question

What is a genetic marker? What are they used to do?

answer

a specific, short sequence of DNA at particular locations on the genome that differ between individuals in the same species; map the locations of genes that control particular traits

question

Who proposed the idea of sequencing the entire human genome? In what year?

answer

Renato Dulbecco; 1986

question

What is the Human Genome Project? In what year was it fully completed?

answer

a funded research effort to produce a complete DNA sequence for the entire human genome; 2003

question

How many chromosomes do prokaryotes usually have? How many chromosomes do eukaryotes usually have?

answer

1; many

question

What did the method that method used to obtain the first human genome sequence use? Who created this method? In what decade? What were the drawbacks of using this method (3) and what did this inspire to happen and what was this and what are the effective characteristics of this (3)?

answer

chemically modified nucleotides; Frederick Sanger; 1970s; it was slow, expensive, and labor intensive, the creation of a new way to sequence DNA, next-generation DNA sequencing, it is fully automated and miniaturized, it conducts massively parallel sequencing, and it is inexpensive and can sequence large genomes

question

What is massively parallel sequencing?

answer

the sequencing of millions of different fragments at the same time in DNA sequencing

question

What is bioinformatics? What is it mainly used to do?

answer

the use of computers and/or mathematics to analyze complex biological information; analyze DNA sequences

question

What is functional genomics? What is it used to do? What are the 5 different types of parts of genomes according to their function and what is each and what is the second identified by and what are the 3 categories within the fifth?

answer

the assignment of functional roles to the proteins encoded by genes identified by sequencing entire genomes; identify the functions of various parts of genomes; 1) open reading frames-the coding regions of genes 2) amino acid sequences of proteins 3) regulatory sequences-promoters and terminators for transcription 4) RNA genes 5) other noncoding sequences, the DNA sequences of open reading frames by applying the genetic code, centromeric regions, telomeric regions, transposons, and repetitive sequences

question

What are open reading frames that code for proteins recognized by in DNA sequences (2)?

answer

1) the start and stop codons for translation 2) introns

question

What is comparative genomics? What can this be used to do (2)?

answer

the comparison of a newly sequenced genome to sequences from other organisms; 1) provide further information about the functions of sequences 2) used to trace evolutionary relationships among different organisms

question

What are the 2 related fields of research that new genomes sequences are used in?

answer

functional genomics and comparative genomics

question

What is genetic determinism?

answer

the idea that a person's phenotype is determined solely by his or her genotype

question

What is proteomics?

answer

the study of the proteome

question

What are the 2 fields of biology that study cells and organisms more closely but complement genomics?

answer

proteomics and metabolomics

question

What is the proteome? What are the 2 methods that are used to analyze proteins and the proteome?

answer

the sum total of all of the proteins produced by an organism; 1) they can be separated according to their electric charge and size by two-dimensional gel electrophoresis and then further analyzed/sequenced//studied 2) mass spectrometry uses electromagnets to determine the structures of proteins

question

Which is more complex, the proteome or the genome?

answer

the proteome

question

What does genomics seek to describe?

answer

the genome and its expression

question

What does proteomics seek to do?

answer

identify and characterize all of the expressed proteins

question

What are both gene function and protein function affected by (cell wise)?

answer

the cell's internal and external environments

question

What is the metabolome? What are the 2 types of metabolites? What is the first involved in and what does it include? What is the second unique to, what is the second involved in, and what is an example of it?

answer

the quantitative description of all of the metabolites in a cell or organism; primary metabolites and secondary metabolites; normal processes, hormones and signaling molecules; particular organisms or groups of organisms, special responses to the environment, chemicals made by plants that are used in defense against pathogens/herbivores

question

What is a metabolite?

answer

the substrates and products of an enzyme's function

question

What is metabolomics? What does it aim to do?

answer

the study of the metabolome as it relates to the physiological state of a cell or organism; describe the metabolome of a tissue or organism under particular environmental conditions

question

Which were the first to have their cellular genomes sequenced, eukaryotes or prokaryotes?

