question

+1 sequence

answer

The site where transcription begins.

question

2-aminopurine (2-AP)

answer

A base analog. An adenine or guanine analog.

question

3' - 5' exonuclease activity

answer

Cuts DNA strands, starting at the 3' termini. The DNA polymerase goes "backwards". Allows for proofreading.

question

5' - 3' exonuclease activity

answer

Cuts DNA strands, starting at the 5' termini.

question

5-bromouracil (5-BU)

answer

A base analog. A thymine analog that pairs with adenine or guanine, depending on if it is in keto or enol form. If it is in enol form before incorporation, it produces C:G > A:T transitions. If it is in enol form after incorporation, it produces A:T > C:G transitions.

question

7-methyl guanosine cap

answer

5' cap
A 7-methyl guanosine residue joined to the initial nucleotide of the transcript by a 5' - 5' phosphate linkage. Added to the nascent RNA transcript during elongation when it is about 30 nucleotides long. Protects the 5' end from degradation.

question

-10 sequence

answer

A promoter. Part of the Pribnow box. An upstream sequence about 10 nucleotides from the initiation site in E. coli. Its consensus sequence is TATAAT. Facilitates localized unwinding of DNA because it is A:T rich.

question

-35 sequence

answer

Recognition sequence
A promoter. Part of teh Pribnow box. An upstream sequence about 35 nucleotides from the initiation site in E. coli. Its consensus sequence is TTGACA. The sigma subunit binds to this sequence.

question

?-amanitin

answer

An inhibitor of RNA polymerase II. A deadly toxin. Found in death angel mushrooms.

question

?-helix

answer

A secondary structure in proteins. Rigid cylinders in which each peptide bond is hydrogen bonded to the peptide bond three/four amino acids away. Proline cannot be present in ?-helices.

question

?-sheet

answer

A secondary structure in proteins. The polypeptide folds back onto itself, sometimes repeatedly, and the parallel segments are held by hydrogen bonds.

question

A-DNA

answer

Right-handed, compact DNA. Created artificially by exposing DNA to salts.

question

Ac/Ds elements

answer

Cut-and-paste transposons found in maize. Discovered by Barbara McClintock. Cause clear corn kernels to become mosaic brown/purple kernels.

question

Acquired immune deficiency syndrome (AIDS)

answer

A disease caused by HIV virus. Affects tens of millions of people. Loss of ability to fight infections from pathogens, including normally benign organisms.

question

Acquired traits

answer

Traits imposed on an organism by environmental factors. Jean Lamarck and Trofim Lysenko thought that they were inherited, but actually they are not.

question

Acridine dyes

answer

A class of chemical mutagens. Intercalates into DNA, sandwiching between base pairs, increasing the probabilit of mistakes in replication. The DNA molecules are more rigid, and may have kinks. Causes frameshift mutations. Includes 2,8-diamino acdiride (proflavin), and acridine orange.

question

Acridine orange

answer

An acridine dye.

question

Activator

answer

The product of regulator genes in positive control mechanisms. They are needed to turn on expression of one or more structural genes.

question

Adenine

answer

Has a common amino form, and a rare imino form, with the H at C6 rather than C1. If treated with nitrous acid, it changes to hypoxanthine, which pairs with cytosine.

question

Alkylating agents

answer

A class of chemical mutagens. Mutagenic to replicating and non-replicating DNA. Donates alkyl groups (ethyl, methyl, et cetera) to other molecuels, altering base pairing, or activating error-prone DNA repair processes that introduce mutations during repair. Induce all types of mutations, including chromosome aberrations. Includes di-(2-chlorethyl) sulfide (mustard gas), ethyl methane sulfonate (EMS), and ethyl ethan sulfonate (EES).

question

Allolactose

answer

The affector molecule of the lac operon. An inducer. Produced from lactose by ?-galactosidase, the product of lacZ, which has a low background level of expression at all times.

question

Allosteric transition

answer

Conformational change in protein structure due to binding with another molecule.

question

Amber mutation

answer

Named after one of the researchers who discovered them. Nonsense mutations in E. coli that produce stop codons, and result in synthesis of truncated polypeptides. Mutant tRNAs that recognize stops codons as amino acids are suppressor mutations for amber mutations.

question

Amino

answer

The common form of cytosine and adenine.

question

Amino acid

answer

The constituent of polypeptides. Has an amino group, a free carboxyl group, and a side group.

question

Aminoacyl site (A)

answer

The A site on a ribosome. Binds incomping aminoacyl-tRNAs.

question

Aminoacyl-tRNA

answer

tRNA with an amino acid attached by a high-energy bond. Created by aminoacyl-tRNA synthetase.

question

Aminoacyl-tRNA synthetase

answer

Catalyzes the binding of amino acids to the correct tRNA, converting ATP into AMP. There is at least one for each amino acid.

question

Anabolic pathways

answer

Biosynthetic pathways
Often repressible. Repressed in the presence of the molecule they produce.

question

Anticipation

answer

Increased copy number of a trinucleotide repeat with each generation, leading to increased severity or early onset of the disease.

question

Antisense strand

answer

Strands of RNA that are complementary to sense strands. Do not code for polypeptides.

question

apo-B

answer

Genes which regulate apolipoproteins: blood proteins in rabbits and humans which carry fat molecules. The mRNA has a change in structure of bases during RNA editing. This enables the mRNA to produce different products in different parts of the body, to perform different functions.

question

ARS elements

answer

Autonomously Replicating Sequences
Sequences in prokaryote DNA that have their own origin of replication, and replicate independently from the rest of the chromosome. About 50 bp in length, with a conserved core A:T rich 11 bp sequences. Found in Saccharomyces cerevisiae.

question

Arthur Kornberg and coworkers

answer

First demonstrated in vivo DNA replication in 1957, and won the Nobel Prize in 1959.

question

Ataxia-telangiectasia

answer

An inherited disease caused by defects in DNA repair mechanism. Radiation sensitivity, chromosome instability, early onset of progressive neurodegeneration, and prone to cancer. Caused by defects in kinases involved in the control of cell cycle. Caused by mutations in ATM.

question

ATM

answer

A gene on chromosome 11 for serine/threonine kinase. Mutation in this gene can lead to ataxia-telangiectasia.

question

AUG

answer

The initiation sequence in eukaryotes. Codes for tRNA_i^Met. The ribosome moves down from the 5' end, scanning for this sequence. At all other positions in the mRNA, it codes for tRNA^Met.

question

Autoradiography

answer

Detecting radioactive isotopes by exposing the experiment to a photographic emulsion containing silver halides. Black spots form where radioactive isotopes are present.

question

Back mutation

answer

A type of reversion. A second mutation at the same site in the genome. Restores the nucleotide sequence of the gene. If back-crossed to a wild-type individual, all progeny are wild-type.

question

Balbiani rings

answer

Puffs
Sites of localized unwinding due to gene transcription in eukaryotes. Occurs in the polytene chromosomes of Drosophila salivary glands.

question

Barbara McClintock

answer

Studied maize chromosome breakage at University of Missouri 1936 - 1941. Discovered Ac/Ds transposable elements in 1940. Proposed the idea of transposable elements. The concept was not accepted immediately; people thought that DNA was stable, and didn't "jump around". Won the Nobel Prize in 1983.

question

Basal transcription factor _ (TFII_)

answer

Transcription Factor for RNA polymerase II [letter of denotation]
Transcription factors which initiate transcription by RNA polymerase II. Must interact with promoters in the correct sequence to initiate translation. Incldues TFII A, B, D, E, F, and H.

question

Base analogs

answer

A class of chemical mutagens. Mutagenic only to replicating DNA. Have structures similar to normal bases, and are incoroprated into DNA during replication. Increase the frequency of mis-pairing. Includes 5-bromouracil (5-BU), and 2-aminopurine (2-AP).

question

Base excision repair

answer

A form of excision repair. Systems remove abnormal or chemically modified bases from DNA. Initiated by DNA glycosylases that recognize abnormal bases in DNA: each recognizes a specific type of altered base. DNa glycosylase cleaves the glycosidic bond between base and deoxyribose, creating apyrimidine sites (AP sites) with missing bases. AP endonuclease acts with phosphodiesterases to excise sugar-phosphate groups.

question

Benno Muller-Hill and coworkers

answer

Showed that O₂ and O₃ operators of the lac operators have effects on levels of transcription in the operon.

question

Bidirectional replication

answer

Replication forks travel in opposite directions from the origin of replication. Mario Schnos and Ross Inman provided evidence for this.

question

bla

answer

A gene on a Tn3 element. Codes for beta lactamase enzyme, which produces resistance to ampicillin.

question

BLM

answer

A gene on chromosome 15 for BLM REcQ helicase. Mutation in this gene can cause Bloom syndrome.

question

Bloom syndrome

answer

An inheritance disease caused by defects in DNA repair mechanism. Chromosome instability, mental retardation, and prone to cancer. Increased chromosome aberration. Alterations in specific DNA helicases. Caused by mutation in BLM.

question

CAAT box

answer

An element of a promoter for RNA polymerase II. A conserved element at about -80. The consensus sequence is GGCCAATCT.

question

Caenorhabditis elegans

answer

A eukaryote which has multi-genic mRNAs that contain many genes.

question

CAF-1

answer

Chromatin assembly factor 1. Carries histones to chromosomal sites of nucleosome assembly during DNA replication.

question

Catabolic pathways

answer

Degradative pathways
Usually catalyzed by inducible enzymes. Induced by presence of the molecule they break down.

question

Catabolite activator protein (CAP)

answer

Cyclic AMP receptor protein
A dimer that binds to the CAP/cAMP binding site on the lac operon in the presence of glucose. It has positive control. It bends the DNA, making it easier for RNA polymerase to attach. It binds to loops formed when lac repressor is bound to O₁ and O₃.

question

Catbolite repression

answer

Glucose effect. In the presenceof glucose CAP prevents induction of the lac (lactose), ara (arabinose), and gal (galactose) operons. Assures that glucose is metabolized in preference to other, less efficient carbohydrates. CAP has positive control of the operons, and cAMp is the effector molecule, present only in the absence of glucose.

question

Central Dogma of molecular biology

answer

First described by Francis Crick.
DNA -(transcription)--> RNA -(translation)--> polypeptides

question

Chain termination codon

answer

UAA, UAG, or UGA
Triggers termination of translation when they enter the A site of the ribosome. Recognize by release factors.

question

Chaperones

answer

Proteins that help some nascent polypeptides fold into their correct formation.

