. Pyrosequencing
4. Data is analyzed using bioinformatics tools. The order of nucleotides provided and the amount of light emitted by pryosequencing gives the sequence.
Reaction mixture: DNA polymerase, nucleotides, luciferase, apyrase, ATP sulfurylase, luciferin, and APS

question

1000 Genomes Project

answer

Their goal is to sequence at least 2500 genomes from people representing ancestral groups from around the world.

question

? subunit

answer

A component of the 20S core particle of a proteasome. Forms the entrance to the inner chamber.

question

? subunit

answer

A component of the 20S core particle of a proteasome. Possessses proteolytic activity.

question

abl

answer

A viral oncogene found in Abelson murine leukemia virus that affects mice. Produces a tyrosine-specific protein kinase.

question

Acetabularia

answer

A genus of green algae with very large cpDNA, about 2000 kb.

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Activator

answer

Binds to enhancer sequences and regulates transcription. Inducible expression. Provides regulated changes in gene expression. Includes HSF1 and steroid hormone receptors.

question

Adenomatous polyposis coli

answer

An inherited condition that often leads to colorectal cancer. Mutation in pACP protein that plays a role in regulating renewal of the lining or epithelium of the large intestine. Cells the produce finger-like projections of the intestinal epithelium remain undifferentiated; they produce polyps.

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Adenosine 5'-phosphosulfate (APS)

answer

ATP-sulfurylase converts PPi into ATP in the presence of APS during pryosequencing.

question

Adenosine deaminase (ADA)

answer

Usually breaks deoxyadenosine into deoxinosine. Overproduction of ADA has no toxic effects.

question

Adenosine deaminase-deficient severe combined immunodeficiency disease (ADA^-SCID)

answer

A disease which was first successfully treated using gene therapy in 1990. A rare autosomal disease of the immune system caused by a single gene defect. The gene is known, cloned, and characterized. In the absence of ADA, toxic levels of deoxyadenosine accumulate in T lymphocytes, killing them. There is no immune system, and even minor infections are fatal. Patients seldom live longer than a few years. Treatment is a bone marrow transplant from a matched donor, to replace lymphocytes.

question

Adenovirus

answer

A vector for gene therapy. Non-integrating DNA tumour virus. Provides transient gene expression. Viral replication can allow cell-to-cell transmission. Causes an immune response, and eventual removal by the host immune system. After a while it becomes more and more ineffective. Can be used to trigger suicide genes in cancer cells.

question

Adrenaline

answer

An endocrine peptide hormone derived from amino acids. Originates in the adrenal medulla. Targets heart muscles, causing increased pulse and blood pressure.

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Aequorea victoria

answer

A jellyfish in which GFP naturally occurs.

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Affymetrix

answer

A company which produces gene chips commercially.

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Agrobacterium tumefaciens

answer

A soil bacteria that causes crown gall disease in dicots. Plants produce tumours, and cells begin to synthesize opine, and arginine derivative. The opine is either nopaline or octopine. Opines are catabolized and used as energy sources for the bacteria. Infection is controlled by the Ti plasmid. Used to produce transgenic plants.

question

Agrobacterium tumefaciens-mediated transformation

answer

The most common procedure for producing transgenic plants, especially in dicots. A segment of DNA is transferred from the bacterium into plant cells.

question

aHSF1

answer

Anti-HSF1 antibody used for a ChIP.

question

Albert Knudson

answer

In 1971, proposed that retinoblastoma was caused by two loss-of-function mutations, one in each of two copies of a tumour suppressor gene. Knudson's two-hit hypothesis.

question

Allele-specific oligonucleotides

answer

Used to detect cystic fibrosis. Used as probes in Southern blotting to differentiate the wild-type codon and the deleted codon.

question

Alternate splicing

answer

Splicing an RNA transcript in different ways. A way of conomizing on genetic information; a single gene can encode many polypeptides. Example: troponin T has several forms from alternate splicing.

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AluI

answer

A restriction endonuclease found in Arthrobacter luteus. Cleaves AGCT, producing blunt ends.

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Amplification

answer

Production of clones of recombinant DNA molecules. One of the parental DNAs must be a cloning vector.

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Anchor markers

answer

STS markers mapped on genetic and physical maps. Anchors the physical map to the genetic map and vise versa.

question

Andrew Fire, Craig Mellow, and colleagues

answer

Discovered RNAi in 1998. Shared the Nobel Prize in Physiology or Medicine in 2006. Performed RNAi in C. elegans. Injected double-stranded RNA into C. elegans, and found that it silenced genes more effectively than either strand individually. This is evidence for a catalytic mechanism, not just stoichiometric interference. Coined the term RNA interference.

question

Angiogenesis

answer

When blood cells are induced to grow among malignant tumour cells. The tumour is nourished and can expand.

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Animal based system

answer

An alternate expression system for recombination protein production. Time consuming and expensive.

question

Anna Nicole Smith

answer

Died in 2007, leaving behind her daughter Dannielynn, and there was uncertainty about who her father was. A paternity test was performed, using Southern blotting of a mixture of VNTR probes.

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Annotation

answer

Making sense of the genome sequence. Assigning protein coding regions, non-coding regions, and regulatory regions to the genome sequence.

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Anopheles gambiae

answer

A mosquito, the host organism of Plasmodium falciparum. Has a sequenced genome.

question

aNS

answer

A non-specific antibody.

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Antennapedia

answer

A homeotic mutation in Drosophila, causing antennae to develop as legs. A homeotic transformation of a protein that regulates expression of genes controlling cell fate during developpment. Has a helix-turn-helix motif.

question

AP1

answer

A protein that consists of a dimer of fos and jun.

question

Apoptosis

answer

"Falling away"
Programmed cell death. Caspases attack proteins in the cell, chromatin becomes fragmented. The cell is usually engulfed by a phagocyte and destroyed. Cells that have potential to become cancerous often undergo apoptosis. The molecular and morphological process leading to controlled cellular self-destruction. Sculpts the developting embryo by removing transient structures, including formation of digits. All physiological cell death occurs by apoptosis.
1. Reduction in nuclear size, condensation of chromatin at nuclear periphery and detachment from surrounding cells.
2. Cell shrinkage, blebbing of cell membrane producing apoptotic bodies.
3. Apoptotic bodies phagocytosed by macrophages.

question

Apoptosome

answer

Cytochrome C bound to APF1 adaptor protein, and oligomerized. Activates caspase 9.

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Apyrase

answer

Degrades unincorporated nucleotides and ATP in pyrosequencing.

question

Arabidopsis biological resource centre (ABRC)

answer

At Ohio State UNiversity. Collets, preserves, reproduces, and distributes diverse and other stocks of Arabidopsis thaliana and related species. Resources are donated by research from around the world. Ships over 100,000 samples annually.

question

Arabidopsis thaliana

answer

Mouse ear cress
A plant model organism with a sequence genome; sequenced in 2000. There are detailed physical maps available for its genome. The mitochondrial genome is 366,924 bp, with 57 genes. The chloroplast genome is 154,478 bp, with 129 genes. Its genome is 119,186,494 bp with 28,152 genes, for a density of 4,200 bp/gene. There are about 1012 protein domains. Insertion sites have been mapped in hundreds of thousands of transgenic plants using reverse genetics with T-DNA. Seed stocks are available to researchers on request.

question

Argonaute

answer

Proteins in a RISC complex. Associates with dicer. Degrades the passenger strand.

question

Ataxia telangiectasia

answer

An inherited cancer syndrome, causing lymphoma. A mutation in ATM (11q22), the product of which functions in DNA repair, monitoring DNA damage.

question

ATP-sulfurylase

answer

Converts PPi into ATP in the presence of APS during pyrosequencing.

question

Avery

answer

Demonstrated that DNA is the genetic material in 1944.

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Bacterial artificial chromosomes (BACs)

answer

A cloning vector. Maximum insert size of 300 kb. Combines multiple cloning sites and selectable marker genes with the essential components of bacterial fertility factors.

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Bacterial expression cassette

answer

One of the cassettes of pcDNA3. Has a pUC origin for plasmid replication in E. coli. Ampicillin resistance for selection of bacateria containing the plasmid.

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BamHI

answer

A restriction endonuclease that produces 5' overhangs.

question

Barr body

answer

A condensed, darkly staining inactive X chromosome. Found in female mammal cells.

question

Basal transcription factors

answer

Transcription factors necessary for accurate initiation of transcription of eukaryotic genes. Binds to a basal promoter sequence in the promoter, and facilitates alignment of RNA polymerase II on the promoter of the template strand of DNA. Controls constitutive gene expression. Helps to assemble the pre-initiation complex. Includs NF1 and SP1.

question

Basal promoter element

answer

DNA sequence elements that bind to transcription factors. Basal factors bind and recruit and properly align RNA polymerase II on the template strand of the DNA. Help assemble the pre-initiation complex. Provides cell-type specific control of gene expression.

question

Basic HLH (bHLH)

answer

Proteins with helix-loop-helix motifs.

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BAX/BAK

answer

Pro-apoptotic. Induces apoptosis by forming channels in the mitochondrial outer membrane, allowing release of cytochrome C.

question

BCL-2

answer

Pro-survival. Inhibitits apoptosis by preventing BAX/BAK oligomerization.

question

Bcl-X

answer

A family of proteins that regulate the life or death decisions controlling apoptosis. The mRNA can be differentially spliced to produce anti-apoptotic Bcl-X_L or pro-apoptotic Bcl-X_S.

question

bcr-abl

answer

Produced by the translocation in CML patients. Tyrosine kinase activity is constitutively activated. Signals cause uncontrolled cell proliferation.

question

Benign

answer

When cells do not detach from a tumour or invade surrounding tissues. Most primary tumours are not life threatening.

question

BH3-only

answer

Pro-apoptotic proteins. Inhibit pro-survival BCL-2 proteins and some directly activate BAX/BAK.

question

Bhanu Chowdhary and colleagues

answer

Concluded that the evolution of mammalian chromosomes involved three classes of conserved synteny:
1. Conservation of entire chromosomes
2. Conservation of large segments of chromosomes
3. Joining of segments of different chromosomes to produce new synteny

question

Bicoid

answer

A protein responsible for development of the head and thorax of Drosophila. The mRNA is localized in the anterior end of the larva.

question

Bioinformatics

answer

Extracting information from nucleotide sequences. The gathering, manipulation, storage, retrieval, and classification of recorded biological information, usually DNA or protein sequences.

question

Bishop and Varmus

answer

Won the Nobel Prize in 1989. Found that a sequence in the chicken genome is homologous to RSV src gene. Found that homologous sequences were also found in the genomes of mammals.

question

Bladder cancer

answer

The fifth most common type of cancer.

question

BLAST search

answer

Basic Local Alignment Search Tool
Used to search GenBank for homologues of genes. Amino acid sequence alignments can identify proteins with related functions.

question

Bloom's syndrome

answer

An inherited cancer syndrome, causing solid tumours. A mutation in BLM (15q26.1), the product of which is DNA helicase, repairs double strand breaks.

question

Bluescript vector

answer

A plasmid cloning vector. A bacterial origin of replication. Small, 3 kb, allowing for large insertions. The selectable marker is lacZ, the gene for ?-galactosidase, which converts the colourless substrate Xgal into a blue product. The MCS is located within the plasmid lacZ gene. Insertion of foreign DNA leads to insertional inactivation. Colonies are selected by colour. Blue colonies contain no inserts; the lacZ is functional. White colonies contain the insert; the lacZ is non-functional.

question

Bombyx mori

answer

A silkworm. An economically important insect with a sequenced genome.

question

Bone and joint cancer

answer

Percent survival of 5 years is 66.6%.

question

Bradyrhizobium japonicum

answer

A soil bacteria capable of colonizing plant root nodules. The genome is 9,105,828 bp with 8,373 genes.

question

BRCA1

answer

Breast cancer 1
Early onset genes encodes a protein involved in DNA repair.

question

Breast cancer

answer

The third most common type of cancer. Percent survival of 5 years is 89.2%.

question

Bt

answer

An endotoxin found in Bacillus thuringiensis bacteria. Safe to mammals and plants, but toxic to the larvae of certain insects, including the European corn borer. Inserted into crop plants to make them resistant to insects.

question

Burkitt's lymphoma

answer

Reciprocal translocation between chromosome 8 and 14. Places the c-myc gene, under control of immunoglobulin gene enhancer, causing overproduction.

question

c-abl

answer

The proto-oncogene on the breakpoint of chromosome 9 in the Philadelphia chromosome. Encodes Abelson intracellular tyrosine kinase.

question

c-Fos

answer

A short-lived mRNA with multiple copies of AUUUA in its 3' UTR. A transcription factor expressed only in rapidly proliferating cells. Deletion of the 3' UTR can stabilize the transcription factor, leading to cancer.

question

c-myc

answer

Overproduced in Burkitt's lymphoma. Controls G1-S phase cycle transition.

question

c-src

answer

The proto-oncogene of src. An intracellular kinase that controls cell proliferation.

question

C5-methylcytosine

answer

Methylated cytosine.

question

CAAT box

answer

CCAAT
A basal promoter sequence. Binds CAAT binding protein transcription factors, such as NF1 and CTF.

question

Caenorhabditis elegans

answer

Roundworm
A see-through nematode. A model organism. Its genome was sequenced in 1998. There are detailed physical maps available for its genome. The mitochondrial genome is 13,794 bp, with 12 genes. The genome is 100,291,841 bp with 20,516 genes, for a density of 4,9000 bp/gene. Has 1090 cells. Cell fate is completely mapped. RNAi can be performed by microinjecting dsRNA, soaking them in media containing dsRNA, or fed bacteria synthesizing dsRNA. RNAi gave new insight into the function of over 400 genes. Used as a model system for the analysis of diseases of protein mis-folding. Used to screen for genetic and chemical modifiers of Huntington's disease.