answer

prokaryotes

question

In what year was the first complete genomic sequence of a free-living cellular organism published?n Who published it? Of what organism was it?

answer

1995; Craig Venter and Hamilton Smith; a bacteria

question

What do prokaryotic sequences reveal about prokaryotes (2)?

answer

1) how they are organized to perform different cellular functions 2) how certain specialized functions of particular organisms are carried out

question

What are the 4 most important features of bacterial and archaeal genomes?

answer

1) they are relatively small and are usually organized into one circular chromosome 2) they are compact 3) their genes usually do not contain introns 4) in addition to the main chromosome, they usually carry smaller circular DNA molecules called plasmids which may be transferred between cells

question

What is a transposon? What is another name for it? Where can it move from and to? What does it do on the whole? What are the ways in which it can move?

answer

a mobile DNA segment that can insert into a chromosome and cause genetic change; a transposable element; it can move from place to place in a genome and can even move from one piece of DNA to another in the same cell; produce significant phenotypic effects by inactivating genes; 1) the transposon can be replicated and then the copy can be inserted into another site in the genome 2) the transposon can splice out of one location and move to another location

question

What happens if a transposon becomes duplicated with two copies separated by one or few genes?

answer

a single larger transposon will form and the additional genes will be carried to different locations in the genome

question

What are microorganisms identified by (2)?

answer

1) their nutritional requirements 2) the conditions under which they will grow

question

What can scientists use now to analyze microbes? What did they used to have to do?

answer

PCR and modern DNA analysis techniques; culture the microbes in the lab

question

What is metagenomics? Who came up with this idea and in what year?

answer

the practice of analyzing DNA from environmental samples without isolating intact organisms; Norman Pace, 1985

question

What are the 2 ways to identify common sequences?

answer

1) look for them in the computer analyses of sequenced genomes 2) take an organism with a simple genome and deliberately mutate one gene at a time to see what happens

question

What are the 4 major differences between eukaryotic and prokaryotic genomes?

answer

1) eukaryotic genomes are larger than prokaryotic genomes 2) eukaryotic genomes have more protein-coding genes 3) eukaryotic genomes have more regulatory sequences and more regulatory proteins 4) much of eukaryotic DNA is noncoding

question

Where have most of the lessons learned from eukaryotic genomes come from, what are all of these/examples? Why?

answer

several model organisms that have been studied extensively, 1) yeast 2) roundworm 3) fruit fly 4) plant; because these model organisms are easy to grow and study in a lab, their genetics are well studied, and they exhibit characteristics that represent a larger group of organisms

question

What are yeasts? What do they have (organelle wise)? What do they live as (haploid/diploid) and what is this determined by?

answer

single-celled eukaryotes, membrane enclosed organelles; they can live as either haploid or diploid, environmental conditions;

question

Which is more complex structurally and functionally, eukaryotic cells or prokaryotic cells?

answer

eukaryotic cells

question

What causes yeasts to have more genes than E. coli?

answer

the compartmentalization of the eukaryotic yeast cell into organelles

question

What are orthologs?

answer

genes with very similar sequences

question

Why do some plants have more protein-coding genes than animals?

answer

in order to create defense mechanisms that produce chemicals to defend themselves from their enemies and adapt to their environments

question

What do half of all eukaryotic protein-coding genes exist as?

answer

one copy in the haploid genome

question

What is a gene family?

answer

a set of similar genes derived from a single parent gene

question

What is a pseudogene? What does it result from?

answer

a DNA segment that is homologous to a functional gene but is not expressed because of changes to its sequence or changes to its location in the genome; mutations that cause a loss of function

question

What 2 types of DNA sequences do eukaryotic genomes contain in regard to their repetitiveness and what is each? How long is the first? Is the first transcribed or not? What is the first often associated with and what is this? What is a type of the first and what is it and where are they located? What does the second type include? What are most of the seconds?