question

Charles Yanofsky and colleagues

answer

First demonstrated evidence for colinearity between genes and polypeptides. Compared the nucleotide sequences of trpA with the amino acid sequence of the polypeptide it codes for in wild-type and mutant E. coli.

question

Charlotte Auberach and associates

answer

Discovered the mutagenic effects of mustard gas. Their research was classified during WWII due to its use as a weapon, and results were not published until after the war.

question

Chemical mutagen

answer

Chemicals which are mutagens. May affect replicating or non-replicating DNA, or replicating DNA only. Includes alkylating agents, base analogs, acridines, deaminating agents, and hydroxylating agents.

question

Chromosome remodeling

answer

Modification of nucleosomes, to interact with proteins and express only genes which need to be expressed. Occurs before transcription.

question

ClB chromosome

answer

An X chromosome in Drosophila which is altered. Examined in the ClB method. Has three characteristics:
C: Crossover suppressor. A long inversion that suppresses recombination between ClB and normal X chromosomes. Causes recombinant progeny to abort.
l: Lethal mutation. Homozygous females and hemizygous males with the ClB chromosome are not viable.
B: Bar-eye phenotype. The eyes are narrowed and bar-shaped. It is partially dominant, so heterozygotes can be identified.

question

ClB method

answer

An accurate method of identifying lethal mutations on the X chromosomes of Drosophila, developed by Hermann J. Muller. Performed with females heterozygous for the ClB chromosome. If there is a recessive lethal mutation on the X chromosome, all progeny from a cross with a normal male will be female.

question

Co-repressors

answer

Effector molecules that cause repression of genes. Cause activators to detach from the RPBS. Cause repressors to attach to the RPBS.

question

Cockayne syndrome

answer

An inherited disease caused by defects in DNA repair mechanisms. UV sensitivity, neurological and developmental disorders, and premature aging. Caused by mutation in CSA or CSB.

question

Codon

answer

A three-nucleotide sequence that specifies an amino acid, according to the genetic code.

question

Cointegrate

answer

A Tn3 element fused to a plasmid. Tn3 is replicated and the cointegrate folds, producing site-specific recombinations at res sites, splitting the cointegrate apart producing two genetic elements with Tn3 genes.

question

Composite transposon

answer

A cut-and-paste transposon found in bacteria. Includes Tn3. Created when two IS elements insert into each other. The region between them can be transposed when the elements act joinly. The flanking IS element may be identical, inverted, or different IS elements.

question

Conjucative R plasmids

answer

Plasmids which transfer genes for antibiotic resistance between bacteria cells. May be rapidly exchanged between bacteria, even across species. Some carry multiple resistance genes. Evolved through IS-mediated recombination events. Cause many bacterial diseases to be difficult to treat for. Includes a resistance transfer factor and R-determinant.

question

Consensus sequence

answer

Sequences which are most often preserved.

question

Conservative replication

answer

A possible method of DNA replication. A completely new DNA molecule is produced. In Meselson and Stahl's experiment, one DNA strand would be heavy density, and the rest would be normal density. There is no evidence to support this.

question

Continuous replication

answer

Occurs on the strand of the replication fork going in the 5' - 3' direction. Synthesizes the leading strand.

question

Constitutive genes

answer

Continuously expressed
Genes which code for housekeeping functions.

question

copia

answer

A retroviruslike element found in Drosophila. Produces copious amounts of RNA.

question

Circk's wobble hypothesis

answer

Hypothesized by Francis Crick. In a tRNA, the first two bases in the codon/anti-codon are very important. Pairing at the third base, the wobble position is less important: supports some, but not all types of base pairing.

question

CSA

answer

A gene on chromosome 5 for DNA excision repair protein. Mutation in this gene can cause Cockayne syndrome.

question

CSB

answer

A gene on chromosome 10 for DNA excision repair protein. Mutation in this gene can cause Cockayne syndrome.

question

Cut-and-paste transposon

answer

Transposition of cut-and-paste transposons. The transposon is excised from one position in the chromosome and inserted into another position.

question

Cut-and-paste transposon

answer

A type of transposon. The element is moved by cut-and-paste transposition. Found in eukaryotes and prokaryotes. Encode for transposase. Includes IS elements, composite transposons, Ac/Ds elements, P elements, hobo elements, piggyBac elements, and Sleeping Beauty.

question

Cyclic AMP (cAMP)

answer

Adenosine-3'-5'-monophosphate
The effector molecule of CAP. An inducer. CAP can only bind to the CAP/cAMP binding site when cAMP is bound to it. It is derived from ATP. Glucose inactivates the enzyme which converts ATP into cAMP.

question

Cytosine

answer

Has a common amino form, and a rare imino form, with the H at C4 rather than C3. If treated with nitrous acid it changes to uracil, which pairs with adenine.

question

David Baltimore, Howard Temin, and Stoshi Mizutani

answer

In 1970, discovered reverse transcriptase. This discovery initiated research into reverse transcription.

question

Deaminating agent

answer

A class of chemical mutagens. Remove amino groups. Mutagenic to replicating and non-replicating DNA. Includes nitrous acid.

question

Death angel mushroom

answer

Amanita sp.
Mushrooms which contain the deadly toxin ?-amanitin.

question

Degeneracy

answer

A characteristic of the genetic code. All amino are specified by more than one codon except methionine and tryptophan. Includes partial degeneracy, where the last nucleotide can be either pyrimidine or either purine, and complete degeneracy, where the last nucleotide can be any base.

question

Delicious Apples

answer

A somatic mutation. The original tree was a genetic mosaic, and vegetative propagation allowed the mutation to be perpetuated.

question

Depression

answer

When a gene is deactivated by a repression.

question

Discontinuous replication

answer

Occurs on the strand of the replication fork going in the 3' - 5' direction. Synthesizes the lagging strand in Okazaki fragments.

question

Dispersive replication

answer

A possible method of DNA replication. Both new DNA strands contain segments from the original molecule. In Meselson and Stahl's experiment, all DNA strands would have hybrid density, decreasing as generations progress.

question

DNA

answer

B-DNA
Found in most cells. Complementary base pairs (A with T, C with G) on antiparallel strands. A right-handed double helix is found in most living cells. There are ten base pairs per turn, 0.34 nm between stacked bases, 3.4 nm length per turn.

question

DNA gyrase

answer

A DNA topoisomerase II in E. coli. A tetramer of two ? subunits encoded by gyrA, and two ? subunits encoded by gyrB.

question

DNA helicase

answer

A component of the primosome and the replisome. Unwinds the DNA strand for replication, using ATP. Two are present: one for each direction of replication. Encoded by dnaB.

question

DNA ligase

answer

Required for DNA replication, repair, and recombination in all organisms. Seals nicks between Okazaki fragments on the lagging strand, using energy from NAP or ATP, depending on species. Cannot work if a nucleotide is missing. Involved in excission repair and mismatch repair.

question

DNA photolyase

answer

The enzyme which carries out light-dependent repair. Activated by light. Uses the energy from blue light to cleave cross-links and repair thymine, cytosine, or cytosine-thymine dimers.

question

DNA polymerase

answer

Can add nucleotides to the 3' end of a primer strand, matching the opposite strand. Can only add in the 5' - 3' direction. A nucleophilic attack of the -OH group of the 3' end. Cannot produce DNA de novo. Makes one mistake out of every 10⁵ - 10⁶ nucleotides. Prokaryotes have 5 DNA polymerases. Eukaryotes have at least 15, some lacking 3' - 5' exonuclease activity.

question

DNA polymerase eta (?)

answer

Replicates damaged DNA. Coded by POLH.

question

DNA polymerase I

answer

Kornberg's enzyme
A replicative polymerase. Has a molecular mass of 103,000. A single polypeptide, encoded by polA. Catalyzes covalent addition of nucleotides to pre-existing DNA strands. Requires Mg²⁺ ions. Plays a role in chromosome replication and DNA. In E. coli it excises RNA primers and replaces then with DNA nucleotides using 5' - 3' exonuclease activity. Also has 3' - 5' exonuclease activity for proofreading. Not highly processive: has short tract synthesis.

question

DNA polymerase II

answer

Involved in DNA repair.

question

DNA polymerase III

answer

A replicative polymerase. A component of the replisome. A complex enzyme of at least 20 subunits. Has a molar mass of 900,000 Da in its holoenzyme form. Catalyzes the addition of DNA nucleotides to RNA primers. Terminates an Okazaki fragment when it encounters the RNA primer of the preceding fragment. The ?-dimer subunit, encoded by dnaN, is a ring that clamps the enzyme to the template strands so that it does not fall off easily. Has 5' - 3' exonuclease activity, only active on single-stranded DNA, and 3' - 5' exonuclease activity for proofreading. Involved in mismatch repair.

question

DNA polymerase IV

answer

Involved in error-prone repair. High error frequency.

question

DNA polymerase V

answer

Involved in error-prone repair. High error frequency.

question

DNA primase

answer

A component of the primosome and the replisome. Synthesizes RNA primers. Encoded by dnaG.

question

DNA repair endonuclease

answer

Involved in excision repair. Recognizes, binds to, and excises damaged base(s).

question

DNA replication

answer

Catalyzed by DNA polymerase
(dNMP)_n + dNTP > (dNMP)_n+1 + PPi

question

DNA topoisomerase

answer

A component of the replisome. Provides axes of rotation for replication of circular DNA by adding nicks ahead of DNA helicase. Prevents DNA from being positively supercoiled as it rotates for DNA replication. Includes DNA topoisomerases I and II. It is necessary for DNA replication.

question

DNA topoisomerase I

answer

A DNA topoisomerase. Catalyzes a single-strand nick in the DNA. The remaining phosphodiester bond acts as a swivel, allowing the supercoil to undwind itself. Removes supercoils one at a time. Energy efficeint.

question

DNA topoisomerase II

answer

A DNA topoisomerase. Produces double-stranded breaks in the DNA, adds a negative supercoil, and reseals the break. Removes positive supercoils two at a time, using ATP. Includes DNA gyrase.

question

dnaA

answer

An E. coli gene that codes for the prepriming protein DnaA, which binds to the 9-bp sequence in oriC, then forms a 20 - 40 protein complex, opening the DNA strand.

question

dnaB

answer

Encodes for DNA helicase, which unwinds the DNA strand.

question

dnaG

answer

Encodes for DNA primase, which synthesizes RNA primers.

question

dnaN

answer

Encodes for the ?-subunit of DNA polymerase III, which clamps the enzyme to the DNA strand.

question

dNTP

answer

Deoxynucleotide triphosphate

question

Downstream

answer

Towards teh 3' end of the RNA transcript.