question

Cancer

answer

A genetic disease. Arises when critical genes are mutated. Mutations alter biochemical processes causing unregulated cell proliferation. Mutations occur due to environmental facotrs, or can be inherited. Avoidable risk factors include tobacco, diet, infections, ionizing UV light, occupation, and pollution. Percent survival of 5 years is 66.1% for all cancers. There are 200,000 new cases of cancer in Canada each year, and 75,000 deats from cancer each year. 41% of women and 46% of men will develop cancer in their lifetimes. Over 50% of all new cancers are lung, prostate, breast, or colorectal cancer. Tumour formation, growth, and metastasis depend on accumulation of mutations in several genes. There are over 100 types of cancer, and abotu 400 cancer-related genes. DNA of cancer causing viruses encode oncogenes. Cancer can be induced by agents that cause mutations to DNA. Certain cancers can run in families. Certain leukemias and lymphomas have characteristic chromosomal alterations. Cancerous state is clonally inherited.

question

Cancer cells

answer

Unregulated cell division, impaired death. Loss of contact inhibition of growth, acquire anchorage-indepdendent growth. Form clumps in cultures, rather than films. Immortal; unlimited passage number in culture, by maintaining telomere length. Overexpress telomerase. Aneuploidy, genetic instability, a source of new mutations.

question

Cancer proteomics

answer

Large-scale, comprehensive study of protein abundance, modifications, and interacting partners in a particular cell. Differences in the proteome are responsible for cancer phenotype.

question

Carcinogens

answer

Agents that cause normal cells to irreversibly transform into cancer cells. Includes radiation, mutagenic chemicals, and certain viruses.

question

Carcinoma

answer

The third stage of colorectal cancer. Appears in patients aged 50 - 70.

question

Cas9 gene

answer

Encodes CRISPR-associated nucleases. Plasmids with Cas9 and the gene for specific sgRNA can be prepared and introduced into cells to direct cleavage of specific genome sequences. Double-stranded breaks are repaired by DNA repaid mechanisms.

question

Caspase

answer

Cysteinyl aspartate-specific proteinase
Proteolytic enzymes that remove small aprts of other proteins, inactivating them. Cysteine proteases responsible for the ordered dismantling of cellular structures during apoptosis. Cleave after aspartic acid (D) residues. Present in an inactive pro-form in healthy cells. Attack many types of protiens, including lamins and the cytoskeleton. Degrade specific proteins that lead to death of the cell. There are two protease subunits, large and small, a cleavage site, and a prodomain with a death fold. Includes ICE sub-family, and CED-3 sub-family. Includes effector and initiator caspases.

question

Caspase 9

answer

An inititator caspase activated by the apoptosome. Cleaves effector caspase 3, leading to apoptotic body formation.

question

CDK inhibitor (CDKI)

answer

Includes INK4 and p21.

question

cDNA

answer

Complementary DNA
Complementary to mRNA. Requires reverse transcriptase to synthesize. DNA molecules created from RNA remplates. The first strand of DNA is created by reverse transcriptase, complementary to the mRNA. Created using oligo(dT) primers that anneal to the poly(A) tail of the mRNA, or gene-specific primers, often annealing to non-coding regions near the poly(A) tail at the 3' end. Gene-specific primers are used for reverse transcriptase-PCR amplification of RNAs. Double stranded DNA molecules are synthesized usign ribonuclease H, DNA polymerase I, and DNA ligase.

question

cDNA library

answer

A genomic DNA library containing only cDNA. This ensures that only coding regions of genes are stored. This is used for organisms with large genomes, to reduce the amount of DNA that is stored. Has different genes, based on the expression of the part of the body from whcih the sample was taken, at the time that it was taken. cDNA is synthesized from mRNA using an oligo-dT primer and reverse transcriptase. Ribonuclease H removes RNA after cDNA synthesis, and a DNA-dependent DNA polymerase is used to synthesize ds cDNA, which is then introduced into bacteria.

question

CED-3 subfamily

answer

A family of caspases including effector and initiator caspases. Responsible for cell death. CED3 needs CED4 to function, and is inhibited by CED9. Has homology to human gene ICE.

question

Celera

answer

A private company established in 1998, lead by J. Craig Venter. Announced a plan to sequence the human genome in 3 years. Developed shotgun sequencing.

question

Cellular oncogene

answer

Cellular genes that have acquired mutations that when expressed promote unregulated cellular proliferation and survival. Encode onco-proteins that no longer resopnd to the normal restraints on cell proliferation and survival.

question

CentiMorgan (cM)

answer

The distance on a chromosome that yields a recombination frequency of 1%.

question

cftr

answer

The gene which causes cystic fibrosis. Localized to a 500 kb region on chromosome 7. CpG islands, exons conserved from other species, and cDNA libraries from sweat glands were used to map the region. Expressed only in epithelial cells of the lungs, pancreas, salivary glands, sweat glands, intestine, and reproductive tract. It is a large gene, 250 kb with 24 exons. It codes for CFTR protein. Over 900 mutations in this gene can cause cystic fibrosis, but 70% of mutants have the same 3 bp deletion, ?F508.

question

CFTR

answer

Cystic fibrosis transmembrane conductance regulator protein
Encoded by CFTR. A membrane channel protein through which ions pass. 1480 amino acids. Some evidence suggests CFTR has a role regulating lipid metabolism and transport. Mutant CFTR caused by a ?F508 mutation is non-functional, and is tagged by ubiquitin for degradation. As a result, salt accumulates in epithelial cells and mucous builds up on the surface of the cell.

question

Chain terminating nucleotides (ddNTP)

answer

2'3'-didoexyribonucleoside triphosphates
Chain terminators used in the Sanger sequencing protocol. Terminates DNA synthesis when incorporated because they have a 3'-H rather than 3'-OH. Labelled with different fluorescent dyes: ddATP is green, ddCTP is blue, ddGTP is black, and ddTTP is red.

question

Checkpoint

answer

A mechanism that halts progression of the cell cycle until a critical process such as DNA synthesis is completed, or until damaged DNA is repaired. Two types of proteins involved: cyclins and CDKs. Cyclin/CDK complexes cause cell cycle to advance. Includes START. Guards the genome from loss of genetic information from unreplicated DNA, DNA damage, chromosome breakage, missing or extra chromosomes from unattached chromosomes.

question

Chimera

answer

Animals that have a mixture of two types of cells; its own, and cells from the cultured potentially transfected ES cells. Breeding of chimeric mice may produce offspring which are transgenic.

question

Chimeric selectable marker genes

answer

Prokaryotic coding sequences flanked by eukaryotic regulatory sequences.

question

ChIP

answer

Can demonstrate regions of chromatin bound by specific transcription factors or bound by histones containing specific modifications.

question

ChIP-chip

answer

Hybridize fluorescently labeled PCR products to a DNA chip containing ordered arrays of chromosomal DNA.

question

ChIP-seq

answer

Sequenced all of the PCR products using next generation sequencing techniques.

question

Chhlamydomonas reinhardti

answer

A green algae. The chloroplast genome is 203,828 bp with 109 genes. It has linear mtDNA. There is one chloroplast per cell, which contains about 100 copies of the cpDNA.

question

Chloroplast DNA (cpDNA)

answer

The DNA of a plant plasmid. Typically 120 - 160 kb in size in higher plants, and 85 - 292 kb in algae. Genes include ribosomal RNA, transfer RNA, ribosomal proteins, polypeptide components of photosystems, enzymes, and chloroplast-specific RNA polymerase. More than 200 cpDNA molecules have been sequenced. The ribosomal RNA genes are usually in an inverted repeat.

question

Chromatin

answer

A mixture of DNA and protein that makes up chromosomes in eukaryotes. Its chemical characteristics differ along the length of the chromosome.

question

Chromatin remodeling

answer

Alteration of nucleosomes in preparation for transcription. Includes HAT and SWI/SNF.

question

Chromosomal gene address

answer

[chromosome number or X/Y][arm of the chromosome, p or q][band number].[sub-band number]["cen if close to the centromere, or "ter" if close to the terminus]

question

Chromosome jumping

answer

Used to speed up long chromosome walks, when the distance from the closest molecular marker to the gene of interest is large. Each jump can cover a distance over 100 kb. A molecular probe like an RFLP, VNTR, or STR is used as a starting point. The fragment is prepared by partial digestion with a restriction endonuclease, and it is circularized by DNA ligase.

question

Chromosome painting

answer

Used for comparative genome analysis. A variation of FISH in which chromosomes are "painted" different colours using DNA hybridization probes labelled with fluorescent dyes of different wavelengths. Different chromosome specific probes are labelled with differently coloured fluorescent dyes. Individual chromosomes or chromosome regions are painted with distinct colours to create a coloured karyotype. This can view the location of several genes on the same FISH array. May be used to paint repetitive sequence or unique, specific probes. Used to diagnose chromosome fusions.

question

Chromosome walks

answer

A scan of a chromosome until the gene is reached. Initiated by selection of a molecular marker close to the gene of interest. Difficult in species with large genomes; the walk is too far. RFLPs close to the gene of interest. Use the cloned RFLP DNA to screen the genomic library. Restriction map the overlapping clones, and use the fragment farthest from the original probe to screen a second genomic library. With each chromosome walk you test the new DNA fragment as a candidate for the disease gene, or search for features indicative of the presence of a gene. Time and labour intensive, compared to shotgun sequencing.

question

Chronic myelogenous leukemia (CML)

answer

Reciprocal translocation of a portion of chromosome 9 and 12, producing the Philadelphia chromosome. The translocation produces a fusion protein, bcr-abl.

question

ClaI

answer

A restriction endonuclease found in Caryophanon latum. Cleaves ATCGAT, producing 5' overhangs.

question

Classical synteny

answer

Linkage
The presence of genes/markers on the same chromosome.

question

Clonal inheritance

answer

Epigenetic states passed on from parental cell to daughter cells during division.

question

Clone

answer

Copies of a recombinant DNA molecule. Created in amplification.

question

Clone library

answer

A collection of DNA restriction enzyme fragments cloned into plasmids, separated into different bacteria isolated in agar plate colonies.

question

Cloning

answer

Isolation and insertion of a gene into a cloning vector in an appropriate host cell, usually E. coli. The gene is incorporated into a small self-replicating chromosome in vitro to form a recombinant DNA molecule. It is amplified by replication in the host cell in vitro. PCR is used to sequence primers.

question

Cloning vector

answer

A small, self-replicating genetic element such as a plasmid or viral chromosome. Used for isolation and amplification of DNA sequences. Must contain an origin of replication, a dominant selectable marker gene, and at least one unique restriction endonuclease cleavage site. Includes plasmids, phagemids, phage lambda, cosmids, BACs, PACs, and YACs. Expression vectors and reporter vectors.

question

Clotting factor VIII

answer

Required to treat hemophilia and AIDS. Until 1992, it was concentrated from donated blood plasma. Initial attempts at expression in E. coli failed to produce functional protein, but it was successfully produced in Chinese Hamster Ovary cells; it must be produced in mammalian cells for glycosylation. A large protein, 186 kb of DNA with 26 exons and 2,351 amino acids. Tissue origin was unknown, and reverse genetics was used to isolate it. Gentech and Genetics Insititute raced to produce factor VIII first.

question

Co-activator complexes

answer

There are two types:
1. Interact with components of basal transcriptional machinery. General transcription factors and mediator complex activate RNA polymerase II.
2. Interact with chromatin to create regions of nucleosome-free DNA. Includes histone modification complex and chromatin remodeling complex.

question

CODIS

answer

Combined DNA Index System
Used by the FBI in forensics. 13 STRs are used. The probability of two individuals having identical fingerprints at all 13 loci is 1 in 5.75 trillion. For each "allele", there is a different number of repeat of the same STR. Loci amplified, dyed with fluorescent dye, and separated with gel electrophoresis. Up to nine loci may be done at a time.

question

Colchicine

answer

Used in cytological mapping. Disrupts micotubules, blocking chromosomes in mitosis.

question

Colony

answer

A group of identical bacterial cells.

question

Colorectal cancer

answer

The fourth most common type of cancer. Evolves through distinct, well-characterized morphological stages associated with a limited number of stage-specific mutations: small adenoma, large adenoma, and carcinoma. Similar genes are mutated at specific stages of tumorigenesis. APC is inactivated early in over 60% cases, as well as tumour suppressor (Wnt siganlling), and increased rate of proliferation. All had activation of one oncogene and inactivation of three tumour suppressor genes. Ordered succession of genetic changes. Many variations in which genes are mutated. It is easy to get a biopsy. FAPC mutation predisposes people to colorectal cancer.

question

Colour karyotype

answer

A karyotype made with chromosome painting with FISH.

question

Comparative genomics

answer

The study of genome evolution. Comparing nucleotide sequences of genomes of organisms. Mining information in genome databases using bioinformatics techniques. Attempts to deduce the structure/function of genes through in silico comparisons of genes. Computer modeling of molecules, based on knowledge of sequence, structure, and function of homologues. Documents change responsible for divergence of species from common ancestors. Construction of phylogenetic trees can be constructed based on sequence comparisons.

question

Complementation screening

answer

A method of screening DNA libraries. The library is exposed to a mutant-type colony, and the DNA which restores the colony to wild-type is selected. Depends on dominance of wild-type alleles over mutant alleles. Often E. coli or yeast is used. E. coli lack machinery requried for excision of introns from eukaryotic genes; this method is limited to cDNA libraries. More likely to work when prokaryotic genes are in a prokaryote or eukaryotic genes are in a eukaryote.

question

Complete nucleosome

answer

A nucleosome core, plus histone H1, which holds it together. Binds 166 bp.

question

Condensins

answer

Links DNA to chromosome scaffolds. When phosphorylated, there is chromosome compaction. There is dissociation of cohesion complexes, and sister chromatid separation for metaphase-anaphase transition.

question

Contig

answer

Overlapping genomic clones. Often found in physical maps.

question

Contig map

answer

A set of contigs. Made using restriction enzyme mapping, DNA sequencing, and STS mapping. Fragments are ordered to reflect the sequence in the genome; compare RE digest patterns for each of the fragments. Each portion of the genomic DNA will be present in sevreal different plasmids since DNA is randomly fragmented. Each clone must be cut with several restriction enzymes; the size of each fragment produced in single and combination digests is used to construct a map of each clone. Computer software is used to order the clones. From a YAC clone, two libraries are produced, each from different restriction enzymes. Southern blots are prepared for both, and used to see which fragments align with each other, to create a contig map.
1. Begin as YAC clones, subcloned into smaller fragments in general purpose cloning vectors
2. Create restriction maps or DNA sequences of each clone
3. Contigs identified by overlapping restriction map patterns and sequences

question

Coomassie blue

answer

A stain that detect proteins. Used in SDS-PAGE; each band represents a differnet protein. Detects only the most abundant proteins; resolving power is limited. 50 mg of the protein are requried in the sample to produce a visible band.

question

Cooperative binding

answer

May be necessary to activate gene expression.

question

Correct DNA insertion

answer

Restriction mapping is used to determine if a gene is inserted in the correct orientation. It is digested with a restriction endonuclease that has a restriction site on the plasmid and on the gene. Electrophoresis is used to note the sizes of fragments, to determine the orientation of the insert.