answer

1) highly repetitive sequences-sequences that are repeated thousands of times in side-by-side arrangements in the genome 2) moderately repetitive sequences; short; not transcribed; heterochromatin, the densely packed and transcriptionally inactive part of the genome; short tandem repeats (STRs), a short moderately repetitive sequence of DNA, they are scattered throughout the genome; the genes that are transcribed to produce tRNAs and rRNAs; transposons

question

What percent of the human genome do transposons make up?

answer

over 40%

question

How many main types of transposons are there in eukaryotes? What are they? What does the first do? What are the 2 types of the first and what does the first have and what does the second not have and what are the 2 types of the second? Are SINEs translated? Are SINEs transcribed? Are LINEs translated/transcribed? What do DNA transposons not use and instead of this what do they do?

answer

2; 1) retrotransposons/Class I transposons 2) DNA transposons/Class II transposons; makes RNA copies of itself which are then copied back into DNA before insertion at new locations in the genome; 1) LTR retrotransposons 2) Non-LTR retrotransposons, long terminal repeats of DNA sequences at each end, long terminal repeats of DNA sequences at each end, 1) SINEs (short interspersed elements) 2) LINEs (long interspersed elements); no; yes; some are into proteins; RNA intermediates, they are excised from their original location and become inserted at a new location without being replicated

question

What percent of the human genome do LTR retrotransposons make up?

answer

8%

question

What percent of the total DNA content of the human genome do SINEs make up?

answer

15%

question

What percent of the human genome do LINEs make up?

answer

17%

question

How many base pairs are in the human genome? How many protein-coding genes? How many base pairs is the average gene? What do all human genes have? What percent of the human genome is functional but noncoding? What percent of the genome is made up of transposons and other repetitive sequences? What percent of the genome is the same in all people?

answer

3.2 billion; 24,000; 27,000; introns; 3.5%; over 50%; 97%

question

What are complex phenotypes determined by?

answer

multiple genes interacting with the environment

question

What are haplotype maps used to do? What are they based on and what are these and what do they arise as?

answer

identify genes involved in disease; single nucleotide polymorphisms (SNPs), DNA sequence variations that involve single nucleotides, point mutations

question

What are SNPs used to do (3)? How are they inherited?

answer

1) create genetic maps of organisms 2) classify organisms and species 3) identify individual organisms carrying specific alleles; they are not inherited independently but a set of SNPs that are close together on a chromosome are inherited as a unit

question

What is a haplotype?

answer

a piece of chromosome with a set of linked SNPs

question

What is a DNA microarray? What do they depend on to do what they need to do which is what?

answer

a grid of microscopic spots of oligonucleotides arrayed on a solid surface; hybridization to identify specific SNPs

question

How are SNPs analyzed in the genomes of individuals (2)?

answer

1) by next generation sequencing methods 2) by DNA microarrays

question

What is pharmacogenomics?

answer

the study of how an individual's genome affects his or her response to drugs or other agents

question

What percent of the yeast proteome is shared by the human proteome? What percent of the worm proteome is shared by the human proteome? What percent of the fruit fly proteome is shared by the human proteome?

answer

46%; 43%; 61%

question

What provides the basic metabolic functions of a eukaryotic cell?

answer

a set of 1,300 proteins

question

What does DNA fingerprinting refer to? What does the most common of these techniques involve?

answer

a group of techniques used to identify particular individuals by their DNA; STR analysis

question

To sequence a genome what must happen (3)?

answer

1) the chromosomes must be cut into overlapping fragments 2) these overlapping fragments are sequenced 3) then the sequenced fragments are lined up to assemble the DNA sequence of the chromosome

question

What happens in next-generation sequencing (3)?

answer

1) short, single stranded DNA fragments are attached to a solid surface 2) a primer and DNA polymerase are added 3) tagged nucleotides are detected by a camera as they are added to the complementary DNA strand

question

What are the 4 elements that genomic sequences include?