question

Downstream sequences (+)

answer

DNA sequences that follow the intiation site.

question

dsRNA

answer

Double-stranded RNA. Rotavirus has dsRNA.

question

Effector molecule

answer

Small molecules such as amino acids, sugars, or other metabolites. Causes allosteric transition in an activator or repressor which affects its ability to bind to RPBS. Includes inducers and co-repressors.

question

Elizabeth Blackburn and Carol Greider

answer

Discovered telomerase in 1985. Won the Nobel Prize in Physiology or Medicine with Jack Szostak in 2009.

question

Elongation factor G (EF-G)

answer

The tRNA at the A site is moved to the P site, the tRNA at the P site is moved to the E site, and the tRNA at the E site is released. Requires GTP. The ribosome changes conformation.

question

Elongation factor Tu (EF-Tu-GTP)

answer

Contains a molecule of GTP. Provides GTP to peptidyl transferase. It is released as EF-Tu-GDP after the polypeptide bond forms, and it is converted back into EF-Tu-GTP by EF-Ts. Interacts with all aminoacyl tRNAs except methionyl-tRNA.

question

Elongation factor Ts (EF-Ts)

answer

Converts EF-Tu-GDP into EF-Tu-GTP.

question

End-product binding site

answer

Regulatory binding site. The site or sites where the end product binds to an enzyme. Often on a separate subunit from where the substrate binds. The enzyme undergoes allosteric transition which reduces its affinity for the subtrate.

question

Endogenous retrovirus

answer

Retrovirus DNA which can be transmitted to subsequent generations of an organism. Some retroviruses lose their ability to produce viral particles, and become innocuous.

question

Enhanceosome

answer

A protein complex in mammals that initiates activation of genes via chromatin remodeling. Adds acetyl groups to histone tails upstream from the promoter region.

question

Enhancer

answer

Modulates the efficiency of transcription initiation in eukaryotes.

question

Enol

answer

The rare form of guanine and thymine.

question

env

answer

A gene in a retrovirus. Codes for protein components of the virus envelope.

question

Equilibrium density-gradient centrifugation

answer

Meselson and Stahl used this method to separate isotopic DNA from regular DNA, using cesium chloride salts, which have approximately the same density as DNA.

question

eRF

answer

The release factor in eukaryotes. Recognizes all three termination codons.

question

Error-prone repair system (SOS response)

answer

A DNA repair mechanism. Activated after extreme damage to DNA: a survival mechanism. DNA repair, recombination, and replication proteins are synthesized. Excision repair may fix much of the DNA. DNA polymerase IV and V replicates across damaged segments. It has a high frequency of replication errors.

question

Ethyl ethane sulfonate (EMS)

answer

An alkylating agent.

question

Ethyl methane sulfonate (EMS)

answer

An alkylating agent.

question

Eukaryotes

answer

Shorter RNA primers and Okazaki fragments. DNA replication occurs only in S phase. There are multiple origins of replications, nucleosomes, and telomeres. Eukaryotes have at least 15 DNA polymerases. DNA polymerase ?, ?, and ? replicate the chromosomes. Eukaryotes have 5 RNA polymerases. Transcription and translation are not coupled, and most transcripts are modified and transported to the cytoplasm.

question

Evolution

answer

Mutations occur in all organisms and viruses, and increases genetic variability. Natural selection preserves combinations of genes adapted to the environment.

question

Excinuclease

answer

A nuclease that cleaves on either side of damaged base(s). Distinct from endonucleases and exonucleases. Involved in nucleotide excision repair.

question

Excision repair

answer

A DNA repair mechanism. DNA repair endonuclease or endonuclease-containing enzymes recognize and bind to damaged strands of DNA as a template. DNA ligase seals the nicks left by DNA polymerase. Includes base excision repair and nucleotide excision repair.

question

Excited state

answer

Electrons in higher energy levels. Caused by nonionizing radiation. Causes increased reactivity in DNA.

question

Exit site (E)

answer

The E site on a ribosome. Binds to the departing uncharged tRNA.

question

Exon

answer

Expressed sequences. Coding sequences. Remain present in mRNA after introns are spliced out.

question

Exonuclease activity

answer

Corrections. Nucleotides are removed. Incorrect base pairs are detected due to their incorrect geometry.

question

Eye

answer

A structure that forms during replication of the linear chromosome of phage T7.

question

F, G, and I elements

answer

A group of retroposons found in Drosophila.

question

FA

answer

Eight genes, A - H, on 5 different chromosomes. Mutations in these genes can cause Fanconi anemia.

question

FACT

answer

Facilitates Chromatin Transcription
A protein which removes H2a and H2b histones as RNA polymerase II passes over nucleosomes, then re-attaches them afterwards.

question

Fanconi anemia

answer

An inherited disease caused by defects in DNA repair mechanisms. Sensitivity to DNA cross-linking agents, chromosome instability, and prone to cancer. Impaired removal of DNA inter-strand cross-links, such as those formed by mitomycin C antibiotic. Caused by mutation in FA.

question

Feedback inhibition

answer

End-product inhibition. The product of a synthetic pathway inhibits the first enzyme in the pathway. Results in an almost instantaneous arrest of synthesis. Not to be confused with repression.

question

Forward mutation

answer

A mutation of a wild-type allele that results in a mutant allele.

question

Frameshift mutation

answer

An insertion or deletion of a number of base pairs that is not a multiple of three within the coding regions of a gene. Alters the reading frame of codons in mRNA translation. Amino acid sequence is dramatically altered, almost always leading to a non-functional protein.

question

Francis Crick

answer

First described the Central Dogma of molecular biology, and suggested that there was an adaptor molecule between RNA and polypeptides (tRNA) in 1958.
In 1961, published the first evidence for triplet codes after doing experiments with T4 bacteriophages: found that single and double-base mutations caused mutant phenotype, but triple-base mutations preserved the wild phenotype. Also proposed the wobby hypothesis.

question

Francois Jacob and Jacques Monod

answer

Developed the operon model in 1961 to explain regulation of genes for lactose metabolism in E. coli. Won the Nobel Prize in 1965.

question

FRAXA

answer

A site on the X chromosome. If there is a CGG trinucleotide repeat, it causes fragile X syndrome, the most common form of inherited mental retardation in humans. Normal X chromosomes have 6 - 50 copies, and fragile X patients can have up to 1000 copies.

question

gag

answer

A gene in a retrovirus. Codes for structural proteins of the virus capsule.

question

GC box

answer

An element of a promoter for RNA polymerase II. Consensus sequence is GGGCGG.

question

Genetic code

answer

Specification of amino acids by codons. Composed of nucleotide triplets, does not overlap, does not have punctuation, has degeneracy, order, start and stop codons, and is nearly universal.

question

George Beadle and Edward Tatum

answer

Won the Nobel Prize in 1958. Irradiated Neruospora crassa spores with X or UV rays, and screened the clones for growth-factor requirements. Each mutation resulted in a requirement of just one metabolite. Demonstrated the one-gene-one polypeptide concept.

question

Gerald Rubin and Allan Spralding

answer

Tried to use a transposon to carry a cloned gene into an organism. They were successful in returning rosy eye colour Drosophila mutants into wild-type by inserting the wild gene from a bacterial plasmid.

question

Germinal mutation

answer

A mutation that occurs in germ-line cells, which gives rise to gametes. If it occurs in the gamete cell, one progeny is affected. If it occurs in a cell which then gives rise to gametes, many progeny may be affected.

question

Guanine

answer

Has a common keto form, and a rare enol form, with the H at the C6 rather than C1. If treated with nitrous acid, it changes to xanthine, which pairs with cytosine, so there is no change.

question

Guide RNAs

answer

RNAs that assist in RNA editing where uridine monophosphate is inserted or deleted from a sequence, dramatically changing the polypeptide it codes for. Has complementary sequence to the transcript being edited, and acts as a template for U insertion.

question

gypsy

answer

A retroviruslike element found in Drosophila. Larger than copia.

question

gyrA

answer

nalA
Encodes for the ? subunit of DNA gyrase. Inhibited by Nalidixic acid.

question

gyrB

answer

cou
Encodes for the ? subunit of DNA gyrase. Inhibited by coumermycin antibiotic.

question

Hermann J. Muller

answer

In 1927, discovered that X rays could induce mutations in Drosophila sperm. This changed the field of genetics. Received the Nobel Prize for Physiology or Medicine in 1946. Developed the ClB method.

question

HeT-A

answer

Regenerates lost chromosome ends in Drosophila.

question

Heterogeneous nuclear RNA (hnRNA)

answer

The populatoin of RNA transcripts in the nucleus of a eukaryote. Vary in size. Mostly pre-mRNA undergoing processing events before leaving the nucleus.

question

hobo elements

answer

Cut-and-paste transposons found in Drosophila.

question

Holoenzyme

answer

The complete enzyme.

question

Housekeeping functions

answer

Gene products such as tRNA, rRNA, ribosomal proteins, RNA polymerase, and enzymes catalyzing basic metabolic processes. Coded by constitutive genes.

question

Human immunodeficiency virus (HIV)

answer

A retrovirus in humans which causes AIDS. Transmitted by blood or semen. Intravenous drug users and sex industry workers are at high risk.

question

Hutchinson-Gilford syndrome

answer

A severe form of progeria. Wrinkles, baldness, and other symptoms of age begin immediately after birth. The patient usually dies in their teens. Caused by a dominant mutation that affects the shape of nuclei in cells.

question

Hydrogen bonds

answer

An element of tertiary structure of proteins. Weak interactions between electronegative atoms and hydrogen atoms bound to other electronegative atoms.

question

Hydrophobic interactions

answer

An element of tertiary structure of proteins. Associations of nonpolar groups with each other in aqueous solution.

question

Hydroxylamine (NH₂OH)

answer

A hydroxylating agent. Produces C:G > A:T transitions. The amino group of cytosine is hydroxylated, producing hydroxylaminocytosine, which pairs with adenine. Due to its specific activity, it can be used to examine the nature of mutations.

question

Hydroxylating agent

answer

A class of chemical mutagens. Add hydroxyl groups. Includes hydroxylamine.

question

I

answer

The repressor gene of the lac operon. Codes for lac repressor, a tetramer with four copies of the gene product. It binds to operators two at a time to prevent RNA transcription, unless allolactose is bound to it. WHen bound to O₁ and O₂, a hairpin is formed in the DNA. When bound to O₁ and O₃, a loop is formed in the DNA. It has mutations I^-, I^-d, and I^s.