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Cos sites

answer

Cohesive ends found on cosmids.

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Cosmids

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A cloning vector. Have a maximum insert size of 44 kb. Contain cos sites in plasmids.

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CpG islands

answer

Clusters of cytosine and guanines, 1 - 2 kb. There are about 30,000 in the human genome, most near transcription start sites. Extensively methylated in inactive gene promoters, and mostly unmethylated in active gene promoters. DNA in the vicinity of CpG islands is hypersensitive to DNase I, there are less H1 histones, and the histones are acetylated. They are found upstream of the CF gene, and were used to map this region.

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CRISPR

answer

Clustered regularly interspaced short palindrome repeats
Short stretches of phage DNA separated by repeated short bacterial DNA sequences. Transcribed into pre-crRNA.

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CSF1P0

answer

An STR loci used in CODIS. On chromosome 5. The motif is TAGA. There are 20 alleles.

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Cyclin

answer

Involved in checkpoints. Allows CDKs to have catalytic activity. Discovered in frog and clam eggs. Abundance of individual cyclins changes through cell cycle. Each cyclin is synthesized and degraded at specific times in the cell cycle.

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Cyclin B

answer

Degraded at the completion of mitosis leading to CDK1 inactivation.

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Cyclin-dependent kinases (CDK)

answer

Involved in checkpoints. Catalytically active components of cell-cycling mechanisms. Regulate activity of other proteins by transferring phosphate groups. Action depends on presence of cyclins. Discovered by isolating temperature-sensitive cell cycle progression defective mutants in yeast. Activity is dependent on association with specific cyclins. Active CDKs phosphorylate specific proteins, controlling cell cycle progression in a temporal and cyclical pattern. Serine/threonine kinases, phosphorylating over 100 proteins. Different CDK/cyciln complexes phosphorylate different substrate proteins. Protien activity is increased or inhibited. Entry into mitosis is regulated by coordinated phosphorylation of a threonine residue by CAK and dephosphorylation of a tyrosine residue by cdc25.

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Cystic fibrosis (CF)

answer

One of the most common inherited diseases in humans. Affects 1 in 2000 newborns of northern European descent. Inherited as an autosomal recessive mutation, and the frequency of heterozygotes in about one in 25 Caucasian populations. Sweat is excessively salty, and the lungs, pancreas, and liver become clogged with mucous, resulting in chronic infections and evenutal malfunction of vital organs. Mucous often builds up in the digestive tract, causing malnourishment. Patients often die of pneumonia. Salt accumulates in epithelial cells and mucous builds up on the surface of cells. With modern medicine, life expectancy is 32, but quality of life is poor, and there is no cure. Many mutations in the CF gene cause CF. In 70% of patients, it is a ?F508 trinucleotide deletion, deleting phenylalanine at position 508. Of the mutations, 20% are common, and the rest are rare.

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Cytochrome C

answer

Binds the adaptor protein APF1, causing oligomerization into the apoptosome.

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Cytogenetic map

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A genetic map anchored to a cytological map. RFLPs are identified that overlap with specific DNA sequences using fluorescent in situ hybridization. These STS sites are used as anchors.

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Cytokine receptor

answer

A receptor that regulates gene expression by activating kinase signalling pathways.

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Cytological map

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Microscopy of the chromosome, staining including Giemsa and quinacrine differential staining. Also uses colchicine.

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Cytoplasmic protein targeting

answer

The default protein targeting. Includes tubulin, actin, and ribosomal protein.

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Cytotoxic T cells

answer

Kill target cells by inducint apoptosis.

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D3S1358

answer

An STR loci used in CODIS. On chromosome 3. The motif is [TCTG][TCTA]. There are 25 alleles.

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D5S818

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An STR loci used in CODIS. On chromosome 5. The motif is AGAT. There are 15 alleles.

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D7S720

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An STR loci used in CODIS. On chromosome 7. The motif is GATA. There are 30 alleles.

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D8S1179

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An STR loci used in CODIS. On chromosome 8. The motif is [TCTA][TCTG]. There are 15 alleles.

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D13S317

answer

An STR loci used in CODIS. On chromosome 13. The motif is TATC. There are 17 alleles.

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D16S539

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An STR loci used in CODIS. On chromosome 16. The motif is GATA. There are 19 alleles.

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D18S51

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An STR loci used in CODIS. On chromosome 18. The motif is AGAA. There are 51 alleles.

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D21S11

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An STR loci used in CODIS. On chromosome 21. The motif is [TCTA][TCTG]. There are 89 alleles.

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Danio rerio

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Zebra fish
Its genome is 1,571,018,465 bp, with 23,524 genes, for a density of 66,800 bp/gene.

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Dark matter

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Areas of the genome with unknown purpose. May code for RNAs of unknown function. Includes chemically modified sequences that control epigenetic expression of genes by modifying chromatin structure.

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David Vetter

answer

Bubble Boy
Born in 1971 with SCID. Lived in a specially sterile enclosure, at first in a hospital, then at home. Everything in the enclosure had to be sterile to prevent infections. Received a bone marrow transplant from his sister at age 12, but died 15 days later from Burkitt's lymphoma caused by a latent Epstein-Barr virus in his sister's bone marrow.

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Deadenylation dependent mRNA decay

answer

A nuclease progressively shortens the poly(A) tail, limiting PABPI binding. When the poly(A) tail is 30 nucleotides long, mRNA is degraded by decapping and 5' > 3' degradation, or exosome mediation 3' > 5' degradation.

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Degradation

answer

Posttranslational control of gene expression. Excess or misfolded proteins targeted for degradation are first polyubiquinated, which targets them for proteasome proteolysis.

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Deoxyadenosine

answer

Toxic to immature lymphocytes. Builds up in ADA-SCID patients.

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Deubiquitylating enzymes (DUB)

answer

Removes ubiquitin chains to allow substrate entry into the 20S core of the proteasome.

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Diagnostics

answer

PCR is used for paternity tests, forensic identification using small amounts of samples, and to detect diseases prenatally, such as Huntington's disease and sickle-cell anemia.

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Dicer

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An RNase that breaks large RNAs into small pieces; siRNAs or miRNAs which can then play a role in RNAi. May act in teh cytoplasm or the nucleus. siRNAs and miRNAs produced are base-paired, except at the 3' ends, where two nucleotides are unpaired. Removes the hairpin loop on the 70 nulceotide pre-miRNA to produce a 22 nucleotide dsRNA associated with Ago2 in RISC complex.

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Dimerization

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Increases the complexity of DNA-binding specifcity; increases the number of possible combinations of transcription factors, each combination with different binding properties.

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Dimerization domain

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A functional domain of a transcriptional factor. Facilitates protein-protein interactions.

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DNA barcoding

answer

Each species has its own unique sequence for cytochrome oxidase, COI. Useful in speciation studies, species domestication, forensics, and quality control of food sources.

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DNA binding domain (DBD)

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A functional domain of a transcriptional factor. Attaches to DNA promoter/enhancer elements.

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DNA DataBank of Japan (DDBJ)

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Established in 1984. It became part of the International Nucleotide Sequence DAtabase Collaboration.

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DNA ligase

answer

Forms the missing phosphodiester bonds during DNA synthesis. Used after complementary overhangs anneal to one another, thus joining restriction fragments together.

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DNA methyl transferase (DNMT)

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Methylates some nucleotides in DNA, inactivating genes. 5' methylcytosine residues bind specific methyl-binding proteins that act as transcriptional repressors and chromatin modifying proteins. Methylate appropriate resideus on newly synthesized DNA strands; methylation pattern is maintained with each cell division.

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DNA methylation

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2% - 7% of cytosine residues are methylated in mammalian genomes. Occurs in 5' CpG 3' dinucleotides. Methylation in promoters of tumour suppressor genes can promote cancer development. An epigenetic modification. Inactive X chromosomes in female mammals are extensively methylated. Repetitive DNA sequences, dormant transposons, are methylated.

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DNA microarray

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Contains thousnads of DNA probes complementary to RNA transcripts on a nylon membrane, glass slide, silicon surface, or array of microbeads. Known ssDNA oligonucleotides that correspond to specific genes are laid out in microscopic quantities, all this is done by a machine. Isolated mRNA is reverse-transcribed into cDNA using fluorescent nucleotides, hybridized to the microarray and quantified by fluorescence. Tells you which genes are expressed in a sample, and the relative abundance of transcripts between two samplse. Includes spotted microarrays and gene chips. Can be used for comparative transcriptomics; use of two differently labelled samples to compare their intensities. Used for transcription profiling, genotyping, drug discovery, toxicology studies, mutation/polymorphism detection, and disease management.

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DNA polymerase I

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Removes RNA primers with exonuclease activity. Fills in the gap by adding deoxynucleotides.

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DNA polymerase III

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Extends RNA primers by adding deoxynucleotides. Catalyzes the formation of phosphodiester bonds.

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DNA polymorphism

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Nucleotide sequence variation among individuals within a population. Includes RFLPs.

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DNA primase

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Adds RNA primers during DNA synthesis.

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DNA probe

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A radioactively or fluorescently labelled probe used in Southern blotting. Hybridizes with the DNA target, in metaphase cells on a glass slide. Detected with autoradiography or fluorescence microscopy. Microscopic observation.

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DNA profile

answer

DNA fingerprint
Specific banding patterns produced by DNA fingerprinting. Individual bands of DNA fingerprints represent different alleles of VNTR/STR loci. The probability of two individuals (not identical twins) having the same DNA fingerprint decreases the more polymorphisms are used. Used for CODIS, used in paternity tests and forensics. Routinely used to identify and/or distinguish individuals.

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DNA profiling

answer

DNA fingerprinting
PCR is used to amplify DNA found in very small tissue samples. Detection of VNTR or STR polymorphisms by PCR and Southern blotting/capillary gel electrophoresis. The use of DNA sequences in personailty identity cases. A valuable tool in cases of uncertain identity including paternity cases, crimes, or disasters. It was used to identify body parts recovered in teh debris after the collapse of the Twin Towers on 9/11.

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DNA replication and DNA damage checkpoints

answer

Cheks for ssDNA, ds breaks, or DNA modifications. Arrests cell cycle, repairs damage, then resumes. If damage is nonrepairable, the cell undergoes apoptosis. Tumour suppressor genes may have loss of expression or express mutant cell cycle inhibitor p53, or pRNB.
p53 > p21 (CDK1) --| CDK2/cyclin E/A

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DNA quantification

answer

Measuring the abundance of a microbe in a sample. Includes qRT-PCR.

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DNA sequencing

answer

Provides conclusive information about gene structure, including coding sequences and regulatory sequences. Comparing amino acid sequences to database, you can identify proteins or potential functional domains within the protein, based on the sequence similarity to other known proteins. Can give information about mutations related to genetic disease. Entire genome sequence can be used to study disease evolution.

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DNA specific motif

answer

An area in a gene's promoter where transcription factors bind.

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DNA synthesis

answer

Begins at the origin of replication. Initiation requires a template primer with a free 3'-OH end. Polymerization occurs in the 5' > 3' direction.

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DNA target

answer

DNA that is complementary to the DNA probe in Southern blotting. Hybridizes with the DNA probe.

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DNase I hypersensitive sites

answer

Specific sites in the DNA where DNase I cleaves. Some lie upstream of transcriptionally active genes, either in promoter or enhancer regions.

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Dolly

answer

A sheep produced by nuclear transfer technology. A clone. Produced by the Roslin Institute in Scotland.

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Domain

answer

An autonomously folding functional module of a protein, usually with several motifs.

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Dominant activator

answer

Mutations in proto-oncogenes that lead to cancer. Most occur spontaneously during the course of cell division.

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Dominant selectable marker gene

answer

A gene that confers drug ressitance to host cell. Found in a cloning vector.

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Dosage compensation

answer

Mechanisms by which gene products from sex chromosomes are equalized in both sexes. Many different genes are coordinately regulated because they are on the same chromosome. Includes inactivation, hyperactivation, and hypoactivation.

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Douglas Hanahan and Robert Weinberg

answer

Proposed six hallmarks to the pathways leading to malignant cancer:
1. Cancer cells acquire self-sufficiency in signalling processes that stimulate division and growth
2. Cancer cells are abnormally insensitive to signals that inhibit growth
3. Cancer cells can evade programmed cell death
4. Cancer cells can acquire limitless replicative potential
5. Cancer cells develop ways to nourish themselves
6. Cancer cells acquire the ability to invade other tissues and colonize them

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Doxorubicin

answer

A drug that kills cells.