answer

1) protein-coding genes 2) RNA genes 3) transcription control elements 4) repeated sequences

question

How can a minimal genome be identified (2)?

answer

1) use transposon mutagenesis to inactivate genes one by one 2) organism is then tested for survival

question

What percent of the human genome codes for proteins? What does much of the rest consist of?

answer

1.5%; repeated sequences

question

What is biotechnology?

answer

any technological application that uses biological systems, living organisms, or derivatives thereof to make or modify products or processes

question

What is recombinant DNA? What are the 3 tools/steps used to make it?

answer

single molecules containing DNA sequences from two or more organisms; 1) using restriction enzymes to cut DNA into pieces that can be manipulated 2) using gel electrophoresis for the analysis and purification of DNA fragments 3) using DNA ligase for joining DNA fragments together in novel combinations

question

What is a restriction enzyme? What is another name for it? What bonds does this enzyme break? Where do restriction enzymes do what they do and how many of these do they have and what does this do? What is left after the restriction enzyme has done its job and what are these called and why?

answer

an enzyme that cuts double stranded DNA at specific sites; restriction endonuclease; the bonds of the DNA backbone between the 3' hydroxyl group of one nucleotide and the 5' phosphate group of the next nucleotide; at a restriction site/recognition sequence, 2 identical restriction sites on 2 subunits, allows them to cut the 2 strands simultaneously; small strands of single stranded DNA, sticky ends, because they are able to form hydrogen bonds with complementary sequences on other DNA molecules

question

What do bacteria use to defend themselves against bacteriophages? How does this work?

answer

restriction enzymes; it cuts the double stranded DNA injected by the bacteriophage into smaller noninfectious fragments

question

What is a recognition sequence/restriction site?

answer

a specific DNA base sequence that is recognized and acted upon by a restriction enzyme

question

What are blunt ends?

answer

the other type of end that a restriction enzyme can create once its done its job

question

How do bacteria protect themselves from their own restriction enzymes?

answer

by modifying the restriction sites in its own DNA by using methylase to add methyl groups to certain bases at restriction sites

question

What is setting up a restriction digest?

answer

the procedure of using restriction enzymes in a lab

question

What is gel electrophoresis? What are the 3 types of information that we receive from this about a DNA sample?

answer

a technique for separating molecules (such as DNA fragments) from one another on the basis of their electric charges and molecular weights by applying an electric field to a gel; 1) the number of fragments-how many times the enzyme's restriction sequence occurs in the sample 2) the sizes of the fragments 3) the abundance of a fragment

question

How can one create a physical map of an intact DNA molecule? What are the steps (2)?

answer

by gel electrophoresis; 1) use restriction enzymes to cut a sample DNA 2) analyze the DNA fragments in gel electrophoresis

question

What is DNA ligase? How can it be used to make recombinant DNA?

answer

an enzyme that unites broken DNA strands by forming phosphodiester bonds between them during replication and recombination; after the DNA strands have been cut by a restriction enzyme they can be spliced together in different combinations by DNA ligase

question

What did the experiment that Stanley Cohen and Herbert Boyer conducted discover? What did they do in the experiment? In what decade?

answer

that recombinant DNA can be a functional carrier of genetic information; 1) restriction enzymes cut out sequences from 2 E. coli plasmids containing different antibiotic resistance genes 2) DNA ligase joined these two fragments together 3) they inserted the resulting plasmid into a new E. coli and it gave that E coli. resistance to both antibiotics; 1970s

question

What is one important goal of recombinant DNA technology? What does this mean? How can this happen (by what process) and what is the first and what is the second?

answer

to clone; to produce many identical copies of a particular DNA sequence; transformation or transfection, the insertion of recombinant DNA into a host's cell, the insertion of recombinant DNA into an animal cell

question

What is a transgenic cell/organism?

answer

a host cell/organism that contains recombinant DNA

question

What are selectable marker genes? What are they included in and why? What larger group to they belong to?