question

I^-

answer

A mutation of I in the lac operon. Causes constitutive synthesis of lac gene products. I⁺ is dominant to it. Can act in cis or in trans. May affect genes on other DNA molecules in the bacteria.

question

I^-d

answer

A mutation in I of the lac operon. Dominant to I⁺ because its products form heteromultimers with I⁺ gene products, forming repressors which can bind to operators, but cannot bind to the affector molecule allolactose.

question

I^s

answer

A mutation of I in the lac operon. Produces uninducible repressors which require high amounts of lactose to produce induction.

question

Imino

answer

The rare form of cytosine and adenine.

question

Induced mutations

answer

Mutations that result from exposure to physical or chemical mutagens.

question

Inducer

answer

Effector molecules that cause induction of genes. Cause activators to bind to RPBS. Cause repressors to fall off the RPBS.

question

Inducible enzymes

answer

Enzymes encoded by inducible genes. Often catalyze catabolic pathways.

question

Inducible genes

answer

Genes whose expression is regulated by induction. Produce inducible enzymes.

question

Induction

answer

The activation of genes with the presence or absence of a subtance. Alters the rate of enzyme synthesis.

question

Initiation codon

answer

Initiates translation. Usually AUG, but in prokaryots it is sometimes GUG. In prokaryotes it cods for tRNA_f^Met.

question

Initiation factors

answer

Proteins in E. coli which are necessary for initiation of translation. Includes IF-1, IF-2, and IF-3
IF-2 interacts with fMet
IF-1 and IF-3 bring the 30S subunit to mRNA using GTP.

question

Inosine

answer

A modified guanine/adenine derivative.

question

Integrase

answer

An enzyme which integrates DNA produced by reverse transcriptase into a random site in the DNA. Coded for by retrotransposons.

question

Intein

answer

Short amino acid sequences that excise themselves from nascent polyptpides. First discovered in Mycobacterium tuberculosis.

question

Intron

answer

Intervening sequences
Non-coding sequences. Found in split genes. Introns can be up to 7,000 nucleotides long. May play a role in gene expression, or are remnants from gene evolution. There can be alternate splicings for one gene, producing multiple products. 60% - 80% of our genes have alternate products. Some introns have sequences that play a role in transcription. There are conserved sequences at the ends of introns: GU-intron-AG. Removed by splicing reactions carried out by splicing endonucleases, self-splicing, or spliceosomes.

question

Ionic bonds

answer

An element of tertiary structure of proteins. Occurs between amino acid side chains with opposite charges. Strong under some conditions, but relatively weak in aqueous environments due to polar water molecules.

question

Ionizing radiation

answer

A mutagen. Lower wavelength, higher energy radiation, including X-rays, gamma rays, and cosmic rays. Penetrates living tissues, causing release of electrons. Produces free radicals: positively charged ions which create more free radicals. Breaks chromosomes and causes deletions, duplications, inversions, and translocations. Dosage is measured in roentgen. Dosage rate is directly correlated with amounts of mutations.

question

IS element

answer

Insertion sequences
Cut-and-paste transposons found in bacteria. Includes IS50. The simplest type of transposon: contains only genes that encode for its own transposition. Inserts at many sites in bacterial chromosomes and plasmids. Short and compactly organized: usually fewer than 2500 bp. There may be up to 10 copies of a single SI element in the genome. Allows for homologous recombination between chromosomes and plasmids, or between plasmids. Causes target site duplications when inserted.

question

J. Herbert Taylor, Phillip Woods, and Walter Hughes

answer

Used autoradiography to examine radioactive chromosomes as they replicate, providing proof of semiconservative replication in the root tips of Vicia faba. Labelled chromosomes with a radioactive isotope of thymine, and transferred it into a solution containing colchicine, causing chromosomes to double in the cell.

question

James Herrick and Ernest Irons

answer

A physician and medical intern in Chicago who discovered sickle cell anemia in 1904.

question

Jean Lamarck and Trofim Lysenko

answer

Believed in the inheritance of acquired traits. Lysenko sold this concept to the Soviet Union from 1937 to 1964. Actually, acquired traits are not heritable, the environment simply selects fro pre-existing mutations. This was proved by Joshua and Esther Lederberg.

question

Jessie Hiatt

answer

An Iowa farmer who discovered Delicious Apples in 1881.

question

Joel Huberman and Arthur Riggs

answer

In 1968, used autoradiography of labelled DNA from Chinese hamster cells to show that in eukaryotes, DNA replication occurs bidirectionally from multiple origins.

question

John Cairns

answer

Established the existence of the origin of replication. In 1963, showed that the chromosome of E. coli was a single molecule of DNA, using autoradiography. Replication of the circular chromosome during cell division produces a ?-shaped structure with two forks.

question

John Lim

answer

Suggested that transposons play a role in the evolution of chromosome structure. Transposons on the same chromosome can have crossing-over to cause deletions. Transposons on sister chromosomes can cause transfer of selections from chromosome to chromosome.

question

Joshua and Esther Lederberg

answer

In 1952, definitively proved that acquired traits were not inherited, by devloping replica plating.

question

Keto

answer

The common form of guanine and thymine.

question

Kozak's rules

answer

Named after Marilyn Kozak, who proposed them. A series of rules of how the efficiency of initiation is changed by changes of bases from the optimal initiation sequence in eukaryotes:
5' - GCC(A/G)CCAUGG-3'

question

L1

answer

A LINE found in humans. 6 kbp long, with internal promoters that are recognized by RNA polymerase II. Two open-reading frames that encode for a nucleic-acid binding protein, and an endonuclease with reverse transcriptase activity. The human genome has 3000 - 5000 L1 elements, and over 500,000 truncated (from the 5' end) non-functional L1 elements. Flanked by short target site duplications.

question

lac^-

answer

Mutations in E. coli caused by inertion of an IS element into lac genes. Reversion to wild-type is caused by excision of the IS element, and occurs at a high rate.

question

lac operon

answer

An inducible operon. Induced only if lactose is present, and glucose is absent. Its products break down lactose. Consists of P, I, three operators O₁, O₂, O₃, and three structural genes lacZ, lacY, and lacA. The operaotrs may have O^c mutation. All structural genes are activated at low background levels at all times. Operators overlap with initiation start sites.

question

lacA

answer

A structural gene of the lac operon. Codes for ?-galactoside transacetylase.

question

lacY

answer

A structural gene of the lac operon. Codes for ?-galactoside permease. Transports lactose.

question

lacZ

answer

A structural gene of the lac operon. Codes for ?-galatosidase. Converts lactose into allolactose. Cleaves lactose into glucose into galactose.

question

Lagging strand

answer

Synthesized by discontinuous replication. Consists of Okazaki fragments.

question

Lariat formation

answer

The 5' phosphate of the G end of the 5' end of the intron is formed to the 2'-OH of the A at the 3' end of the intron by the spliceosome.

question

Leading strand

answer

Synthesized by continuous replication.

question

Light-dependent repair

answer

Photoreactivation
A DNA repair mechanism found only in bacteria. Works only in light. Carried out by DNA photolyase. Repairs thymine, cytosine, or cytosine-thymine dimers caused by nonionizing radiation. Used as a tool to detect thymine dimers.

question

LINEs

answer

Long interspersed nuclear elements. Retroposons found in humans. Includes L1.

question

Linus Pauling

answer

Thought that DNA may have been triple-stranded. This does sometimes occur in deformed cells.

question

Maria Schnos and Ross Inman

answer

Used A:T rich markers in phage ? to prove that it is bidirectional replicatio. A:T pairs separate at high temperatures or pH, where C:G pairs do not, causing denaturation bubbles. Exposed replicating chromosomes to high pH at different stages of replication and examined the denaturation bubbles.

question

Marilyn Kozak

answer

Proposed Kozak's rules.

question

Marshall Nirenberg, Severo Ochoa, H. Ghobind Khorana, Philip Leder, and colleagues

answer

Worked out the meaning of all 64 codons of the entire genetic code. Nirenberg and Khorana shared the Nobel Prize in Physiology or Medicine in 1968.

question

Mary Lou Pardue, Robert Levis, Haral Beissman, James Mason, and colleagues.

answer

Showed that HeT-A and TART regenerate lost chromosome ends in Drosophila.

question

Masayasu Nomura and colleagues

answer

Disassembled the E. coli 30S ribosomal subunit into its individual proteins and rRNAs to study it.

question

Matthew Meselson and Franklin Stahl

answer

In 1958, proved that E. coli replicates its DNA using semiconservative replication. Grew E. coli in a solution containing a heavy isotope of nitrogen, ¹⁵N. DNA which contains this isotope is denser than regular DNA. They separated it using equilibrium density-gradient centrifugation with cesium chloride salts. Results were consistent with semiconservative replication: two DNA strands had intermediate density, and the rest had normal density.

question

Merozygotes

answer

Partially diploid bacteria with F' factors.

question

Messenger RNA (mRNA)

answer

A type of RNA. It is translated into proteins on ribosomes. The product of pre-mRNA processing: removal of introns, modification of termini.

question

Methionine

answer

One of the only amino acids which is specified by a single codon.

question

Micro RNA (miRNA, siRNA, RNAi)

answer

A type of RNA. 20 - 22 nucleotide segments. Cleaved from small hair-pin shaped precursors. Block the expression of complementary or partially complementary mRNAs by either causing their degradation or repressing translation.

question

Minimal medium

answer

Ionic salts, a simple sugar, and the vitamin biotin. Wild-type Neurospora crassa can survive in this medium.

question

Mismatch repair

answer

A DNA repair mechanism. A backup to replicative proofreading. A universal mechanism. Scans for and corrects mismatched nucleotides in DNA post-replication. The template strand and non-template strand are differentiated by their methylation patterns after DNA replication: the newly synthesized strand is unmethylated. In E. coli, MutS, MutH, MutL, UvrD, exonuclease, DNA polymerase III, and DNA ligase are involved.

question

Missense mutation

answer

A mutation that changes a codon to produce a different amino acid. Causes impaired function of the gene product.

question

MSH1

answer

A gene on chromosome 3 for a homolog of E. coli mismatch repair protein MutL. Mutation of this gene can cause nonpolyposis colon cancer.

question

MSH2

answer

A gene on chromosome 2 for a DNA mismatch recognition protein, similar to MutS in E. coli. Mutation in this gene can cause nonpolyposis colon cancer.

question

MSH6

answer

A gene on chromosome 2 for MutS homolog 6. Mutation in this gene can cause nonpolyposis colon cancer.