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Drosha

answer

An RNase that crops the ends of the hairpin on the pre-miRNA to produce a 70 nucleotide pre-miRNA that is exported out of the nucleus by exportin-5.

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Drosophila melanogaster

answer

A fruit fly. A model organism with a sequenced genome; genome sequenced in 2000. There are detailed physical maps available for its genome. The mitochondrial genome is 19,517 bp with 37 genes. Its genome is 131,000,899 bp with 13,792 genes, for a 9,500 bp/gene density. 18% of its genome is highly repetitive DNA. There are about 1035 protein domains. Salivary glands have polytenes: huge chromosomes, many chromosomes stuck together. Heat shock puffs are the location of the heat shock genes.

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Drosophila virilis

answer

A relative of Drosophila melanogaster. 45% of its DNA is highly repetitive.

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E2F

answer

A transcription factor inactivated by binding to pRB early in G1. Growth factors stimulate signal transduction pathways leading to expression of cyclin D. CDK4/cyclin D complex hyper-phosphorylates pRB, which prevents it from binding to E2F, which is now able to activate transcription of genes requried to enter S phase, including cyclin E and E2F. CDK2/cyclin E complex phosphorylates pRB, allowign cells to pass the restriction point; capable of growth factor independent G1-S progression.

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Ecdysone

answer

A steroid hormone. An insect molting hormone. Responsible for metamorphosis of larval tissue into adult structures. Binds to ecdysone receptor protein. Its DNA response element is EcR.

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Ecdysone receptor protein

answer

An intracellular receptor that binds to ecdysone.

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EcoRI

answer

A restriction endonuclease found in E. coli strain RY13. Cleaves GAATTC, producing 5' overhangs.

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EcR

answer

Ecdysone response DNA element. Present in promoters of ecdysone responsive genes.

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Edwin Southern

answer

Published the Southern blot procedure in 1975 which allowed identification of genes and other DNA sequences on restriction fragments separated by gel electrophoresis. The separated DNA is transferred onto a nitrocellulose or nylon membrane. Bands showing the positions of hybridized DNA sequences are developed using radioactively labelled DNA and X-rays, similar to in situ colony hybridization.

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Effector caspase

answer

Executioner caspase
Cleaves specific cellular proteins, leading to cellular inactivation. Includes caspases 3, 6, and 7.

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Electropherogram

answer

A graph made by a laser during Sanger sequencing. It is decoded to get nucleotide sequences. Each peak represents a strand one nucleotide longer then the previous one, and the colour determines the end nucleotide of that strand.

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Electrophoresis

answer

An electric field is generated in agarose (for DNA) or polyacrylamide (RNA or protein) gel. Separates macromolecules based on size. DNA is negatively charged, and will migrate to the anode (positive electrode). Rate of migration is inversely proportional to the length of the fragments; shorter fragments move faster. Used to determine the sizes of RNA fragments, isolate fragments, and in preparation for Southern or Northern blotting.

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Electroporation

answer

A procedure for producing transgenic plants. A short burtst of electricity is used to get the DNA into cells.

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Elizabeth Stweard and coworkers

answer

Published a map of 10,478 STSs in human chromosome 1 in 1997, based on radiation and hybrid mapping data.

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Embryonic stem cell (ES)

answer

Pluripotent cells derived from the inner cell mass of a blastocyst. Able to differentiate into all three primary germ layers of the embryo: ectoderm, endoderm, or mesoderm. May be isolated from mouse embryos at day 4.5. Can be cultured in vitro, transfected or injected with DNA, and introduced into other developing mouse embryos. Some of the transgenic cells may be contributed to formation of adult tissues.

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Encyclopedia of DNA elements (ENCODE)

answer

A consortium founded by Francis Collins. Their goal is to identify all non-genic functional elements in the human genome, such as promoters, enhancers, silencers, methylation and acetylation sites, and other factors involved in chromatin structure and gene expression.

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Endocrine signaling

answer

Signaling molecules produced and secreted into the blood stream where they travel to and affect targeting cells large distances from their site of synthesis. Includes adrenaline, insulin, EGF, and prostaglandins.

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Endometrial cancer

answer

The tenth most common type of cancer.

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Endonucleolytic cleavage

answer

Removes the distal segments of a nascent mRNA 10 - 30 down from the polyadenylation signal AAUAAA.

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Enhancer

answer

DNA sequence elements located in the vicinity of a gene. Binding to activating transcription factors, providing gene specific control of gene expression. 50 - 200 bp long, and can bind multiple different factors. Act over relatively large distances, up to several thousand bp from regulated genes. Influence on gene expression is independent of orientation in the DNA. Effects are independent of position; may be upstream, downstream, or in an intron. May be large, up to sevreal hundred bp. May contain repeated sequences with partial regulatory activity by themselves. Most function in specific tissues. Proteins bind to enhancers, influencing the activity of proteins that bind to promoters, including basal transcription factors and RNA polymerases. Enhancers cannto work properly if they, plus associated genes, are transported to a different chromosomal location.

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env

answer

A retroviral gene that encodes an envelope protein.

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Epidermal growth factor (EGF)

answer

A peptide endocrine hormone. A growth factor. Originates in multiple cell types. Targets epidermal cells and others, causing cell growth.

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Epidermal growth factor receptor (EGFR)

answer

Truncation of the ectodomain in glioblastoma, lung, and breast cancer. Overexpression results in elevated AKT and MAPK signaling.

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Epigenetic

answer

"Above'
A heritable state other than the actual sequence of the gene regulates the gene's expression. Includes chromatin organization, acetylation of histones, and methylation of histones or nucleotides.

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Epigenotype

answer

Twins with identical genotypes can have different epigenetic factors.

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Epitwin

answer

A project that began in 2010. Led by scientists in the UK and China. Searchign for epigenetic modifications that influence susceptibility to diseases and conditions. Five thousand twins will be analyzed.

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erbA

answer

A viral oncogene found in avian erythroblastosis virus that affects chickens. Produces an analog of thyroid hormone receptor.

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erbB

answer

A viral oncogene found in avain erythroblastosis virus that affects chickens. Produces a truncated version of epidermal growth factor receptor.

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Escherichia coli

answer

The best-known cellular microorganism. The genome of strain K12 has 4,638,675 bp with 4,467 genes. The genome of strain O156 is 5,528,910 bp with 5,463 genes.

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Estrogen

answer

A steroid hormone.

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Euchromatin

answer

"True"
Lightly stainign chromatin. Most eukaryotic genes are located in euchromatin. Generally active.

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Euglena gracilis

answer

A unicellular organism with about 15 chloroplasts per cell, each with about 40 copies of the cpDNA.

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Eukaryote

answer

Multicellular, diversity of cell types and organs with specialized functions. Gene expression is regulated during development to allow cells to differentiate into specific cell types, and to allow cells to respond to changes in their environment. Tissue architecture depends on maintainging proportions of cell types, and replacing missing cells. Decisions in growth and differentiation are made in response to signals from neighboring cells. Eukaryotic cells can respond to diverse environmental signals and signals from other cells. Cells respond to signals by changing metabolism, cell shape and migration, and cell type. Eukaryotes have greater level of transcriptional control; cells are compartmentalized allowing for differential control of transcription and translation.

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Eukaryotic expression cassette 1

answer

One of the cassettes of pcDNA3. Contains GFP. pCMV is a eukaryotic cytomegalovirus promoter. MCS for insertion of eukaryotic genes. BGH pA is a eukaryotic bovine growth hormone polyadenylation sequence.

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Eukaryotic expression cassette 2

answer

One of the cassettes of pcDNA3. Contains neomycin resistance. SV 40 pA is a polyadenylation sequence.

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Eukaryotic mRNA

answer

Ribosomes scan 5' > 3' until it reaches a start codon. The mRNA is post-transcriptionally modified to have 5' methylated guanine caps and 3' poly(A) tails. The start codon has an upstream Kozak sequence which interacts with initiator tRNA to increase efficiency. The primary transcript contains introns that are removed by splicing. There are 5' and 3' non-translated sequences. mRNA is translated into the cytoplasm.

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European Molecular Biology Laboratory (EMBL)

answer

Set up in Germany in 1980. It became part of the International Nucleotide Sequence Database Collaboration.

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Evasion of apoptosis

answer

An essential alternation for tumorigenesis. Inactive pro-apoptotic genes (FasR). Activate anti-apoptotic proteins (Bcl-2). Growing tumours initially have high rates of apoptosis (stressful environment, oncogene activation, genomic instability). Virtually all cancer cells have mutations in apoptosis-regulatory genes.

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Expressed-sequence tags (EST)

answer

Short cDNA sequences used as hybridization probes to anchor physical maps to genetic maps and cytological maps. Usually short, less than 1000 bp, single-pass sequence reads from mRNA. Typically produced in large batches. Represents a snapshot of genes expressed in a cell at a certain time. They are tags, some coding, others not, of expression for a cDNA library. Represent portions of cDNAs generated by sequencing cDNA fragments. Used for gene mapping, studying transcripts and SNPs, discovering putative gene products, comparing gene expression patterns, and as probes for microarrays or gene chips.
To generate an EST library:
1. Isolate total mRNA, using an oligo dT column to trap all poly(A) containing mRNAs
2. Add reverse transcriptase and oligo dT primers, to generate a single-stranded cDNA for each mRNA
3. Convert ss cDNA into ds cDNA (with DNA polymerase)
4. Generate a ds cDNA library by cloning products into a vector
5. Select specific ESTs as markers

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Expression vector

answer

Designed for expression of proteins in bacteria, yeast, plant, or animal cells. Myst be able to replicate in bacteria to amplify the plasmid. Must contain a cloning site located downstream from a promoter appropriate for the host cell to allow the inserted gene to be expressed. Usually also contains a selectable marker (antibiotic resistance gene), to allow for selection of cells with the plasmid in their genome.

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Extrinsic death pathway

answer

Death-receptor induced apoptosis. Instructive apoptosis, enables cells to direct other cells to self-destruct.

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FADD

answer

Binds to receptors, activating effectors for extrinsic apoptosis.

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Familial adenomatous polyposis (FAP)

answer

An inherited cancer syndrome, causing colorectal cancer. A mutaton in APC (5q21), the products of which regulate ?-catenin. Occurrence of numerous tumours in the colon. Predisposed to form polyps, and there is a high probability that one will become malignant. Frequency is about 1 in 700 in Western countries. Median age of onset is 42.

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Familial breast cancer 1

answer

An inherited cancer syndrome, causing breast cancer. A mutation in BRCA1 (17q21), the product of which functions in DNA repair. About 50% of mutations in this gene are private mutations.

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Familial breast cancer 2

answer

An inherited cancer syndrome, causing breast cancer. A mutation in BRCA2 (13q12), the product of which functions in DNA repair.

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Familial melanoma

answer

An inherited cancer syndrome, causing melanoma. A mutation in P16 (9p21), the product of which is an inhibitor of CDKs.

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Familial retinoblastoma

answer

An inherited cancer syndrome, causing retinoblastoma. A mutation in RB (13q14.3), the products of which regulate cell cycle and transcription.

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FASTA

answer

A program used for rapid searches of huge databases. Used in bioinformatics.

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fes

answer

A viral oncoene found in ST feline sarcoma virus that affects cats. Produces a tyrosine-specific protein kinase.

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FGA

answer

An STR loci used in CODIS. On chromosome 4. The motif is CTTT. There are 80 alleles.

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fgr

answer

A viral oncogene found in Gardner-Rasheed feline sarcoma virus that affects cats. Produces a tyrpsine-specific protein kinase.

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Fibroblast growth factor (FGF)

answer

A growth factor secreted by tumour cells to encourage blood vessel growth to promote oxyen and nutrient delivery.

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Fibroblast growth factor receptor

answer

Amino acid substitutions in multiple myeloma, bladder and cervical cancer. Incldues FGF-R.

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Fluorescent probe (FISH)

answer

Fluorescent in situ hybridization. Hybridization of biotin-bound DNA probe to cells on a glass slide. Incubate with avidin-bound to a fluorescent dye. Microscopic observation with fluorescent microscope.

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FMRP

answer

Fragile X Mental Retardation Protein
An RNA-binding protein, playing a role in transporting mRNA molecules, or in regulating their translation. In Fragile X syndrome patients, it builds up in the dendrites of neurons.

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fmr

answer

A viral oncogene found in McDonough feline sarcoma virus that affects cats. Produces an analog of colony stimulating growth factor receptor.

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Forward genetics

answer

Beginning with a mutant phenotype, and attempting to identify the mutant gene responsible for the phenotype. Can provide clues to the normal function of the gene product.

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fos

answer

A viral oncogene found in FJB osteosarcoma virus that affects mice. Produces a transcriptional activator protein.

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fps

answer

A viral oncogene found in Fuginami sarcoma virus that affects chickens. Produces a tyrosine-specific protein kinase.

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Fragile X syndrome

answer

The second most common form of inherited mental retardation in humans. Significant mental impairment, and facial and behavioural abnormalities. Occurs in one in 4000 males, and one in 7000 females. Caused by dominant X-linked mutation that is incompletely penetrant. 20% of hemizygous males, and 30% of heterozygous females show no symptoms. There is a constriction near the tip of the long arm of the X chromosome, with an unstable trinucleotide repeat, CGG. Normal tip of the chromosome has 6 - 59 copies, fragile X syndrome chromosomes have 200 - 1500 copies. Due to "slippage" of the repeats, DNA repair systems may expand the repeats, making the number of copies unstable. The gene produces FMRP protein.