answer

genes that can be used to identify cells that contain recombinant DNA from among a large population of untransformed cells; the recombinant DNA that is put into the host cell, so that they can help create an organism from the transgenic cells by allowing only them to grow; reporter genes

question

What are the 4 types of organisms that are most commonly used as host cells for the introduction of DNA?

answer

1) bacteria 2) yeasts 3) plant cells 4) cultured animal cells

question

What are the 4 ways to insert recombinant DNA into a host cell?

answer

1) chemically treating the host cells so that their membranes are more permeable and then mixed with the DNA 2) electroporation can be used-a short electric shock is used to create temporary pores in the host's membrane through which DNA can enter 3) viruses and bacteria can be altered so that they carry or insert the DNA into host cells 4) transgenic animals can be produced by injecting recombinant DNA into the nuclei of fertilized eggs

question

What is a replicon?

answer

a region of DNA replicated from a single origin of replication

question

What are the 2 ways in which the newly introduced recombinant DNA can become part of a replicon within the host cell?

answer

1) the DNA can be inserted into a host chromosome 2) the DNA can enter the host cell as part of a carrier DNA sequence called a vector and can either integrate into a host chromosome or have its own origin of DNA replication

question

What is a vector? What are the 3 types of vectors that can be used to get recombinant DNA into cells and why is each used (4 for first) (1 for second) (2 for third)?

answer

a plasmid or virus that carries an inserted piece of DNA into a bacterium for cloning purposes in recombinant DNA technology; 1) plasmids as vectors-they are small and therefore easily to manipulate, they have one or more restriction enzyme recognition sequences that each occur only once in the plasmid sequence which makes it easy to insert additional DNA into the plasmid, they contain genes that are resistant to antibiotics and therefore serve as selectable markers, they have an origin of replication and therefore can replicate independently of the host chromosome 2) plasmid vectors for plants (the plasmid found in the bacteria A. tumefaciens)-it has genes that allow the bacteria to infect plant cells and then insert a region of its DNA into the chromosome of infected cells 3) viruses as vectors-it is bigger and therefore can accommodate larger eukaryotic DNA sequences that plasmids can't, they infect cells naturally

question

After introduction of recombinant DNA to host cells, how can one identify which host cells actually incorporated the recombinant DNA into their genome?

answer

by inserting selectable markers such as antibiotic resistance genes in the recombinant DNA that allows us to observe how many host cells were infected after treating all of the cells with the chemical that the antibiotic gene is resistant to and seeing which ones live

question

What is a reporter gene? What are 2 types of reporter genes? What are the 2 other ways in which reporter genes are used?

answer

a genetic marker included in the recombinant DNA to indicate the presence of recombinant DNA in a host cell; 1) a selectable marker containing a gene for antibiotic resistance 2) a green fluorescent protein that normally occurs in a jellyfish and emits a green light to indicate that the host cell has been effectively transformed; 1) they can be attached to promoters to study how promoters function under different conditions 2) they can be attached to proteins to study how an where those proteins become localized within eukaryotic cells

question

What is the goal of cloning by recombinant DNA?

answer

to clarify the functions of specific DNA sequences

question

What is a genomic library?

answer

a collection of DNA fragments that together comprise the genome of an organism

question

What is a complementary DNA? Does it have introns? What is its shorthand? What does it make and how (2 steps)?

answer

DNA formed by reverse transcriptase acting with an RNA template; no; cDNA; a small DNA library that only includes the genes transcribed in a particular tissue, 1) the mRNA of the particular tissue is isolated from its cell 2) cDNA copies of the mRNA are made by complementary base pairing using the enzyme reverse transcriptase

question

What is a cDNA library? What is it really? What are they used to do?

answer

the collection of cDNAs from a particular tissue at a particular time in the life cycle of an organism; a snapshot of the transcription pattern of the cell; used to compare gene expression in different tissues at different stages of development

question

What element is necessary in the creation of artificial DNA?