question

Mustard gas

answer

Di-(2-chlorethyl) sulfide
An alkylating agent. Its effects were studied by Charlotte Auberach and associates.

question

Mutagen

answer

Physical or chemical factors which cause induced mutations. Increases frequency of mutation up to 1% per gene. Includes ionizing radiaton, nonionizing radiation, and chemical mutagens.

question

Mutant

answer

An organism which exhibits a novel phenotype as a result of a mutation.

question

Mutation

answer

A change in genetic material, and the process by which this change occurs. The ultimate source of all genetic variation: the raw material for evolution.

question

MutH

answer

Involved in mismatch repair in E. coli. Joins the complex formed by MutS. Cleaves unmethylated strand at hemi-methylated GATC sequences on either side of the mismatch, comparing old and new strands based on methylation.

question

MutL

answer

Involved in mismatch repair in E. coli. Joins the complex formed by MutS.

question

MutS

answer

Involved in mismatch repair in E. coli. Recognizes mismatches and binds to initiate the repair process.

question

Mycobacterium tuberculosis

answer

The bacteria which causes tuberculosis. Inteins were first discovered in this species.

question

Nap-1

answer

Nucleosome assembly protein 1. Transports new histones from the cytoplasm to the nucleus during DNA replication.

question

Negative control mechanism

answer

Repressors are needed to shut off expression of structural genes.

question

Neurospora crassa

answer

A salmon-coloured bread mould. Can survive in minimal medium. George Beadle and Edward Tatum used this species in their experiments proving the one geneone polypeptide concept.

question

Neutral mutation

answer

A mutation that causes a change in amino acid to an amino acid with similar properties. The function of the mutated polypeptide is not altered.

question

Nick

answer

A break in the phosphoriester bond of one of the strands of DNA. All nucleotides are present. DNA ligase seals the nick.

question

Nijmegan breakage syndrome

answer

An inherited disease caused by defects in DNA repair mechanisms. Chromosome instability, microcephaly, and prone to cancer. Increased chromosome aberrations. Caused by mutation in NBSI.

question

Nitrous acid (HNO₂)

answer

A deaminating agent. A potent mutagen. Causes oxidative deamination of amino groups in adenine, guanine, and cytosine. Converts amino groups into keto groups. Adenine changes to hypoxanthine. Cytosine changes to uracil. Guanine changes to xanthine.

question

Nonionizing radiation

answer

A mutagen. Higher wavelength, lower energy radiation, including ultraviolet radiation. Does not have enough energy to cause ionizations. Penetrates only the surface layer of cells of the body, but can be highly damaging to single-celled organisms. Raises electrons into an excited state. PRoduces pyrimidine hydrates and dimers. Hydrates cause mis-pairing. Dimers disturb the structure of DNA, interfering with replication and repair.

question

Nonpolyposis colon cancer

answer

Lynch syndrome
An inherited disease caused by defects in DNA repair mechanism. High rist of familial colon cancer. Occurs in 1/200 individuals. Caused by mutation in MSH2, MSH1, MSH6, PMS2, or PMS1.

question

Nonsense mutation

answer

A mutation that produces chain-termination codons. Results in truncated polypeptides.

question

Nontemplate strand

answer

Sense strand
The DNA strand which is not transcribed. Identical to the RNA transcript, but has T rather than U.

question

NPSI

answer

A gene on chromosome 8 for DNA double strand break recognition protein. Mutation in this gene can cause Nijmegan breakage syndrome.

question

Nuclear organizer regions

answer

Regions of the chromosome with redundant, tandem rRNA coding sequences. There may be multiple.

question

Nuclease activity

answer

Synthesis
Nucleotides are added.

question

Nucleolus

answer

A region of rRNA synthesis and ribosome assembly in the nucleus.

question

Nucleoside

answer

A pentose sugar and a nitrogenous base, without a phosphate group.

question

Nucleotide

answer

A pentose sugar and a nitrogenous base, with a phosphate group.

question

Nucleotide excision repair

answer

A type of excision repair. Removal of larger defects such as thymine dimers. Involves excinucleases. In E. coli three proteins are involved, and in humans twelve are involved, including XPA. Mutation in nucleotide excision repair genes can cause xeroderma pigmentosum.

question

O₁

answer

An operator in the lac operon discovered by Jacob and Monod. Located between P and lacZ.

question

O₂

answer

An operator in the lac operon. Located downstream from O₁ within lacZ.

question

O₃

answer

An operator in the lac operon. Located upstream of P.

question

O^c

answer

A mutation of any of the operators in the lac operon. Causes constitutive synthesis of lac gene products. Acts only in cis; cannot affect genes on other DNA molecules.

question

Octamer box

answer

An element of a promoter for RNA polymerase II. Consensus sequence is ATTTGCAT.

question

Okazaki fragments

answer

Short fragments of DNA 100 - 200 bp on the lagging strand. Replicated in the 5' - 3' direction, overall in the 3' - 5' direction.

question

One gene-one polypeptide

answer

A concept demonstrated by George Beadle and Edward Tatum. Each gene encodes one polypeptide. Modified from "one gene-one enzyme" concept, because some enzymes are multimeric.

question

Operator

answer

A gene which is contiguous with structural genes that it regulates. Repressors bind to the operator to turn off transcription. An operon may have several operators.

question

Operon

answer

A negative control system. Consists of structural genes, operators, and a promoter. In an inducible operon, free repressors turn off transcription. In a repressible operon only a repressor/effector complex can turn off transcription. All genes in the operon are transcribed onto a single mRNA molecule, so all genes are expressed simultaneously, and products are in equal proportions in the cell.

question

Operon model

answer

A negative control mechanism proposed by Francois Jacob and Jacques Monod. A regulator gene encodes for a repressor which binds to an operator. This controls expression of the operon.

question

Order

answer

A characteristic of genetic code. Amino acids with similar properties have similar codons. Evolved as a way of minimalizing mutation lethality.

question

oriC

answer

The origin of replication in E. coli. 245-bp, with two conserved repeat sequences. An A:T rich 13-bp sequence is repeated four times, facilitating formation of the replication bubble. A 9-bp sequence is repeated four times, facilitating binding of prepriming proteins.

question

Origin of replication

answer

The site of initiation of DNA replication. There is usually one per chromosome on bacterial and viral DNA. There are multiple per chromosome in eukaryotes, each controlling one replicon. In eukaryotes, origins of replication may be very long. In E. coli it is oriC.

question

Oscar Miller, Barbara Hamkalo, and colleagues

answer

Developed imaging techniques to allow observation of transcription and translation occuring on the same RNA molecule in a prokaryote.

question

P

answer

The promoter of the lac operon.

question

P elements

answer

Cut-and-paste transposons found in Drosophila. Cause mutations.

question

Paula DeLucia and John Cairns

answer

In 1969, discovered that DNA polymerase I was not the only DNA polymerase in E. coli.

question

Peptide

answer

Two or more amino acids.

question

Peptide bond

answer

Covalent linkage between amino acids and polypeptides. Formation on ribosomes is catalyzed by peptidyl transferase.

question

Peptidyl site (P)

answer

The P site on a ribosome. Binds the tRNA to the growing polypeptide.

question

Peptidyl transferase

answer

Enzymatic activity built into the 50S subunit of the ribosome, on an rRNA molecule. Catalyzes the formation of a covalent peptide bond between the amino acid at the P site and the aminoacyl-tRNA at the A site, uncoupling the amino acid and tRNA at the P site. Uses GTP provided by EF-Tu-GTP.

question

piggyBac elements

answer

Cut-and-paste transposons found in moths. Can be a transition vector for many species.

question

Plasticity

answer

Ability to turn genes on and off rapidly to acheive maximal growth and reproduction under a wide range of environmental conditions. In prokaryotes, there may be preprogrammed circuits or cascades of gene expression. Genes cannot be turned on out of sequence.

question

PMS1

answer

A gene on chromosome 2 for a yeast mismatch repair protein homolog. Mutation in this gene can cause nonpolyposis colon cancer.

question

PMS2

answer

A gene on chromosome 7 for endonuclease PMS2. Mutation in this gene can cause nonpolyposis colon cancer.

question

Point mutation

answer

A mutation at a speciifc site in a gene. Substitution of one base pair for amother, or the insertion or deletion of a few nucleotide pairs at a specific site in the gene.

question

pol

answer

A gene of a retrovirus. Codes for reverse transcriptase or integrease.

question

POLH

answer

XPV
Codes for DNA polymerase eta. Loss of this gene leads to xeroderma pigmentosum.

question

Poly(A) polymerase

answer

Performs polyadenylation: adds poly(A) tails to the cleaved 3' end of transcripts following a AAUAAA sequence.

question

Poly(A) tail

answer

A polyadenosine tract 20 - 200 nucleotides long, joined to the cleaved 3' end of an RNA transcript. Gives the transcript stability, and plays a role in transport out of the nucleus. Added by poly(A) polymerase. Binds to proteins and protects the 3' end from degradation.

question

Polyadenylation

answer

The addition of poly(A) tails to the cleaved 3' end of mRNAs in eukaryotes.

question

Polypeptide

answer

The constituents of proteins. Long chains of amino acids.

question

Positive control mechanisms

answer

Activators are needed to turn on expression of structural genes.

question

Postreplication repair

answer

A DNA repair mechanism. Activated in mutants deficient in more than one repair system. DNA polymerase III stops when it encounters a thymine dimer, and replication is continued past the dimer, forming a gap in the nascent strand. RecA mediates exchange of singel strands between homologous DNA molecules. There is recombination, inserting the sequence for the nascent strand, and the thymine dimer remains on the other side. If the nucleotide excision repair system does not repair it, this process is repeated at each replication of the DNA.

question

PPi

answer

Pyrophosphate

question

Pre-mRNA

answer

The product of transcription in eukaryotes. It is processed by excision of introns, and modification of termini before translation.

question

Prepriming proteins

answer

Aid in the formation of the replication bubble by forming multi-protein complexes that bend the DNA molecule. In E. coli, they bind to the 9-bp repeat sequences. Includes DnaA.

question

Pribnow box

answer

The -35 sequence and the -10 sequence.

question

Primary structure

answer

A level of structure in proteins. The amino acid sequence, specified by the nucleotide sequence.

question

Primary transcript

answer

The product of transcription in prokaryotes.

question

Primer DNA

answer

Provides DNA polymerase with a 3' terminus with a free -OH.

question

Primosome

answer

A protein complex containing DNA primase and DNA helicase. DNA helicase unwinds the DNA, and DNA primase adds RNA primers to the lagging strand, initiating Okazaki strands.