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Frame-shift mutation

answer

A mutation which is an addition or deletion of nucleotides of a number which is not a multiple of three. Shifts the frame of downstream codons, altering amino acid sequence.

question

Francis Collins

answer

Led the research teams that identified the gene for cystic fibrosis, and characterized some of the mutations that cause CF with Lap-Chee Tsui and Jack Riordan.

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Frederick Sanger and colleagues

answer

Published a dideoxy termination sequencing protocol in 1977. Sanger shared the Nobel Prize in Chemistry in 1980 for this protocol.

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Fugu rubribes

answer

A puffer fish. An organism with a sequenced genome.

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Functional genomics

answer

The study of genome function. Spawned proteomics. Includes the analysis of the transcriptome and proteosome. Uses the information from genome sequencing to describe the gene and protein functions and interactions.

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G protein

answer

Have GTPase activity. Conformation is altered by GDP/GTP binding. GDP bound is inactive. GTP bound is active.
GTP > GDP

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G protein-coupled receptor (GPCR)

answer

A receptor that regulates gene expression by activating kinase signalling pathways.

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G1

answer

A phase in cell cycle. Cell growth, preparation for S phase. Early in G1, E2F is activated by binding to pRB.

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G1/S transition

answer

Requires nutrient/growth factor independent synthesis of late G1 cyclin (cyclin E). Checks if cell division is compatible with function of tissue and well-being of the organism. Oncogenes may overexpress or produce hyperactive signalling molecules or transcription factors controlling the expression of cyclin D.
Growth factors > cyclin D --| pRB --| E2F > cyclin E

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G2

answer

A phase in cell cycle. Preparation for mitosis.

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gag

answer

A retroviral gene that encodes for the capsid protein.

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Gain-of-function

answer

A mutation where the mutant form of the protein has a different effect than the normal protein.

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GAL4

answer

A transcription factor that activates Gal1 genes in the presence of galactose in Saccharomyces cerevisiae. A positive regulator for gene expression of the galactose-induced genes, GAL1, GAL2, GAL7, GAL10, and MEL1, which encode enzymes that convert galactose into glucose. Recognizes a 17 bp sequence upstream from the activating sequence. Functional domains are interchangeable, and can be used to screen for protein-protein interactions.

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Gallus gallus

answer

Red jungle fowl
An ancestor of domestic chickens. An organism with a sequenced genome.

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GC box

answer

GGGCGG
A basal promoter sequence. Binds SP1 basal transcription factor.

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GEF

answer

REmoves bound GDP allowing GTP binding to occur.

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GEnbank

answer

ncbi.nlm.nih.gov/genbank
Proposed by Walter Goad in 1979. Contains all sequenced genes. Can be used to design special primers. Maintained by NCBI. By 2011, it contained over 117 billion bp of sequenced DNA. It became part of the International Nucleotide Sequecne Databse Collaboration.

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Gene addition therapy

answer

Adding functional copies of the defective gene, not replacing the gene. GEnes are inserted at random, or nearly random sites. All current protocols are gene-addition. Can be used for dominant disorders, such as Huntington's disease.

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Gene chip

answer

A form of DNA microarray. Produced by Affymetrix. Can detect thousands of SNPs at once. Thousands of probes are synthesized on silicon wafers 1 - 2 cm² in size. Target RNAs from samples are labelled with fluorescent dyes, and a laser scans the chips to collect data. A single chip can be used to study the expression of a thousand genes. Over 400,000 oligonucleotides can be spotted onto a single chip, each spot 10 nm apart. A high-resolution array can have over 6 million probes.

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Gene editing

answer

Precise targeting of transgenes using CRISPR.

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Gene expression profiling

answer

Can predict the outcome of breast cancer. There is correlated gene expression and tumour data by cluster analysis. Provides a strategy to select patients who would benefit from more aggressive therapy.

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Gene imprinting

answer

Expression of a gene is determined by its parental origin. During development of somatic tissues, one alleles from one parent remain methylated, while the allele from the other parent is unmethylated. In somatic cells, only the unmethylated allele is expressed. During development of the germ line, the methylation imprint is released, and methylation is re-established during either oogenesis or spermatogenesis, but not both. Sex-specific factors are responsible for imprinting methylation. There are over 20 imprinted genes in mice and humans. Includes Igf2.

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Gene replacement therapy

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The ideal gene therapy protocol. The dysfunctional gene is replaced with a functional copy. Would be mediated by homologous recombination. Uses homologous recombination to replace the defective gene with a functional copy.

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Gene therapy

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The most promising approach to successful treatment of diseases where a protein must be synthesized within the cell to function properly. Involves adding a normal copy of the gene into the genome. More research is needed before it becomes a routine protocol. Includes somatic-cell and germ-line gene therapy. Insertion is random, and could activate nearby oncogenes, leading to cancer.

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General transcription factor

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Transcription factors that bind to basal promoter sequences. First forms a pre-initiaon complex, then binds. Includes TATA binding protein adn several TFIIs.

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Genetech

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Founded in 1976. Raced with Genetics Institute to produce clotting factor VIII first.

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Genetic code

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Triplet codons of mRNA. There are 64 codons; 61 specify 20 amino acids, and 3 are termination codons.

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Genetic Information Non-discrimination Act (GINA)

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An American bill passed in 2008, protecting individuals from discrimination from employers and insurance companies based on genetic studies and DNA tests.

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Genetic map

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Based on relative positions of genes, RFLPs, STRs, VNTRs, and SNPs, based on lineage studies. Genetic techniques are used to construct maps showing the relative positions of genes and other sequence features in the genome. Cross-breeding, or pedigree analysis is used to determine recombination frequencies. Map distance is the frequency of recombination between two loci on the same chromosome, due to crossing over. Loci that are farther apart have greater chance of crossing over. Good for mapping the gene order and relative distance of genes. Distances do not always correlated with phsycial distances.
1 cM = about 1 mb = 1 million bp

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Genetic marker

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Includes genes, DNA polymorphisms such as RFLPs, VNTRs, STRs, STSs, and SNPs.

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Genetic selection

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The simplest method of screening DNA libraries. The library is exposed to a wild-type colony, and the DNA which produces a mutant phenotype is selected. Isolate a mutant strain which lacks the ability to grow in the absence of glucose, transform the cells with the DNA library. Screen for colonies by growing in the absence of glucose.

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Genetics Computer Group (GCG)

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A group at the University of Wisconsin. Developed some of the most popular programs used in bioinformatics, including Map.

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Genetics Institute

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Founded in 1980. Raced with Genetech to produce clotting factor VIII first.

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Genome

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One complete copy of the genetic information, or one complete set of chromosomes, monoploid or haploid. The entire DNA genetic material of an organism.

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Genome evolution

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Occurs through mutation and selection for new traits. Gene duplication and evolution through mutation can produce paralogues with new functions. Source of complexity is not due to the number of genes, but rather the complexity of gene product processing: alternative RNA splicing, and posttranslational processing of protein.

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Genomic DNA library

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A set of amplified DNA clones collectively containing the entire genome. Some are chromosome-specific. The DNA and cloning vector are treated with restriction enzymes, combined so that they anneal, and sealed with DNA ligase. The cloning vector is introduced to an appropriate host for amplification. If the host is E. coli, the bacteria are first trated with chemicals or a short pulse of electricity to make them permeable to plasmids. Cells will produce multiple plasmids per cell, allowing for high level plasmid amplification. The cells are then cleaned of vector-lacking cells by exposing the cells to conditions where the vector is essential for growth. Each colony contains clones of cells replicating a unique fragment; the library can contain thousands of different recombinant clones. Contains the same genes, no matter what part of the body the sample is taken from, or when the sample is taken.

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Genomic sequence

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Ordered contigs for each chromosome, measured in base pairs.

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Genomics

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A phrase coined by Thomas Roderick in 1986. The sub-discipline of genetics mapping, sequencing, and analyzing the functions of entire genomes. The name of a journal dedicated to communicating new information in this sub-discipline, began in 1978. Includes structural, functional, and comparative genomics.

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Genotyping

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Diagnostics
An application of DNA microarrays. Labelled genomic DNA of a gene is hybridized into an array of alleles of gene. A one-nucleotide difference in a SNP can prevent hybridization.

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Germ-line gene therapy

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Heritable gene therapy
A type of gene therapy. Performed experimentally in mice and other animals, never in humans. Moral and ethical considerations are involved.

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GFP reporter

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Studies the regulation of gene expression by cloning GFP open reading frame after different promoters, and measuring the intensity of GFP fluorescence.

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GFP tag

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Allows visualizaion of proteins in real time. Studies the subcellular localization of proteins by cloning GFP "in frame" with the open reading frame of a specific gene, and viewing by UV fluorescence microscopy. Many colours can be used at once, for different proteins.
1. Clone the open reading frame of the gene of interest, "in frame" with the GFP open reading frame
2. Transfect the plasmids into cells
3. Visualize in real time with fluorescence microscopy

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Giemsa staining

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Used in cytological mapping. Shows "G" bands in the human karyotype. A meiotic or mitotic chromosome smear is treated with protease trypsin, stained with Giemsa, and observed by light microscopy.

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Gilbert

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Developed chemical degradation sequencing protocol in 1977. Chain termination and chemical degradation concepts were developed. Polyacrylamide gel electrophoresis was used to separate DNA tracts.

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globin

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A long-lived mRNA with repeats of CCUCC in its 3' UTR.

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Glucocorticoid

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A steroid hormone.

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Glucocorticoid receptor (GR)

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A transcription factor that binds to GRE. Recruits a HAT to the DNA, which acetylates the histones of nucleosomes near the transcription start site.

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Glucocorticoid response element (GRE)

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Upstream of GR-regulated genes. GR binds to it, recruiting a HAT to acetylate the histones near the transcription start site.

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Glutamine (Q, Gln)

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An amino acid which is encoded by the CAG repeat in the huntingtin gene.

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Glyphosate

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A herbicide which inhibits ESPS synthase, needed for synthesis of aromatic amino acids phenylalanin, tyrosine, and tryptophan.

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Glyphosate resistant crops

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Roundup Ready
An EPSP synthase gene resistant to glyphosate is transferred into crop plants using Ti plasmid mediated transformation. The crops can be sprayed with glyphosate to kill weeds, without affecting growth of the crop. It is not allowed to save Roundup Ready seeds from a crop to plant them next year.

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Golden Rice

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Rice which is genetically modified to have higher ?-carotene content to prevent blindness.

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Graham Moore and colleagues

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Compared the high density genetic maps of several cereal grasses, and discovered that linkage relationship of blocks of unique DNA sequences were conserved. Repetitive DNA sequences were highly variable.

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Green fluorescent protein (GFP)

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A naturally occurring fluorescent protein of the jellyfish Aequorea victoria. About 27 kDa. A powerful tool to study gene expression at protein level. Used to monitor synthesis and localization of specific proteins in living cells. Genes are fused with the sequence that encodes GFP, and the chimeric gene introduced to cells by transformation. Fluorescence is studied by exposing the cells to blue or UV light; it fluoresces bright green. Because it is a small protein, it can often be coupled to proteins without interfering with their activity or interaction with other components. Variants of GFP, in different colours, allow the study of more than one protein simultaneously. Includes GFP reporter and GFP tags.

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Green spot

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In DNA microarrays for comparative transcriptomics of cancer vs. normal tissues, signifies a transcript that is more abundant in normal cells than cancer cells.

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Guide strand

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Base-pairs to homologous mRNA sequences as dsRNA is unwound, usually in 3' UTR, either impairing mRNA translation or causing its destruction.

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Gut microbiome

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All the microorganisms in the gut.

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H-ras

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A viral oncogene found in Harvey murine sarcoma virus that affects rats. Produces a GTP-binding protein. One homolog was discovered to be a proto-oncogene for bladder cancer in humans; when mutated it transmits information that stimulates cells to divide uncontrollably.

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H. Robert Horvitz, John E. Sulston, and Syndey Brenner

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Won the Nobel Prize in Physiology or Medicine in 2002, for genetic regulation of organ development and programmed cell death. Brenner introduced C. elegans as a model organis, and mapped its cell fates.

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Haemophilus influenza

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The first cellular organism with its entire genome sequenced. Sequenced in 1995.

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Hamilton Smit and Daniel Nathans

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Discovered restriciton endonucleases in 1970. In 1986 they shared the Nobel Prize in Physiology or Medicine with Werner Arber, who carried out research that lead to their discovery.

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Haplotype

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Sets of SNPs and other genetic markers on a chromosome that tend to be inherited together.

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Heat-shock protein

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Proteins produced when organisms are subjected to high temperatures, or other protein damaging stresses. Stabilize the internal cellular environment. Expression is regulated at the transcriptional level; heat induces transcription. Some of the most conserved polypeptides: human HSP70 and E. coli DnaK proteins are 50% identical. Among the first mammalian protein-coding genes to be cloned and characterized. In eukaryotes there is a conserved consnsus sequence, (nGAAnnTTCnnGAA); a transcription factor, HSF1 binds to this sequence to activate the gene.

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Heat-shock response element (HSE)

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Nucleotide sequences upstream of heat-shock protein coding genes. When heat-shock transcription factors bind to these sequences, transcription is promoted.

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Heat-shock transcription factor (HSTF)

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Activates heat shock protein gene expression in response to heat treatment in Drosophila melanogaster. Includes HSF1.

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HeLa

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A line of cancer cells that have been grown for years.

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Helix-loop-helix

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A stretch of two ? helixal regions, separated by a non-helical loop. Helical regions permit dimerization between two polypeptides. Often adjacent to a stretch of basic amino acids, so they can bind to DNA. PRoteins with this structure are basic HLH. Contain a basic DNA-binding domain adjacent to the motif.

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Helix-turn-helix

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A structural motif characteristic to eukaryotic transcription factors. A stretch of three short ? helices, separated from each other by turns. Helical segments close to the C-terminus are required for DNA binding. The other helices are involved in formation of protein dimers. Often coincides with a homeodomain.