answer

recombinant DNA

question

What is a knockout experiment? What types of organisms does it only occur in? What is another name for it? What does this experiment discover? How does it occur in mice (3 steps)? Who developed these steps?

answer

a molecular genetic method in which a single gene of an organism is permanently inactivated; animals; transposon mutagenesis designed to describe the minimal genome; the function of a gene; 1) the normal gene of interest from the mouse is inserted into a plasmid 2) restriction enzymes insert a fragment containing a reporter gene/selectable marker into the middle of a normal gene which disrupts the gene's coding region so that it no longer codes for a functional protein 3) once the recombinant plasmid has been made it is used to infect mouse embryonic stem cells; Capecchi, Evans, and Smithies

question

What is homologous recombination? What is it used to do?

answer

the exchange of segments between two DNA molecules based on sequence similarity between the two molecules during crossing over; conduct a knockout experiment in small animals

question

What is a stem cell?

answer

an unspecialized cell that divides and differentiates into specialized cells

question

What is another way of studying the expression of a specific gene? How is this done (2 steps)?

answer

to block the translation of the gene's mRNA; 1) an antisense RNA is made artificially in a lab to be complementary to the mRNA that carries that gene of interest whose translation needs to be blocked 2) the antisense RNA is inserted into the cell and blocks the translation of the mRNA and the gene of interest

question

What is an antisense RNA? What is an example of this?

answer

a single stranded RNA molecule that is complementary to as mRNA of interest to block its translation; microRNA

question

What is RNA interference? What is its shorthand? What are the small molecules that help it occur and what does it do and how?

answer

a mechanism for reducing mRNA translation where a double stranded RNA is processed into a small single stranded RNA whose binding to a target mRNA results in the latter's breakdown; RNAi; small interfering RNAs (siRNAs) that are short double stranded RNAs, it acts as an antisense RNA, 1) it is turned into 2 single stranded RNA molecules by a protein complex 2) it is guided to its target mRNA by the protein complex 3) the siRNA bings to the target mRNA and breaks it down into much smaller fragements

question

Which is preferred siRNA or antisense RNA? Why?

answer

siRNA; because they are more stable

question

What is DNA microarray? What is it used to do?

answer

a small glass or plastic square onto which thousands of single stranded DNA sequences are fixed so that hybridization of cell-derived RNA or DNA to the target sequences can be performed; to analyze, discover, and study the patterns of gene expression in different tissues at different times

question

What is an expression vector? What do they include for bacterial hosts (3)? What do they include in eukaryotic hosts (3)? What 3 other features can an expression vector include?

answer

a DNA vector such as a plasmid that carries a DNA sequence for the expression of an inserted gene into mRNA and protein in a host cell; a promoter, a signal for transcription termination, and a special sequence that is necessary for ribosome binding on the mRNA; the poly-A addition sequence, transcription factor binding sites, and enhancers; 1) an inducible promoter which responds to a specific signal 2) a tissue-specific promoter which is expressed only in a certain tissue at a certain time 3) signal sequences that direct the gene product to an appropriate destination

question

What is pharming?

answer

the production of pharmaceuticals in farm animals or plants

question

What are the 3 advantages that recombinant RNA technology has over traditional methods of breeding?

answer

1) the ability to identify specific genes using selectable markers which makes breeding more precise and rapid 2) the ability to introduce any gene from any organism into a plant or animal species which expands the range of possible new traits 3) the ability to generate new organisms quickly by cloning which is much faster than traditional breeding

question

What are the 3 claims about genetic alteration of organisms that are the center of concerns about the safely of genetically modifying crops and other organisms

answer

1) genetic manipulation is an unnatural interference with nature 2) genetically altered foods are unsafe to eat 3) genetically altered crop plants are dangerous to the environment

question

What is bioremediation?

answer

the use by humans of other organisms to remove contaminants from the environment

Biology Chapters 12-13 – Flashcards

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