question

Proflavin

answer

2,8-diamino acridine. An acridine dye.

question

Progeria

answer

A disorder in humans characterized by premature aging. Exact mechanism is unknown. The most severe form is Hutchinson-Gilford syndrome. A less severe form is Werner syndrome.

question

Prokaryotes

answer

Have on RNA polymerase. Transcription and translation are tightly coupled, and may take place simultaneously on the same RNA transcript. No modification of the transcript occurs: mRNA is short-lived.

question

Promoters

answer

Specific nucleotide sequences that bind to RNA polymerase. Near transcription start sites. More complex in eukaryotes than in prokaryotse. Includes the -10 and -35 sequences in E. coli. Promoters for RNA polymerase II includes the TATA box, CAAT box, GC box, and octamer box.

question

Proofreading

answer

Uses 3' - 5' exonuclease activity by DNA polymerase I and III. Reduces the expected error rate of DNA replication from 1/10⁴ times to 1/10⁶ times. The nascent strand is scanned for errors, which are corrected using 3' - 5' exonuclease activity.

question

Protein

answer

Made of polypeptides.

question

Quaternary structure

answer

A level of structure in proteins. The association of two or more polypeptides in a multimeric protein.

question

R-determinant

answer

A component of a conjugative R plasmid. Genes for antibiotic resistance.

question

R loop

answer

A region where RNA binds to one of the strands of DNA, displaicng the other strand. Can be visualized using electron microscopy. First observed by Shirtley Tilghman, Philip Leder, and colleagues.

question

Reading frame

answer

Where each codon beings and ends on an mRNA. If there is a frameshift mutation, the reading frame is altered, producing a mutant phenotype. If there is a mutation involving a number of nucleotides that is a multiple of three, the reading frame is not altered.

question

RECQLA

answer

A gene on chromosome 8 for RecQ helicase L4. Mutation in this gene can cause Rothmund-Thomson syndrome.

question

Regulator genes

answer

Encode products that regulate the expression of other genes. Bind to RPBS. Regulators produced are either activators or reprssors. Their ability to bind to RPBS is affected by effector molecules.

question

Reiji and Tuneko Okazaki

answer

In the 1960s, discovered discontinuous relpication using isotope labelling in T4-infected E. coli.

question

Release factors (RFs)

answer

Recognize termination codons. Attach a water molecule to the carboxyl terminus of the polypeptide, releasing the polypeptide from the tRNA at the P site. Prokaryotes have two: RF-1 and RF-2. Eukaryotes have one: eRF.

question

Replica plating

answer

A technique developed by Joshua Esther Lederberg in 1952. Demonstrates the presence of antibiotic resistant mutants in bacterial cultures prior to introduction of antibiotic. Cultures that had been exposed to the antibiotic were much more likely to contain antibiotic resistant bacteria that ones which had not been exposed. If mutations for resistance occured after exposure to the drug, and were not randomly pre-existing in the population, then cultures that had not been exposed to the antibiotic would be just as likely to contain resistant bacteria as cultures that had been.

question

Replication bubble

answer

The two strands of DNA come apart for replication. Facilitated by prepriming proteins. In E. coli it is facilitated by A:T rich in 13-bp repeat sequences in oriC.

question

Replication fork

answer

Y-shaped structures that occur during DNA replication. They have bidirectional replication, in opposite directions. One side of the fork has continuous replication, and the other has discontinuous replication.

question

Replicative transposition

answer

Transposition of replicative transposons. Catalyzed by transposases. The element is replicated and one copy is inserted at the new site, and one copy remains at the original site.

question

Replicative transposon

answer

A type of transposon. The element is moved by replicative transposition. Found in prokaryotes. Contain genes for transposase. Includes Tn3 elements.

question

Replicative polymerases

answer

DNA polymerases I and III. Involved in DNA replication. They both add 30,000 nucleotides per minutes: one error per 10⁸ - 10⁹ nucleotides.

question

Replicon

answer

A segment of DNA which is replicated by one origin of replication. In prokaryotes the entire chromosome is one replicon. Eukaryotes have around 10,000 replicons. The number of replicons is not fixed throughout growth and development.

question

Replisome

answer

The complete replication apparatus that moves along the replication fork: topoisomerase, DNA helicase, SSB proteins and other prepriming proteins, DNA primase, and replicative polymerases, DNA I and III.

question

Repression

answer

The deactivation of a gene. Produces depression of a gene. Anabolic pathways are often repressed. Not to be confused with feedback inhibition.

question

Repressor

answer

The product of regulator genes in negative control mechanisms. It is needed to shut of expression of one or more structural genes.

question

res

answer

Resolution site
Sites on the Tn3 element where site-specific recombination occurs in the cointegrate.

question

Resistance transfer factor (RTF)

answer

A component of a conjugative R plasmid. Genes needed for conjugative transfer between cells.

question

Retroposon

answer

Non-LTR retrotransposons
A type of retrotransposon. Not related to viral genes. Large and widely distributed. Codes for reverse transcriptase and endonuclease activity. Flanked by untranslated regions (UTR), and homogenous sequences of A:T base pairs at the ends, derived from poly(A) tails of the RNAs from which they are produced. Include F, G, and I elements, telomeric retrotransposons, LINEs, and SINEs.

question

Retrotransposition

answer

Transposition of retrotransposons. The RNA of the element is used as a template to generate DNA that is inserted into new chromosomal sites.

question

Retrotransposon

answer

"Backwards"
A type of transposon. The element is moved by retrotransposition. Found only in eukaryotes. Includes retrovirus like elements and retroposons.

question

Retrovirus

answer

Viruses whose life-cycle depends on retrotransposition. Their genomes are RNA strands, which are retrotransposed into the DNA of their host. Genes include gag, pol, and env. Includes HIV.

question

Retrovirus-like elements

answer

LTR retrotransposons
A type of retrotransposon. Related to viral genes. Found in many eukaryotes, including yeasts, plants, and animals. Codes for reverse transcriptase and integrase, flanked by a long terminal repeate (LTR) and short target site duplications. There are about 400,000 in the human genome. Includes Ty1, copia, and gypsy.

question

Reverse transcriptase

answer

Catalyzes the reverse transcription of RNA into DNA. Goes backwards from the central dogma. Discovered by David Baltimore, Howard Temin, and Satoshi Mizutani. Coded for by retrotransposons.

question

Reversion

answer

Reverse mutation
A mutation which restores a mutant allele to the wild-type allele. Includes back mutations and suppressor mutations; distinguished by back-crossing the mutation to a wild-type individual. Genes vary in which type of reversion is more common.

question

RF-1

answer

A release factor in prokaryotes. Recognizes UAA and UAG.

question

RF-2

answer

A release factor in prokaryotes. Recognizes UAA and UGA.

question

Rho (?)

answer

A protein that binds to rut near the 3' end of a transcript, and then moves 5' - 3' down the nascent strand RNA, after RNA polymerase. When RNA polymerase slows at the hairpin, it uses helicase activity to unwind the DNA/RNA base-pairing at the terminus.

question

Rho-dependent terminator

answer

A type of termination signal in E. coli. Termination occurs only in the presence of rho.

question

Rho-independent terminator

answer

A type of termination signal in E. coli. Termination can occur without rho. Contains a C:G rich region followed by six or more A:T base pairs, with A's in the template strand. When transcribed, it forms a hairpin in the nascent RNA. This slows RNA polymerase, and the weak A:U section causes RNA polymerase and the nascent RNA strand to simply fall off the DNA.

question

Ribonucleoside triphosphate (RTP)

answer

The precursors for RNA synthesis.

question

Ribosomal RNA (rRNA)

answer

A type of RNA. A structural and catalytic component of ribosomes.

question

Ribosome

answer

Intricate macromolecular machines composed of 3 - 5 rRNAs, and 50 - 90 proteins. Perform translation. Found throughout the prokaryote cells, and in the cytoplasm and ER of eukaryote cells. Composed of rRNA and proteins. Consists of two subunits, one large and one small, which associate when they bind to mRNA and dissociate when they detach. Size and structure of ribosomes varies between species. Size is measured in Svedberg units. Has an A, P, and E site.

question

Ribozyme

answer

An RNA enzyme. In self-splicing, the intron is a ribozyme for its own splicing reaction.

question

RNA editing

answer

Alteration of the content of RNA transcripts by changing the structure of bases (rare), or by inserting or deleting uridine monophosphate residues. Example: apo-B.

question

RNA polymerase

answer

Catalyzes the addition of RTPs to 3' end of an RNA strand. Moves in the 5' - 3' direction on the DNA, using it as a template. A nucleopilic attack of the 3'-OH on the nucleotide phosphorus atom of the RTP. Eliminates pyrophosphate. Binds to promoters on DNA. Eukaryotes have five RNA polymerases for different types of RNA, and prokaryotes have one. Produces a transcription bubble by winding DNA ahead of the polymerization side, and rewinding it behind. RNA polymerase holoenzyme in E. coli has a molecular weight of 480,000, consisting of 5 polypeptides, two of which are identical. Includes the tetrameric core and sigma factor. Adds 40 ribonucleotides per second. The region where RNA and DNA are base-paired is about 3 base pairs in length.
n(RTP) - (DNA template, RNA polymerase) > (RMP)_n + n(PP)

question

RNA polymerase I

answer

Found in almost all eukaryotes. Located in the nucleolus. Produces rRNAs, but not 5S rRNA.

question

RNA polymerase II

answer

Found in almost all eukaryotes. Located in the nucleus. Produces nuclear pre-mRNAs, and other hnRNAs.

question

RNA polymerase III

answer

Found in almost all eukaryotes. Located in the nucleus. Produces tRNA, 5S rRNA, and other snRNAs.

question

RNA polymerase IV

answer

Found only in plants and some fungi. Plays a role in chromatin remodeling. Located in the nucleus. Produces siRNAs.

question

RNA polymerase V

answer

Found only in plants and some fungi. Plays a role in chromatin remodeling. Located in the nucleus. Produces some siRNAs, plus noncoding transcripts of siRNA target genes, which interact and condense chromatin in chromatin remodelling.

question

RNA primer

answer

RNA segments bound to the lagging strand which initiates an Okazaki strand. Synthesized by DNA primase. 10 - 60 nucleotides long in prokaryotes, about 10 nucloetides long in eukaryotes.

question

Robert W. Holley and colleagues

answer

In 1965, published the proposed cloverleaf structure of tRNA. Holley shared the Nobel Prize in Physiology or Medicine in 1968.