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Hemoglobin

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(?/? globins)
Store oxygen in blood.

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HER1

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Overexpressed in about 30% of carcinomas. Includes erbB-1 and EGFR.

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HER2

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Overexpressed in about 25% of breast cancer. Amplified copy number is correlated with poor prognosis for breast cancer patients. Includes erB-2 and neu.

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Herceptin

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An anti-Her2 specific humanized monoclonal antibody. Promotes receptor internalization. Reduces AKT and MAPK signaling. Increases radiation response.

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Hereditary nonpolyposis colorectal cancer (HNPCC)

answer

An inherited cancer syndrome, causing colorectal cancer. A mutaiotn in MSH2 (2p16), MLH1 (3p21), PMS1 (2q32), or PMS2 (7p22), the products of which function in DNA mismatch repair. A dominant autosomal condition occurring in 1 in 500 people. Occurrence of a small number of polyps, one of which eventually progresses into a cancerous condition. Median age of occurrence is 42.

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Heterochromatin

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"Different"
Darkly staining chromatin. Represses gene function, perhaps because it is condensed into a form that is not accessible to transcriptional machinery. Rich in repetitive DNA, mostly located in centromeres or telomeres. Generally inactive.

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HincII

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A restriction endonuclease found in Haemophilus influenza strain R_c. Cleaves GTPyPuAC, producing blunt ends.

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HindII

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A restriction endonuclease found in Haemophilus influenza strain R_d. Cleaves AAGCT, producing 5' overhangs.

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Histone

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Pack up the DNA. Have tails, which can be in contact with DNA or not.

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Histone acetyl transferase (HAT)

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Histone acetylases
A mechanism of chromatin remodeling. Enzymes that transfer acetyl groups to lysine at specific positions in histones of nucleosomes. This is associated with increased gene expression. Loosens DNA-histone associations in nucleosomes, and "opens" the chromatin. Acetylation of histones is correlated with increased gene expression. Creates open chromatin to allow transcription factor binding to promoters/enhancers.

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Histone deacetylases (HDAC)

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Deacetylates histones, inactivating genes. Removes acetyl groups from lysine residues of histones. Creates closed chromatin to restrict transcription factor bindign to promoters/enhancers.

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Histone methyl transferase (HMT)

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Methylates histones, inactivating genes.

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Histone modification complex

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A co-activator complex that includes histone acetyltransferases and methylases.

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Homeodomain

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A region of about 60 amino acids, encoded by homeotic genes of Drosophila, which determine developmental fates of cells. Often has helix-turn-helix motifs.

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Homo neanderthalensis

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A close evolutionary relative of humans. Two thirds of the genome was sequenced and published in 2010.

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Homo sapiens

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Humans
The genome is sequenced. There are detailed physical maps available for the genome. The mitochondrial genome is 16,571 bp, with 37 genes. The genome is 2,851,330,913 bp with 22,287 genes, for a density of 127,900 bp/gene. There are about 1262 protein domains.

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Homologous

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Genes or proteins that are similar in different species because they evolved from a common ancestral gene or protein. Identified using Southern blotting.

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Homologues

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Groups of homologues genes.

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Hood

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Developed partially automated sequencing system in 1986. Sequencing reactions were optimized. Assorted sequencing strategies were applied and computer assisted data handling was started.

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Hormone

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MOlecules which circulate through the body, making contact with target cells, initiating series of events that regulate expression of genes. In animals, includes steroid hormones and peptide hormones.

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Hormone receptors

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Cytoplasmic or nuclear proteins that interact with steroid hormones. When bound in a complex with their hormone, they act as transcription factors, regulating expression genes.

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Hormone response element (HRE)

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Specific sequences in the DNA in promoters of the genes they regulate. Bind to proteins or hormone/protein complexes which act as transcription factors. Can be activated by proteins that are not part of hormone signal transductions. Vigour of transcriptional response depends on the number of HREs present.

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Hoxc8

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A transcription factor that regulate expression of genes encoding proteins that control development of thoracic vs. cervical vertebrae in animals. Subtle differences in enhancer sequences in the promoters cause different number of vertebrae in animals. Subtle differences in enhancer sequences in the promoters cause different numbers of vertebrae in the neck and chest in mice than in chickens. Expressed during embryonic development. Mice have 7 cervical and 13 thoracic vertebrae. Chickens have 14 cervical and 7 thoracic vertebrae.

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HpaII

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A restriction endonuclease found in Haemophilus parainfluenzae. Cleaves CCGG, producing 5' overhangs. Cleaves only if the second cytosine is not methylated. Can be used to detect methylation in DNA.

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HSF gel shift

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HeLa cells incubated at 37 - 44?C for 1 hour. Cell ectracts prepared and mixed with 32 P labelled DNA probe containing the heat shock element. Mixtures separated on a 4% polyacrylamide gel, dried, and exposed to X-ray film.

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HSF1

answer

A heat-shock transcription factor that is constitutively expressed, and negatively regulated in non-stressed cells. Trimerization is mediated by interactions between hydrophobic heptad repeats in the oligomerization domain. Repressed in non-stressed cells by HR-C interaction. Regulatory domains inhibit transcriptional activation domain (TAD). To activate, it must trimerize to gain DNA-binding capability, and undergo posttranslational modification to gain transcriptional activation ability.

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hsp70

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Genes in Drosophila that code for HSP70, heat shock protein molecular weigth 70 kDa. Transcribed when temperatures exceed 33? C.

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Htt

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huntingtin
Used to be called IT15 (Interesting Transcript 15)
The mutation is called mhtt. The gene responsible for HUntington's disease. Located at 4p16.3. Being homozygous mhtt leads to more rapid onset of symptoms. One of the first human genes to be shown to be linked to an RFLP. Spans abotu 210 kb near the end of the short end of chromosome 4. Healthy individuals have 11 - 34 copies of the CAG repeat. Individuals with Huntington's disease have 42 - 100 copies, and age of onset is negatively correlated with number copies. Number of copies can expand and contract between generations. The gene encodes for HTT.

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HTT

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Huntingtin protein
It is 3144 amino acids in length, with a polyglutamine tract. Important for transcription, cell signalling, and transport. The mutant form of the protein has an excessive polyglutamine region that causes inability to fold properly, leading to accumulation of aggregates of huntingtin protein in brain cells, loss of neurotransmission, and atrophy of neuronal tissues.

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Human cell

answer

Has about 20,000 protein coding genes, and expresses about 12,000 proteins. There are 2x10⁹ total proteins per cell. Some proteins are very abundant, such as cytoskeletal proteins (actin, tubulin), histones, and ribosomal proteins. Most proteins are less than 0.1% of total cellular protein.

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Human Genome ORganization (HUGO)

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Human Genome Sequencing Project Consortium
Established in 1993 by Francis Collins to coordinate the efforts of human geneticists around the world. Used chromosome walking to sequence.

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Human Genome Project

answer

Initiated by Watson in 1990. Their original goal was to sequence the entire genome by 2005. It was expected to take 20 years, and to cost over $3 billion. Two first drafts were published in 2001. By 2004, 99% of the genome was released. It has serves as an umbrella for similar mapping and sequencing projects for model organisms. Found that 1.1% of genes code for proteins. There are about 25,000 coding regions, 44% derived from transposable genetic elements. Some noncoding DNA sequences are conserved between humans and mice. 80% of the genome is transcribed into RNA of unknown function. 40% of gene sequences associated with disease are intergenic.

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Human growth hormone (hGH)

answer

A protein deficient in certain types of dwarfism. A single polypeptide chain 91 amino acids long. Prior to 1985, the major source was human cadavers. It can be produced using recombination protein production. hGH made this way was approved for use in humans in the US in 1985. The vector used to produce hGH in E. coli must have an open reading frame, promoter, Ori, and Amp^r (ampcillin resistance, a selectable marker). When expressed in transgenic mice, it results in increased somatic growth; the transgene is expressed under control of a gene promoter regulated by zinc.

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Human Proteome Organization (HUPO)

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Formed with the goal of determining the structures and functions of all the proteins encoded by the human genome.

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Huntington's disease (HD)

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A genetic disorder caused by an autosomal dominant gain-of-function mutation in Htt. Occurs in one in every 10,000 individual of European descent. Progressive degeneration of the central nervous system, usually beginning at age 30 - 50, causing death 10 - 15 years later. It is untreatable. The patient suffers from uncontrolled movement and shaking. Can be detected using PCR of repeat regions, and determining the repeat number with gel electrophoresis.

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Hylobates concolor

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White-cheeked gibbon
Comparison with human chromosomes revealed at least 21 translocations that occurred between our two species from our common ancestor.

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Hyperactivation

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A type of dosage compensation. Found in Drosophila. Genes on the single X chromosomes of male Drosophila are transcribed more vigorously. Requiers five genes, in which null mutations result in male-specific lethality. Protein complexes bind to the X chromosome, enhancing gene expression. Involved chromatin remodeling and acetylation of histone H4.

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Hypoactivation

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A type of dosage compensation. Found in C. elegans. Genes on the two X chromosomes of hermaphrodite C. elegans are transcribed less vigorously. Protein complexes bind to the two X chromosomes, inhibiting gene expression. Does not bind to the single X chromosome of males, nor to any autosomes.

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ICE subfamily

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A family of caspases includin inflammatory caspases.

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Igf2

answer

Insulin-like growth factor
A gene that has gene imprinting. Methylated in the female germ line, and not in the male germ line. The copy inherited from the father is expressed. The copy inherited from the mother is methylated and not expressed.

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Immortalization

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An essential alteration for tumorigenesis. Cells that have acquired limitless replicative potential. Loss of p53, inhibition of Rb. In normal cells telomere length degreases with each cell division; cancer cells overcome this intrinsic program that limits unlimited cell divison. Requries overexpression of telomerase to maintain telomere length.

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Immunofluorescence imaging

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Detects where in the cell a protein is localized.
1. Grow cells on a glass slide
2. Fix cells with paraformaldehyde
3. Block with a protein solution
4. Incubate with a primary antibody, which detects a protein of interest
5. Wash to remove unbound antibody
6. Incubate with conjugated secondary antibody, which detects the primary antibody
7. Wash
8. Analyze with a fluorescence microscope

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In frame deletion

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A mutation which is a deletion of a multiple of three nucleotides. Downstream codons are the same as the original gene.

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In situ colony hybridization

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A method of screening DNA libraries. Used with libraries of plasmid and cosmid vectors. Colonies are transferred onto a nylon membrane and hybridized with a radioactively or fluorescently labelled DNA or RNA probe. DNA from lysed cells bind to the nylon membrane before hybridization; only probes bound to complementary target DNA will stay after it is washed with a buffered salt. The exact location of the hybrid colony is detected using X-ray autoradiography, thus identifying the location of the correct colony on the original plate.

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Inactivation

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A type of dosage compensation. Found in mammals. One of the two X chromosomes in female mammals is randomly inactivated. Inactivation begins at the X inactivation centre, and spreads in opposite directions to ends of the chromosome. XIST gene remains active on the inactivated chromosome.

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Inherited bilateral retinoblastoma

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Childhood tumours in both eyes. Inherited predisposition. High risk of osteosarcomas. Small deletion of chromosome 13. Requires somatic mutaiton of the other allele. Treatment is to remove both eyes, and there is still risk of tumours.

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Initiation factor (IF)

answer

Binds to PABPI, stabilizing the RNA.

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Initiator caspase

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Processes effector caspases. Includes caspase 9 (intrinsic pathway), caspase 8 and 10 (extrinsic pathway) and caspase 2 (DNA damage).

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Injection of DNA into the nucleus

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A method of producing transgenic animals. DNA is injected into the nucleus of zygotes; DNA integration occurs during early development, and not all germ cells have the transgene. G₀ offspring are chimeras, and are mated to produce G₁, which are screened for the presence of the transgene.
1. Remove the eggs from the female mouse, and fertilize in vitro, producing a diploid fertilized egg.
2. Microinject DNA into the nucleus of the zygote
3. Implant the zygote into a pregnant mouse
4. Screen offspring for transgenic mice

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INK4

answer

A CDK inhibitor. Binds CDK4, preventing binding to cyclin B.

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Insect cell lines

answer

An alternate expression system for recombination protein production. Uses simple media. High yield, cost effective.

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Insensitivity to antigrowth signals

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An essential alteration for tumorigenesis. TGF? inhibits G1-S progression by inibiting pRB phosphorylation, inhibiting c-myc expression, and increasing expression of CDKIs (p21).

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Insertional inactivation

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A gene becomes non-functional due to the insertion of foreign DNA.

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Insertional mutagenesis

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The induction of null mutaitons, "knockout" mutations. Insertion of foreign DNA into genes. The same whether perofmed with a Ti plasmid, or transposon.

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Insulator

answer

Marks boundaries of transcriptional units and prevents activators from influencing the activity of other genes.

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Insulin

answer

A peptide endocrine hormone. Originates in pancreatic ? cells. Targets multiple tissues, causing glucose uptake into cells. Required to treat diabetes. Until 1982, it was obtained from pig or cow pancreases. Today it is produced using recombination protein production.

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Interactome

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All interactions in the cell: protein/protein, protein/nucleic acid, protein/ligand.

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Interactomics

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The study of the interactome.

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International Consortium of Scientists

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The first eukaryotic genome (yeast) was sequenced in 1996. Collaborations between teams of scientists.

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International HapMap Project

answer

Initiated by researchers from around the world. Their goal is to identify and map SNPs using DNA samples from many human populations. Make a catalog of common genetic variants that occur in humans. Used for tracing evolutionary history, predicting an individual's susceptibility to diseases, and genetic markers to map disease genes. Helped in the discovery of the Huntington's disease gene.

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International Human Genome Sequencing Consortium

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Published a nearly complete sequence of the human genome in 2004. It covered 99% of the human genome.