question

Roentgen (r)

answer

The unit in which dosage of ionizing radiation is measured. Equal to 2.083 x 10⁹ ion pairs produced in one cm³ of air at 0? C and a pressure of 760 mmHg.

question

Rolling-circle replication

answer

Used by many viruses, in bacteria during genetic exchange, and in some amphibians during amplification of extracrhomosomal DNA during oogenesis. A circular DNA segment stays intact, and "rolls" as it acts as the template for DNA synthesis. It may roll more than once, producing a linear DNA longer than the parent DNA, with its sequences repeated.

question

Rotavirus

answer

A virus that contains dsRNA. Kills infants in 3rd world countries.

question

Rothmund-Thomsun syndrome

answer

An inherited disease caused by defects in DNA repair mechanisms. Chromosome instability, mental retardation, and prone to cancer. Alterations in specific DNA helicases. Caused by mutation in RECQL4.

question

RPBS

answer

Regulator protein-binding sites. Sites adjacent to promoter regions for genes, where activators or repressors bind.

question

rut

answer

Rho utilization
A binding site for rho.

question

Saccharomyces cerevisiae

answer

A test organsim in which splicing endonucleases were studied.

question

Science

answer

If you cannot disprove a hypothesis, you must accept it.

question

Secondary structure

answer

A level of structure in proteins. The spatial interrelationship of amino acids in segments of the polypeptide, maintained by hydrogen bonds. Includes ? helices and ? sheets.

question

Self-splicing

answer

Autocatalytic activity
Discovered by Thomas Check and Sidney Altmari. Splicing reactions are intrinsic to the RNA, and occur without enzymes in rRNA, tRNA, and mRNA of mitochondria and chloroplasts. Uses no energy source: a series of phosphoester bond transfers occur, requiring guanosine nucleoside or nucleotides (GTP, GDP, GMP, or guanosine), with a free 3' -OH group. Splicing depends on the secondary structure of the RNA precursor to bring reactive groups together: the intron is a ribozyme. Rapid degradation of excised introns drive the reaction. Studied in Tetrahymena thermophila.

question

Selenocystein

answer

An additional amino acid to the regular 20. Contains a trace element of selenium. Coded by UGA. Terminates the polypeptide.

question

Selenoproteins

answer

Proteins that contains selenocystein. The selenium usually plays a role in binding at active sites. Play an important role in all organism.

question

Semiconservative replication

answer

A possible method of DNA replication. Two strands are unwound, and a complementary nascent strand is formed to each, producing 2 identical DNA molecules. In Meselson and Stahl's experiment, two DNA strands have hybrid density, and the rest have normal density. There is evidence that this method is used in bacteria, and all eukaryotes.

question

Sense strand

answer

Strands of RNA that code for polypeptides.

question

Sequence-specific protein-nucleic acid interactions

answer

Bonds between proteins and nucleic acids, such as between RNA polymerase and promoters, CAP/cAMP and its binding site, or repressors/activators and operators. Proteins bind to specific DNA sequences, alter the structure of DNA to stimulate or repress transcription.

question

Seth Wright

answer

A sheep farmer from Dover, Massachusetts who in 1791 discovered a germinal mutation in sheep that causes short legs.

question

Shine-Dalgarno sequence

answer

AGGAGG
Named after the scientist who discovered it. A conserved sequence 7 nucleotides upstream from the initiation codon in prokaryotes. Forms base-pairing with an rRNA on the 30S subunit during initiation.

question

Shirley Tilghman, Philip Leder, and colleagues

answer

Hybridized purified mouse ?-globulin mRNA to the DNA that coded for the gene. Observed two R loops, demonstrating the existence of introns.

question

Sickle-cell anemia

answer

Caused by a missense mutation in one of the proteins that make up hemoglobin in red blood cells.

question

Side groups (R)

answer

Radicle
The group that differs between amino acids. Highly varied, producing the structural and functional versatility of proteins. Can be hydrophobic, hydrophilic, acidic, or basic.

question

Sigma (?) factor

answer

A component of RNA polymerase in E. coli. A subunit involved only in initiation of transcription. It is released after initiation. Recognizes and binds to promoters. If absent, the tetrameric protein will initiate transcription at random sites on the DNA in vitro.

question

Signal sequence

answer

A short amino acid sequence at the amino or carboxyl terminus of a nascent polypeptide which signals for transport into a specific cellular compartment. Often it is removed when the polypeptide reaches its destination.

question

Silencer

answer

Modulates the efficiency of transcription initiation in eukaryotes.

question

Silent mutation

answer

A mutation that has no effect on phenotype. This is due to degeneracy in genetic code.

question

Simple tandem repeats

answer

Repeated sequences of 1 - 6 nucleotide pairs. Dispersed throughout the human genome.

question

SINEs

answer

Short interspersed nuclear elements
Retroposons found in humans. Less than 400 bp. Do not encode proteins: rely on retrotransposition activity of LINEs. Includes Alu.

question

Single-strand DNA-binding proteins (SSB proteins)

answer

A component of the replisome. Bind to single-strand DNA strands in the replication bubble, after DNA helicase has opened it, preventing it from binding to itself, forming hairpins, and slowing or halting DNA replication. Binding of one SSB leads to the binding of another SSB. Encoded by ssb.

question

Sleeping Beauty

answer

A cut-and-paste transposon found in salmon. A transition vector which works well in many vertebrates. Potentially useful for human gene therapy.

question

Small interfering RNA (siRNA)

answer

A type of RNA. Important regulators of gene expression. Interact with proteins to modify chromatin structure.

question

Small nuclear RNA (snRNA)

answer

A type of RNA. Structural components of spliceosomes. Found in the nucleus. Includes U1, U2, U4, U5, and U6.

question

Small nucleolar RNA (snoRNA)

answer

Small nuclear RNAs. Found in the nucleolus. Function in rRNA and tRNA modification.

question

snRNPs

answer

Small nuclear ribonucleoproteins
"Snurps"
Complexes of snRNA and protein that are the constituents of spliceosomes.

question

Somatic mutation

answer

A mutation that occurs in somatic cells, which do not give rise to gametes. Mutant phenotype occurs only in cells that descent from that cell, and will not pass onto progeny. Incldues Delicious apples, and navel oranges: the original mutants were genetic mosaics, and the mutation is reproduced by vegetative propagation.

question

Spliceosomes

answer

Macromolecular structures containing about 40 different proteins and five snRNAs. Composed of snRNPs. Carry out splicing reactions, removing introns in nuclear pre-mRNA. Recognition of the correct site involves base-pairing between the consensus sequence and complementary sequence at the 5' end of an snRNA. The lariat formation is formed using ATP. The 3' end of the intron is cut, and the 5' end on the exon is joined to the 3' end on the other side by a normal 5' - 3' phosphodiester linkage.

question

Splicing endonucleases

answer

Carry out splicing reactions in tRNAs. Two cuts are made at the ends of the intron, and splicing ligase joins the two halves. Studied in Saccharomyces cerevisiae.

question

Splicing ligase

answer

Joines the to halves cut by splicing endonuclease.

question

Splicing reactions

answer

Carried out by spliceosomes. Removes introns.

question

Split genes

answer

Gene which have introns. Almost all eukaryotic genes have introns, some as many as 50.

question

Sponanteous mutation

answer

Mutations with no known cause. May result from a low level of metabolic errors, or be caused by unknown agents in the environment. Occurs infrequently, but frequency varies with gene and organism. For bacteria and phages, frequency is 10^-8 - 10^-10, and for eukaryotes 10^-7 - 10^-9 per nucleotide.

question

ssb

answer

Encodes for SSB proteins, which bind to single-stranded DNA in the replication bubble.

question

Suppressor mutation

answer

A type of reversion. A second mutation at a different location in the genome compensates for the effects of the first muation, producing wild-type phenotype. Restores the reading frame, or changes the anticodon on a tRNA. If back-crossed to a wild-type individual, half the progeny are wild-type, a quarter have the muation, and a quarter have the second mutation without the first mutation.

question

Suppressor tRNA

answer

tRNA which have a mutated anticodon that recognizes a termination codon: UAG, UAA, or UGA with varying efficiency. A suppressor mutation that negates nonsense mutations.

question

Svedberg unit (S)

answer

The unit that the size of ribosomal complexes are measured in. A sedimentation coefficient = (velocity/centrifugal force) of 10^-13 seconds.

question

Sylvie Doublie and colleagues

answer

In 1998, determined the structure of phage T7 polymerases, similar to DNA polymerase I of E. coli. Found its shape is somewhat like a hand grasping the primer DNA.

question

Tanning beds

answer

Cause cancer. Are as dangerous as cigarettes or asbestos.

question

Target site duplications

answer

2 - 13 bp repeats caused by staggered cleavage of DNA when transposons are inserted.

question

TART

answer

Telomere-assited retrotransposition. Regenerates lost chromosome ends in Drosophila.

question

TATA box

answer

An element of a promoter for DNA polymerase II. A conserved element at -30. The consensus sequence is TATAAAA (5' - 3' on the nontemplate strand). Plays a role in positioning the transcription start point.

question

Tautomeric shift

answer

A hydrogen atom moves its position on a nucleic base, changing its propertis. Rare, but causes alteration in pairing of bases. A change from keto to enol form, or from amino to imino form. The more rare forms are less stable, and exist only for short amounts of time, and have irregular base pairing. Form A:C and G:T base pairs, due to altered numbers of hydrogen bonds from the moved hydrogen.

question

Telomerase

answer

An RNA-containing enzyme which adds telomeres to a new DNA strand. Discovered in 1985 by Elizabeth Blackburn and Carol Greider. It extends the 3' end of the telomere with repetitive sequences. In humans the sequence is TTAGGG. Without telomerase, the chromosome would become shorter with every replication, since DNA polymerase cannot work without a 3' end. Somatic cells have low telomerase activity. Cancer cells have high telomerase activity. There is a correlation between telomere length and the age of cells. Shortening of the telomere with age leads to death.

question

Telomeric retroposons

answer

A retroposon found in Drosophila.

question

Template strand

answer

Anti-sense strand
The DNA strand which is transcribed. Complementary to the RNA transcript.

question

Template strand

answer

Anti-sense strand
The

question

terA

answer

Blocks movement of the replication fork in a counter-clockwise direction.

question

terB

answer

Blocks movement of the replication fork in a clockwise direction.

question

Termination signal

answer

A DNA sequence which causes the RNA polymerase to dissociate with the DNA, releasing the nascent RNA molecule. In E. coli this includes Rho-dependent and Rho-independent terminators.