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International Mouse Phenotype Consoritum (IMPC)

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Building the first comprehensive, functional catalogue of the mouse genome.

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International Nucleotide Sequence Database Collaboration

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The joined forces of GenBank, EMBL, and DDBJ.

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International Rice Genome Sequencing Project and Syngenta

answer

Published the first drafts of the genomes of two rice subspecies in 2002.

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Intrinsic death pathway

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Mitochondrial-induced apoptosis. Removes damaged cells, excess cells, or cells that are no longer needed.

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J. Craig Venter and colleagues

answer

Sequenced the first bacterial genomes in 1995. Automated fluorescent sequencing instruments and robotic operations were applied to the process. PCR sequencing concept was introduced. Announced the formation of Celera Genomics in 1998. Became interested in the minimal gene set, and constructed a synthetic bacterial genome of Mycoplasma mycoides, which was introduced to Mycoplasma capricolum. The synthetic genome contained lacZ gene from E. coli to allow for blue-white selection.

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JAK/STAT

answer

A cytokinine receptor signal.
1. Interferon (IFN) binds to a cell surface receptor
2. IFN binding causes receptor dimerization
3. The Jak kinase associated with the intracellular domain of the receptor becomes activated by phosphorylation
4. Activated Jak kinase phosphorylates tyrosine residues on the intracellular domain of the receptor
5. PHosphorylated tyrosine residues bind to STAT transcription factors
6. Jak phosphorylates the bound STATs
7. Phosphorylated STAT dimers enter the nucleus, bind to specific DNA elements, and activate transcription of downstream genes

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Jacob and Monod

answer

In the 1960s, made the operon model.

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James Guesella, Nancy Wexler, and coworkers

answer

In 1983, demonstrated that Htt was linked with an RFLP. Mapped chromosome 4, and showed that linkage was about 96% complete. Wexler spent years in Venzuela, collecting data to map the chromosome. The discovery allowed for development of a method to genetically screen patients for Huntington's disease.

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James Watson and Crick

answer

Discovered the double-helix structure of DNA in 1953. Watson initiated the HUman genome project in 1990, and was the first director.

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Jefff Healy

answer

Had retinoblastoma.

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Jeffrey Carroll

answer

A Canadian scientist with Huntington's disease. He is working to help find a cure, and perhaps extend his own life. He is the father of healthy identical twins, using in vitro fertilization with pre-implantation genetic diagnosis.

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Jesse Gelsinger

answer

An 18-year-old boy with ornithine transcarbamylase deficiency, a genetic disease causing a build-up of ammonia in his blood. Died in 1999, for days after an experimental gene therapy treatment, after a severe immune reaction to the adenovirus vector, causing organ failure. The researchers involved were found responsible for his death due to negligence.

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jun

answer

A viral oncogene found in avian sarcoma virus 17 that affects chickens. Produces a transcriptional activator protein.

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K-ras

answer

A viral oncogene found in Kirsten murine sarcoma virus that affects rats. Produces a GTP-binding protein.

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Kan^r

answer

A gene from E. coli transposon Tn5, encoding neomycin phosphotransferase, which phosphorylates and inactivates kanamycin. Used as a selectabel marker in modified Ti plasmids for gene transfer.

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Kary Mullis

answer

Tried to write science fiction, and tried to open a bakery. Worked for a biotech company in San Francisco. Got a PhD from Kerley. Was a research scientist at Cetus Corporation in the 1980s. Was interested in developing a method to detect a single bp change responsible for sickle cell anemia, from small samples, so developed PCR. Received bonuses and sold the idea. Won the Nobel Prize in Chemistry in 1993, but his girlfriend Jenny broke up with him.

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Kidney cancer

answer

The eighth most common type of cancer.

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Kinase

answer

Enzymes that transfer phosphate groups to molecules. May play a role in chromatin-remodeling complexes.

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Klenow fragment

answer

DNA polymerase I of E. coli. Used in the original PCR protocol. It is denatured during the first step of PCR, so it must be re-added. Its optimum activity is at 37? C.

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Knockout (KO)

answer

Directed site specific recombination, integrating DNA into a gene at random, or down-expressing a gene using RNAi. Used to study the effect of removing a gene from an organism.

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Knudson's two-hit hypothesis

answer

Rate of appearance of retinoblastoma tumours is consistent with a single random event for familial tumours, and requires two random hits for sporadic tumours.

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KpnI

answer

A restriction endonuclease that produces 3' overhangs.

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Lactose

answer

Genes for lactose metabolism in E. coli are specifically transcribed when lactose is given to cells. It is an inducer of gene transcription. This was studied by Jacob and Monod.

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Lamin

answer

Normally forms a mesh. When phosphorylated, there is disassembly of the lamina.

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Lap-Chee Tsui, Jack Riordan, and colleagues

answer

From the Toronto Hospital for Sick Children. Synthesized oligonucleotides complementary to the mutant and wild-type alleles of the cftr gene and demonstrated that at 37? C under specific conditions, the probes hybridized with their corresponding alleles. This can be used to analyze the DNA of CF patients and their parents. The research team was led by Francis Collins.

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Large adenoma

answer

The second stage of colorectal cancer. Appears in patients aged 40 - 50.

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Legionella pneumophila

answer

Legionnaire's disease
The genome of strain Paris is 3,503,610 bpw ith 3,136 genes.

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Leucine zipper

answer

A stretch of amino acids with leucine at every seventh amino acid. The polypeptide forms dimers by interactions between leucines in zipper regions. Usually adjacent to a stretch of positively charged amino acids. The two zippers interact and form a surface that can bind to DNA.

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Leukemia

answer

The ninth most common type of cancer.

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Li-Fraumeni syndrome

answer

An inherited cancer syndrome, causing sarcomas and breast cancer. A mutation in TP53 (17p13.1), the product of which is a transcription factor. A rare dominant condition in which any of seveal types of cancer may develop. Mutation in p53, which controls cell cycle apoptosis.

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Ligand-binding domain

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A functional domain of a transcriptional factor. Signal sensing domain. Binds to external signals, such as hormones.

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LIM-only gene 2 (LMO2)

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A gene associated with T cell acute lymphoblastic leukemia: a translocation between chromosome 7 and 11, placing a strong promoter of TCR? gene close to the LMO2 gene, causing overexpression that stimulates cell proliferation, causing cancer. Some gene therapy recipients have elevated levels of LMO2 expression due to insertion of the IL2R?c transgene close to the LMO2 gene.

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Lin-4

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A gene in C. elegans that controls lin-14. Produces a noncoding 70 bp RNA precursor, which is trimmed to produce a 22 bp miRNA that is imperfectly complementary to a 3'-UTR in lin-14. Binding suppresses translation of lin-14.

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Lin-14

answer

A gene in C. elegans which has repressed translation due to binding of miRNA to the mRNA transcript. Encodes a transcription factor that controls development. Expression is controlled by lin-4.

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Liposomes

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A vector for gene therapy. Artificial lipid-coated vesicles. Delivers enclosed transgenes by fusing with cell membranes. There is some dose-dependent toxicity. Commonly used in cell cultures; not widely used in humans.

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Locus control region (LCR)

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Regions upstream of human ?-globin genes which have DNase I hypersensitive sites. Contains binding sites for transcription factors that pre-activate individual genes for transcription. Pre-activation is detected by an increased sensitivity to DNase. It must be upstream of the gene, and in correcct orientation in order to work, however if it is transposed with its gene to another chromosomal location, it still works.

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luc+

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A gene for firefly luciferase. Luciferase protein can be assayed by measuring light. Converts luciferin to light. Light intensity is proportional to the concentration of luciferase mRNA, which is proportional to its transcriptional activity.

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Luciferase

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Converts luciferin into oxy luciferin in the presence of ATP during pyrosequencing.

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Luciferin

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Converted into oxy luciferin by luciferase in the presence of ATP during pyrosequencing.

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Lung cancer

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The most common type of cancer. In large measure it is due to the effects of cigarettes. Percent of survival of 5 years is 16.8%.

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Lymphoma

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The sixth most common type of cancer.

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MacKeigan et al

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Knocked down expression of kinases in HeLa cells using RNAi. Tested cells for resistance to chemotherapeutic drugs. Identified 73 kinases, 11% of the kinome, which enhanced apoptosis when ablated. Suggests possibility of using RNAi/drug combination therapy for cancer treatment.

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M

answer

A phase in cell cycle. Chromosome segregation, cell division.

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Male-specific lethality (msl)

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Genes that code for proteins that bind to the X chromosomes in male Drosophila for hyperactivation, remodeling chromatin near genes on the X chromosome, leading to hyperactivation. Includes a HAT that acetylates H4.

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Malignant

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When cell detach from a tumour and invade the surrounding tissues. Can be life threatening. A number of mutations must occur before a tumour becomes malignant.

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Mammalian cell lines

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An alternate expression system for recombination protein production. Produces low yields of foreign protein.

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Map

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A program developed by GCG that can be used to translate ds DNA in all six reading frames. Used in bioinformatics.

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Marchantia polymorpha

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Liverwort
A primitve, non-vascular plant. The mitochondrial genome is 186 kbp, with 94 open reading frames. The chloroplast genome is 121,024 bp, with 134 genes. One of the first chloroplast genomes to be sequenced.

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Mark Groudine and Harold Weintraub

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Demonstrated in 1976 that transcriptionally active DNA is more sensitive to DNase I than non-transcribed DNA. Exposed chicken blood to DNase, and probed the chromatin fragments for ?-globin and ovalbumin genes. Found that 50% of ?-globin genes were digested, but 10% of ovalbumin genes were digested. This implied that the actively transcribing segments of gnes were more "open" to nuclease attack.

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Maxam Gilbert sequencing

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A labour-intensive process which involves offensive chemicals.
1. DNA is radioactively labelled
2. Strands are separated
3. Four separate reactions modify and destroy specific bases
4. DNA is cleaved at the position of the missing base
5. DNA is separated by polyacrylamide gel electrophoresis, dried, and exposed to X-ray film

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mCpG

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Methylated CpG group.
m = methylated
p = phosphodiester bond

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Mediator complex

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A multimeric complex consisting of at least 20 different protein. It bends the DNA in a way that proteins bound to an enhancer are juxtaposed to those bound at a promoter, allowing them to control transcription. Acts as bridge between transcriptional factors and RNA polymerase II, to stimulate RNA synthesis. Different subunits interact with specific transcription factor activation domains. One of the subunits has histone acetylase activity to maintain nucleosome-free DNA. Other subunits contract general transcription factors and RNA polymerase II to assist in the assembly of the pre-initiation complex.

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Melanoma

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The seventh most common type of cancer.

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Membrane-bound receptor proteins

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Transmit peptide hormones into cells.

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Membrane localization protein targeting

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Includes peptide hormone receptor.

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Messing

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Developed M13 cloning vectors in 1980. Cloning system was applied.

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Metabolome

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All metabolic pathways and intermediaries in an organism.

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Metabolomics

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The study of the metabolome.

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Metagenomics

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The study of aggregate genomes from a complex of organisms, such as a gut microbiome.

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Metastasis

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"Change state"
When malignant tumours spread to other locations of the body to form new tumours. Cancer cells detach from the primary tumour and travel through the bloodstream to other locations. The most serious occurrence in the progression of a cancer. Most tumours originate from epithelial cells.
1. Tissue invasion
2. Intravasation
3. Survival in the blood
4. Extravasation
5. Colonization

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Methylation

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Protects cleavage sites from the organisms' own restriction endonucleases. One or more nucleotides in each sequence recognized by a restriction endonuclease is methylated. Methylation occurs after replication, catalyzed by site-specific methylases.

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Methylation specific restrition enzyme

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Detect methylated CpG dinucleotides. HpaIII and MspI recognize CCGG, and cut between the two Cs. HpaIII cannot cleave if the second C is methylated, however MspI can.

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Microprojectile bombardment

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Gene gun
A procedure for producing transgenic plants. A DNA-coated tungsten or gold particle is shot into a plant cell.

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MicroRNA (miRNA)

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Small RNA, 21 - 28 bp. Produced from larger double stranded RNA that are processed. There are hundreds of genes which encode miRNAs. Exist in nematodes, flies, plants, mammals, and some viruses. There are 2588 miRNAs in humans, each capable of binding to many different mRNA transcripts. Each mRNA transcript can potentially bind to many miRNAs. Perform dsRNAs in vitro. Synthesized as a large pre-miRNA with a hairpin. The functions of many miRNAs are under investigation. RISC-associated RNAs that result in inhibited translation of mRNA. THere is imperfect base-pairing between RISC and mRNA. Involved in post-transcriptional regulation of genes; endogenous gene regulation system in which short RNAs produced in the cell are used to interfere with mRNA translation. Base pair with mRNA 3' UTRs, and interfere with translation.
miRNA gene silencing:
1. Recruit deadenylases leading to mRNA degradation
2. Recrut proteases to degrade the nascent peptide
3. Inhibit translational inhibition and/or elongation

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Miescher

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Discovered DNA in 1868.

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mil

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mht
A viral oncogene found in MH2 virus that affects chickens. Produces a serine/threonine protein kinase.

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Minimal gene set

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The minimum number of genes that would support life of a single-celled organism.

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Mir

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Genes that produce miRNAs that produce small RNA molecules that induce RNAi. Have little or no protein-coding potential. Contain a short stretch of nucleotides repeated in opposite orientations around a short intervenign segment of DNA. The inverted repeat structure of transcribed RNA folds back on itself to form a double-stranded stem at the base of a single-stranded loop. The stem-loop region is excised from the transcript by a Drosha enzyme, and cleaved to form miRNA. Many mir genes were identified using computer-based genomics.

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Missense mutation

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A mutation which is a substitution of a nucleotide that changes the codon of one amino acid into another mutation.

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Mitochondrial DNA (mtDNA)

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Discovered in the 1960s using electron micrographs. One mitochondrion has several copies of mtDNA. Most mtDNA are circular, but some are linear.

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Model organism

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Enables scientists to compare their results with other scientists; many people studying the same organism. Studying model organisms can give clues to how things work in humans. Includes yeast, nematodes, fruit flies, mice, and humans.

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Molecular chaperone proteins

answer

Heat shock proteins
Play an essential role in assisting proteins reach their properly folded conformation. Overexpression can alleviate the toxic consequences of misfolded proteins in cell and animal models of protein -misfolding diseases. Assist in de novo folding of proteins, their intercellular transport and assembly, refolding of proteins damaged by proteotic stress and delivery of irreversibly damaged proteins to the ubiquitin proteasome system or autophagy machinery for destructino. Act as surveillance factors or misfolded proteins. Not present in the folding protein's final structure. Multicomponent molecular machines that act through ATP and co-factor regulated binding and release cycles. Recognizes hydrophobic amino acids exposed by non-native proteins. May be constitutively expressed or stress-inducible. Includes HSP70, HSP90, chaperonin/HSP60, and HSP families.

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Molecular hybridization

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A method of screening DNA for genes of interest. Radioactively labelled DNA or RNA probes are used to hybridize DNA bound to a nylon plate. A replica plate is made ona nylon membrane, cells are lysed and DNA is denatured. The cDNA probe (made with radioactive nucleotides) is added and incubated to allow hybridization with membrane-bound DNA. Unbound probe is washed away, and the membrane is exposed to X-ray film. When developed, dark spots will reveal where positive colonies are located on the original plate.

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Molecular pharming

answer

Transgenic plants that produce vaccines.

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Molecular synteny

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Conserved gene order

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Monozygotic

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Identical twins
Twins which originated from a single fertilized egg. Have the same genome.

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mos

answer

A viral oncogene found in Moloney sarcoma virus that affects mice. Produces a serine/threonine protein kinase.

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Motif

answer

A pattern in a protein structure associated with its secondary structure.

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mRNA

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Messenger RNA
Codes for proteins.

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Multiple clonign site (MCR)

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Polylinker
A cluster of unique restriction sites on modern cloning vectors.

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Murder

answer

Cells are instructed to die by cytotoxic T cells. Autoreactive immune cells during differentiation, expanded populations of immune cells at the end of immune responses, virus-infected cells transformed into cancerous cells.

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Mus musculus

answer

Mice
A model organism with a sequenced genome. The first draft of the sequence was released in 2002. Its genome is 2,932,368,526 bp long, with 25,396 genes, for a density of 115,500 bp/gene.

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Mutant mosquitoes

answer

Mosquitoes with genomes modified by an efficient Cas9-mediated gene. Resist malaria, which kills 500,000 thousand people per year.

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myb

answer

A viral oncogene found in avian myeloblastosis virus that affects chickens. Produces a transcription factor.

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myc

answer

A viral oncogene found in MC29 myelocytomatosis virus that affects chickens. Produces a transcription factor.

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Mycobacterium tuberculosis

answer

Causes tuberculosis, the cause of more human deaths than any other infectious bacteria. The genome of strain CDC has 4,403,835 bp with 4,293 genes.

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Mycoplasma capricolum

answer

Was used to test the synthetic genome produced for Mycoplasma mycoides.

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Mycoplasma genitalium

answer

Has a genome 580,076 bp, with 525 genes, the smallest genome of any non-symbiotic bacteria.

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Mycoplasma mycoides

answer

A faster-growing relative of Mycoplasma genitalium. A synthetic genome was constructed by J. Venter and colleagues.

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N-myc

answer

Amplified 30% of childhood neuroblastomas.

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Nanoarchaeum equitans

answer

An archae. An obligate symbiont witha genome that is 490,885 bp, with 582 genes.

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Nasui Morcos

answer

A man who chose to take his own life rather than suffer from the disabling effects of Huntington's disease. He died in September 2012.

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National Centre for Biotechnology Information (NCBI)

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Maintains GenBank at the NIH in Maryland. Encompasses the bibliographic database PubMed.

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National Institute of Health (NIH)

answer

A project funcded by the US government. Developed strict guidelines for gene therapy protocols: there must be gene characterization, an effective delivery mechanism, minimal risk, no other treatment strategies available, and preliminary data on effectiveness.

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Neo^r

answer

A targeting vector inserted into genes of mice, disrupting coding sequence, inactivating the gene. Split segments of hte genome provide homology for recombination with the genomic copy. Provides resistance to the antibiotic neomycin. The ES cells are then screened for the transgene and injected into the blastocyst to produce a transgenic mouse.

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Neurofibromatosis type 1

answer

An inherited cancer syndrome causing neurofibromas. A mutation in NF1 (17q11.2), the product of which regulates Ras-mediated signalling. A disease characterized by benign tumours and skin tumours.

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Neurofibromatosis type 2

answer

An inherited cancer syndrome causing acute neuromas and meningiomas. A mutation in NF2 (22q12.2), the products of which function in linkage of membrane proteins to the cytoskeleton.

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Next generation sequencing

answer

Massively parallel sequencing. DNA molecules are attached to solid surfaces or beads to be sequenced. Allows for millions of sequencing reactions to happen in parallel. Includes 454 technology.

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Nicotania tabacum

answer

Tobacco
The chloroplast genome is 155,844 bp, with 150 genes. One of the first chloroplast genomes to be sequenced.

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Noc

answer

A gene on the T-DNA of a Ti plasmid. Involved in catabolism of nopaline.

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Nonhomologous ending joining (NHEJ)

answer

Results in insertions or deletions, creating a mutation that will inactivate the targeted gene.

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Nonsense mutation

answer

A mutation which is a substitution of a nucleotid that changes the codon of one amino acid into a termination codon.

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Northern blotting

answer

Invented in 1977. Similar to Southern blotting. RNA molecules are transferred to the membrane from an electrophoresis gel. Detects RNA accumulations, but provides no information on why they have accumulated. RNA is less stable than DNA, so care must be taken to prevent degradation. Used to detect the length and types of transcripts of a specific gene, and to measure the transcription level of a gene. Measures mRNA abundance in different tissues. Detects length and type of transcripts from a specific gene. Measures change in gene expression as a result of differences in developmental stage, environmental stress, and drug treatment.

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Nos

answer

A gene on the T-DNA of a Ti plasmid. Involved in nopaline biosynthesis.

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NotI

answer

A restriction endonuclease found in Nocardia otitidis. Cleaves GCGGCCGC.

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Nuclear pore proteins (NUP)

answer

When phosphorylated, there is dissambly of the nuclear core complex.

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Nuclear transfer technology

answer

Reproductive cloning
Transfer of a nucleus from an adult cell to an egg cell with its nucleus removed. Artificially constructs a zygote. The animal has the nuclear genome inherited from the nucleus donor. The animal has developmental abnormalities and shortened life span. Dolly the sheep was produced this way.

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Nuclear translocation protein targeting

answer

Includes histones and cell cycle regulating proteins.

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Nucleosome core

answer

An octamer of histones: two H2a, two H2b, two H3, two H4. 11 nm in diamter. Binds to 146 bp.

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Nucleotide

answer

Composed of a purine (G or A), or a pyrimidine (C, T, or U) base linked to a pentose sugar. The bases absorb light, and this property is used to measure DNA concentration.

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Oligo-dT primer

answer

A primer often used when synthesizing cDNA. mRNAs all contain a 3' poly(A) tail.

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Oligonucleotide sequencer

answer

Can produce oligonucleotides 50 bp long before it starts to make errors.

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Oliver Smithies and coworkers

answer

First used homologous recombination in 1985 to target DNA sequences to the ?-globin locus of human tissue-culture cells. The frequency of targeted gene transfers was very low, about 10^-5. Later, with Mario Capecchi, developed improved selection strategies for efficient targeted gene replacements, and methods to identify cells with the desired gene replacement.

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Oncogene

answer

"Tumour"
Mutant genes that actively promote cell division. An over-expression or activation of a proto-oncogene, causing cancer. Arises by point mutation, chromosomal translocation, or amplification. Can cause activation of signal transduction pathways leading to cell proliferation that are no longer growth factor dependent. Includes viral oncogenes and cellular oncogenes. Carcinogens mutate proto-oncogenes to turn them into oncogenes.

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Open reading frame (ORF)

answer

A contiguous, non-overlapping string of codons. Translation starts at the 5' start codon (AUG), and ends at the 3' stop codon.

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Operon model

answer

Made by Jacob Monod in the 1960s. Regulatory proteins bind operator sequences and repress expression of structural genes. Induction requires removal of the repressor. Inducible systems are under negative control.

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Origin of replication

answer

An essential component of a cloning vector.

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Orthologous genes

answer

Orthologues
Homologues present in different species. Includes tubulin genes of Arabidopsis and Chlamydomonas.

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Oryza sativa

answer

Rice
The mitochondrial genome is 491,515 bp with 96 genes. The chloroplast genome is 134,525 bp with 159 genes.

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Oskar

answer

A protein responsible for development of germ cells in Drosophila. The mRNA is localized at the posterior end of the larva.

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p

answer

The short arm of a chromosome.

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P-bodies

answer

Small cytoplasmic granules where deadenylation, decapping, and degradation occur.

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p21

answer

A CDK inhibitor. Binds to CDK2/cyclin B complex and inhibits CDK2 kinase activity. Keeps cells inactive in mitosis.

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p53

answer

A tumour suppression gene. The guardian of the genome. Controls cell proliferation and cell death. Produces miRNAs that inhibit proliferation, survival, angiogenesis, and epithelial to mesenchymal transition. It is inhibited by miR-380 and miR-504. Mutating it caused experimental mice to die faster. Inherited mutation in p53 is associated with Li-Fraumeni syndrome. Encodes a transcription factor that binds to DNA as a homo-tetramer. Has a short half-life, ubiquinated by MdM2 proteins for degradation. Stress conditions such as DNA damage prevent p53 degradation, resulting in increased accumulation. Induces expression of genes controlling DNA repair, cell cycle progression (p21), and apoptosis (BAX). Mutated in over 50% of all cancers. 95% of all p53 mutations are within the DNA binding domain; one mutant allele has a dominant negative effect, part of tetrameric complexes that cannot bind DNA (if there is one mutation, 15 out of 16 possible tetramers are mutated). If mutated, cells escape apoptosis and divide with damaged DNA; these cells are then able to accumulate additional mutations that increase the probability of tumour formation.

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Palindromes

answer

Nucleotide pair sequences that read the same forward or backward from a central axis of symmetry. Restriction endonucleases commonly recognize palindromes. After the DNA is broken into restriction fragments, the overhangs are complementary and may anneal to one another.

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Pamel Greyer and Victor Corces

answer

Showed that the yellow gene is regulated by several enhancers, some of which are located within an intron. Enhancers allow expression to be controlled in specific tissues.

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Pan troglodytes

answer

Chimpanzee
The closest living relative of humans. Its genome was sequenced in 2006. The genome is 2,928,563,828 bp, with 21,098 genes for a density of 139,000 bp/gene.

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Pancreatic cancer

answer

The eleventh most common type of cancer.

question

Paralogous genes

answer

Paralogues
Homologues within a species.

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Parkinson's disease (PD)

answer

A disease caused by mis-folding of proteins.

question

Parmecium aurelia

answer

A ciliate. Has linear mtDNA.

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Passenger strand

answer

Degraded by the Argonaute protein as ds RNA is unwound.

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Paul Berg

answer

First produced recombinant DNA moleucles in 1972 at Stanford University. Berg and his research team combined DNA of phage lamba and simian virus 40. Berg was co-recipient of the Nobel Prize in Chemistry in 1980.

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pBR322

answer

An early bacterial cloning vector.

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pcDNA3

answer

Human cells grown in vitro express GFP from an expression plasmid. There are three cassettes: eukaryotic expression cassette 1 and 2, and bacterial expression cassette.

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Pedigrees

answer

Used to track inheritances, to see if individuals in a family share markers.

question

Peptide hormones

answer

A class of animal hormones. Polypeptides encoded by genes. Water soluble. Too large to pass through cell membranes; must be transmitted into cells by membrane-boudn receptor proteins. Peptide hormones cause conformational changes in receptors, leading to changes in other proteins in the cell. Causes signal transduction. Includes endocrine signalling. Includes insulin, somatotropin, and prolactin.

question

PerkinElmer, Inc.

answer

Developed 96-capillary sequencer in 1998. Fully automated 96-capillary electrophoresis sequencing system became available to research laboratories.

question

Peyton Rous

answer

Discovered the first tumour-inducing virus in 1910. It was Rous sarcoma virus, the causative agent of a bird sarcoma. Won the Nobel PRize in 1966. Extract from chicken sarcoma could cause tumour formation in chickens after passage through a filter capable of retaining bacteria.

question

Pfu polymerase

answer

A thermostable polymerase found in Pyrococcus furiosus. Has a lower error rate than Taq polymerase. Used when high fidelity is needed, such as for gene cloning. Has 3' > 5' proofreading activity.
Efficiency = 60%
Error rate = 7 x 10^-7
Maximum fragment length = 20 kb

question

Phage lambda

answer

A cloning vector. Has a maximum insert size of 23 kb. Widely used for several years.

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Phage P1 artificial chromosomes (PAC)

answer

A cloning vector. Maximum insert size of 300 kb. Combine multiple cloning sites and selectable marker genes with the essential components of phage P1 chromosomes. Those with sacB can be used for negative selection.

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Phagemids

answer

A cloning vector. Has a maximum insert size of 15 kb. Combines components of phages, such as M13, with components of plasmids.

question

Phenylalanine (F)

answer

The amino acid which is deleted in ?F508 mutation that causes cystic fibrosis.

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