question

Tertiary structure

answer

Conformation
A level of structure in proteins. The overall folding of the polypeptide. Ionic bonds, hydrogen bonds, hydrophobic interactions, Van der Waals interactions, and covalent disulfide bonds are elements of tertiary structure.

question

Tetrahymena thermophila

answer

A test organism in which self-splicing was studied.

question

Tetrameric core (?₂??')

answer

A component of RNA polymerase in E. coli. The ? subunit is involved in its assembly. The ? subunit is the RTP binding site. The ?' subunit is the DNA template binding site. Catalyzes transcript elongation.

question

TFIIA, B, D, and F

answer

Basal transcription factors. Forms a pre-initiation complex that prepares DNA for unwinding and recruits RNA polymearse and TFIIE to form a transcription bubble and initiate transcription.

question

TFIIE

answer

A basal transcription factor. It is recruited by TFIIA, B, D, and F to form a transcription bubble and initiate transcription.

question

TFIIH

answer

A basal transcription factor. Associates and aids in DNA helix unwinding.

question

Thermus thermophilus

answer

A bacteria. The structure of its 70S ribosome was solved to a resolution of 0.55 nm using X-ray crystallography.

question

Thomas Cech and Sidney Altmari

answer

Discovered self-splicing in 1982. Won the Nobel PRize in Chemistry in 1989.

question

Thymine

answer

It has a common keto form, and a rare enol form, with the H at C4 rather than C3.

question

Tn3 element

answer

A replicative transposon in bacteria. Terminate in simple inverted 38 - 40 bp repeats. Contain three genes: tnpA, tnpR, and bla. Fuses with plasmids to form cointegrates. The plasmid and chromosome are split at the res site, thus replicating and passin Tn3 on to the other plasmid.

question

tnpA

answer

A gene in a Tn3 element. Codes for transposase.

question

tnpR

answer

A gene in a Tn3 element. Codes for resolvase or repressor. Binds to the res site to prevent transcription.

question

Transcript

answer

A strand of RNA produced by transcription. Identical sequence to the nontemplate strand of DNA. In prokaryotes, the half-life of a transcript is less than 5 minutes. In eukaryotes, the transcripts have proteins bound to them which protect them from degradation, increasing their half-life to 5 hours.

question

Transcription

answer

An RNA transcript is produced, using DNA as a template.

question

Transcription bubble

answer

A locally unwound segment of DNA where RNA transcription takes place. Produced by RNA polymerase. In E. coli it is about 18 nucleotide pairs wide.

question

Transcription factor

answer

Proteins that bind to the promoter region and form a complex before RNA polymerase II can bind in eukaryotes. Forms a locally unwound segment of DNA. Includes basal transcription factors.

question

Transcription unit

answer

A segment of DNA that is transcribed to produce on RNA molecule. May be equivalent to one gene, or include several genes. Large transcripts with many genes are common in bacteria.

question

Transfer RNA (tRNA)

answer

A type of RNA. Small RNA molecuels. Adaptors between amino acids and the codons in mRNA during translation. Have 1 - 4 unusual nucleotides that are modified post-transcriptionally by enzymes. Attach to amino acids by high energy bonds. Have an anticodon.

question

Transition

answer

A mutation caused by a tautomeric shift where a pyrimidine is replaced by the other pyrimidine, or a purine is replaced by the other purine. There are four possible transitions.

question

Transition vector

answer

The transposon used to carry genes into an organism. Gerald Rubin and Allan Spralding used a P element from bacteria. Different transition vectors work differently for different species.

question

Translation

answer

The sequence of nucleotides in an mRNA is converted into amino acids of a polypeptide, based on the genetic code. Takes place on ribosomes in the cytoplasm.

question

Translesion polymerase

answer

Replicate over lesions or defects which block replciation by most DNA polymerases.

question

Transposase

answer

A protein that enables cut-and-paste and replicative transposition. Encoded by cut-and-paste and replicative transposons. Binds at or near the ends of the element and cuts both strands of the DNA.

question

Transposition

answer

The movement of transposons.

question

Transposon

answer

Transposable element
Transposable genetic element
Discovered by Barbara McClintock. DNA elements that can move from site to site in the genome. Constitute over 40% of the human genome, 85% of the maize genome. Insertion of a transposon into a gene often renders genes non-functional. Can confer selective advantage, or act as a genetic parasite. Many mutations are caused by transposon insertion. Includes cut-and-paste transposons, replicative transposons, and retrotransposons.

question

Transposon tagging

answer

Identifying genes by using transposon-insertion mutations as markers.

question

Transversion

answer

A mutation caused by a tautomeric shift where a pyrimidine is replaced with a purine, or vice versa. There are eight possible transversions.

question

Trichothiodystrophy

answer

An inherited disease caused by defects in DNA repair mecahnisms. UV sensitivity, neurological disorders, and mental retardation. Individuals have short stature, brittle hair, and scaly skin. Caused by mutations in TTD, XBA, or XPD.

question

Trinucleotide repeats

answer

Simple tandem repeats with 3 nucleotide pairs. Increase in copy number causes inherited diseases. The higher the copy number, the more severe the symptoms. There can be anticipation. Incldues FRAXA.

question

Triplet code

answer

The nucleotide codons. Evidence for this was first found by Francis Crick in 1961.

question

tRNA_f^Met

answer

The aminoacyl-tRNA that the initiation codon codes for in prokaryotes. Adds a methionine with a formyl group. The amino terminus amino acid in prokaryotes is alwas f-methionine, and is often cleaved post-translationally.

question

tRNA_i^Met

answer

The aminoacyl-tRNA that the initiation codon, AUG, codes for in eukaryotes. Adds a methionine without a formyl group.

question

tRNA^Met

answer

The aminoacyl-tRNA that AUG codon codes for, excepting the initiation codon in prokaryotes. Adds methionine without a formyl group.

question

trpA

answer

A gene in E. coli that encodes for the ? subunit of tryptophan synthetase. It was studied by Charles Yanofsky and colleagues.

question

trpB

answer

A gene in E. coli that encodes for the ? subunit of tryptophan synthetase.

question

Tryptophan

answer

One of the only amino acids which is specified by a single codon.

question

Tryptophan biosynthesis

answer

The genes for biosynthesis of tryptophan are depressed in the presence of tryptophan.

question

TTDA

answer

A gene on chromosome 6 for basal transcription factor IIH. Mutation in this gene can cause trichothiodystrophy.

question

Ty1

answer

A retrovirus-like element found in yeast. 5.8 kbp, with 340 bp LTRs. Creates a 5 bp target site duplication when inserted. Most yeast strains have about 35 copies of it. Incldues TyA and TyB genes, homologous to gag and pol, respectively.

question

Ultraviolet radiation (UV)

answer

A nonionizing radiation. Induces mutations through excidation of electrons. Causes cross-linking of adjacent thymines, to form thymine dimers that can block DNA replication and activate DNA repair mechanisms.

question

Unidirectional replication

answer

One replication fork remains stationary while the other moves away. Occurs in the circular chromosome of coliphage P2.

question

Universal

answer

A characteristic of genetic code. Virtually all organisms use the same genetic code. Exceptiosn in mitochondria and yeast. Mutations in tRNA cause deviations from the genetic code, and can arise as suppressor mutations.

question

Upstream

answer

Towards the 5' end of the RNA transcript.

question

Upstream sequence (-)

answer

DNA sequences that precede the initiation site.

question

UvrD

answer

MutU
DNA helicase
Involved in mismatch repair in E. coli. Necessary for excision.

question

Van der Waals interactions

answer

An element of tertiary structure of proteins. Weak attraction between atoms in close proximity.

question

Vernon Ingram

answer

In 1957, demonstrated that in a normal person, the 6th amino acid of the ?-subunit of hemoglobin is gluatmine, but in someone with sickle-cell anemia, it is valine.

question

Vicia faba

answer

Broad beans. Used in the experiments of Taylor, Woods, and Hughes.

question

Werner syndrome

answer

An inherited disease caused by defects in DNA repair mechanisms. Chromosome instability, progressive neurodegeneration, and prone to cancer. A less severe form of progeria. Sensesnce begins in the patient's teen years, and death occurs in the patient's 40s. Alterations in specific DNA helicases. Caused by a recessive mutation in WRN.

question

Wobble position

answer

The third base in a codon. It is not as important as the other bases, according to Crick's wobble hypothesis.

question

WRN

answer

A gene on chromosome 8 for WRN RecQ helicase. Mutation in this gene can cause Werner syndrome.

question

X-ray diffraction

answer

Used to create models of proteins.

question

X-ray radiation

answer

An ionizing radiation. Induces mutations through ionization.

question

Xenopus laevis

answer

South African clawed toad
Its nuclear organizer region is on the sex chromosome.

question

Xeroderma pigmentosum (XP)

answer

An inherited disease caused by defects in DNA repair mechanisms. UV sensitivity, early onset of skin cancers, and neurological disorders. DNA polymerase eta is absent. Caused by mutations in XPA, XPB, XPC, XPD, XPE, XPF, XPG, or XPV: genes for nucleotide excision repair.

question

XPA

answer

A gene on chromosome 9 for DNA damage recognition protein. Mutation in this gene can lead to xeroderma pigmentosum.

question

XPB

answer

A gene on chromosome 2 for 3' - 5' helicase. Mutation in this gene can lead to xeroderma pigmentosum or trichothiodystrophy.

question

XPC

answer

A gene on chromosome 3 for DNA damage recognition protein. Mutation in this gene can lead to xeroderma pigmentosum.

question

XPD

answer

A gene on chromosome 19 for 5' - 3' helicase. Mutation in this gene can lead to xeroderma pigmentosum or trichothiodystrophy.

question

XPE

answer

A gene on chromosome 11 for DNA damage recognition protein. Mutation in this gene can lead to xeroderma pigmentosum.

question

XPF

answer

A gene on chromosome 16 for nuclease 3' incision. Mutation in this gene can lead to xeroderma pigmentosum.

question

XPG

answer

A gene on chromosome 13 for nuclease 5' incision. Mutation in this gene can lead to xeroderma pigmentosum.

question

XPV

answer

A gene on chromosome 6 for translesion DNA polymerase ?. Mutation in this gene can lead to xeroderma pigmentosum.

question

Z-DNA

answer

Left-handed, open DNA. Found in some living cells.

Foundations in Molecular Biology and Genetics: Final – Flashcards

Unlock all answers in this set

Haven't found what you were looking for?

Search for samples, answers to your questions and flashcards