genetics exam 2

what gives rise to comparative genomics?

gene functions have been conserved across evolution, so when nature solves a problem it typically continues to reuse the solution

what is it called when you establish gene function and can transfer that understanding to other species

comparative genomics

conserved genes for glycolysis is an example of what?

comparative genomics

when the eyeless mutation was first sequenced, it was recognized as a gene that regulates what?

transcription

which gene was sequenced first, the human aniridia gene or the drosophila eyeless mutation?

drosophila eyeless mutation

if you were to take a fruit fly with the eyeless mutation and replace the gene with a human gene in the correct location, what would happen?

human gene makes up for absence of fruit fly gene, develops normal compound eyes

what would happen if you express fruit fly gene or human gene in the wrong location?

ectopic expression of gene

do ectopic eyes work?

no

flies with human eyeless homolog do not develop what?

human eyes

fruit fly eye genes control not just presence/absence of eyes, but also what?

the kind of eye the human gene generates within the fruit fly

gene products function as a part of what?

pathways, cascades

what drives the formation of either compound eyes or irises?

subsequent genes/pathways

the function of many genes is conserved across what?

immense evolutionary distances

the function of a gene is affected by its...?

environment

what has an impact on what the genes upstream affect?

downstream regulators

the function of a gene can be impacted by what?

external and internal environment, context

who conducted an experiment that led to the realization that DNA encodes genetic information?

frederick griffith

early in the 20th century, what was accepted about genetic material?

DNA cannot encode genetic material, it was proteins

why was it thought that DNA couldn't encode genetic information?

unit sequence of DNA and RNA was just repeats of GATC over and over again, nothing more

transforming principle in experiment strains

streptococcus pneumoniae

two strains: smooth - virulent (S) and rough - non-virulent (R

once you get beyond the genes that encode proteins, they are almost all what kind?

structural (scaffolding) RNAs or regulatory (gene expression, RNAs, protein function)

what happens if you were to inject the S strain into a mouse?

it dies

what happens if you were to inject the R strain into a mouse?

it lives

how does the smooth strain evade the recognition of the immune system to kill the mouse?

makes a complex mucosal surface on bacteria to hide from the mouse's immune system

how does the mouse live when injected with the R strain?

R strain does not make a mucosal surface to evade the immune system so the immune system detects and kills it

during the experiment, what happens when the S strain is heat killed?

the mouse survived

during the experiment, what happens when the heat killed S strain and the R strain were put into the mouse?

the mouse died

principle of Griffith's experiment

something from the dead S strain transforms the R strain to virulent S strain

avery-macleod-mccarty experiment

identified the transforming principle by extracting components from the smooth virulent strain

what happened when the S strain was treated with protease and RNase?

nothing, genetic material was not affected and transformation still occurred

what happened when S strain was treated with DNase?

S strain was killed, transformation did not occur

purpose of avery-macleod-mccarty experiment

DNA is the genetic material

what experiment used a bacterial phage T2 to infect bacteria to see what the genetic material of the cell is?

hershey-chase experiment

components of bacterial virus (phage) T2

protein coat surrounding, DNA core

during the hershey-chase experiment, what was labeled with sulfur?

virus protein

during the hershey-chase experiment, what was labeled with phosphate?

virus DNA

steps of hershey-chase experiment

label virus protein and DNA, allow attachment of phage long enough to permit infection, blender to sheer off phage particles, see which molecule was left in bacteria

was radioactive phosphate or sulfur found in the bacteria?

phosphate

where did the protein go during the hershey-chase experiment?

supernatant

what is the genetic material of the cell?

DNA

what is the genetic material of some viruses like HIV?

RNA

why was it originally believed that nucleic acids could not be the genetic material?

DNA only has 4 components and is just repeated sequences, protein has 20

DNA, RNA, and proteins encoded by RNA have what?

directionality - a beginning and an end encoded in the DNA

directionality of DNA

5' to 3'

from DNA directionality, what is determined?

RNA transcription

from RNA directionality, what is determined?

RNA translation

proteins have directionality depending on what?

RNA

what end of DNA/RNA contains the phosphate group or some other modification?

5' end

what end of DNA/RNA contains the OH group?

3' end

relationship of DNA strands

antiparallel

what holds double stranded DNA together?

hydrogen bonds

base pairing rules

A-T (2 bonds)

G-C (3 bonds)

what is the difference between a deoxyribose sugar and a ribose?

deoxyribose lacks a hydroxyl (-OH) group at the 2' carbon position

where does the next nucleotide attach onto DNA?

the 3' OH group

where is the triphosphate attached to on the incoming nucleotide?

5' end

what does the formation of a phosphodiester bond release?

a diphosphate

what does the released phosphate do?

contributes the energy to make the phosphodiester bond

when does the formation of the phosphodiester bond occur?

DNA formation and repair

what are chargaff's rules?

amount of purines = amount of pyrimidies

amount T = amount A

amount G = amount C

however, A+T does not equal G+C

who discovered x-ray diffraction?

rosalind franklin and maurice wilkins

what permits deduction of structure of the DNA crystal and provides evidence that DNA has long fibers that run adjacent to each other and are helical?

x-ray diffraction

what attributes of DNA do you have to maintain to replicate DNA?

double stranded, antiparallel, 5' and 3' ends, base pairing, ribose-phosphate backbone, hydrogen bonding, and hydrogen interactions

what is the DNA backbone composed of?

charged phosphate residues

what are DNA sugars linked by?

phosphodiester bonds

how do phosphodiester bonds link?

link 5' methyl group to 3' OH group

what is the main site on DNA for protein binding where proteins interact with several nucleotides?

major groove

what is the area on DNA where bases are closer together and not easily accessed?

minor groove

purpose of major and minor grooves

allows proteins to recognize specific sequences without pulling strands apart

what synthesizes DNA in the 5' to 3' direction and copies DNA to DNA?

DNA polymerase

does DNA polymerase require a primer?

yes

what synthesizes primers?

primase

do RNA polymerases require primers?

no

what does DNA polymerase needing a primer and RNA polymerase not needing a primer suggest?

life itself started out using RNA as the fundamental genetic material

is RNA chemically more or less stable than DNA?

less stable

where is replication initiated?

defined origins of replication

function of DNA polymerase I

repair and replace RNA primer

function of DNA polymerase 2

repair

function of DNA polymerase 3

replicate chromosomal DNA - multisubunit enzyme

what can ONLY synthesize DNA in one direction by adding the 5' end of the next nucleotide to the 3' end of an existing strand?

DNA polymerase

what synthesizes a short RNA primer to initiate DNA synthesis?

primase

what separates annealed (bound) double stranded DNA - permits access of primase and DNA polymerase?

helicase

what binds and stabilizes single stranded DNA and prevents reannealing?

single stranded DNA binding protein

what relieves torsional stress induced by unwinding of DNA?

gyrase (topoisomerase II)

what covalently bonds DNA synthesized to replace RNA primer?

DNA ligase

bacteria have ______ origins of replication while eukaryotes have _______

single, multiple

eukaryotes have ______ chromosomes while bacteria have _______

linear, circular

what is the impact of DNA polymerase's ability to only synthesize DNA in the 5' to 3' direction?

forces DNA replication to be asymmetrical: creating a leading and lagging strand

how does replication of the leading and lagging strand differ?

the leading strand is synthesized continuously and the lagging strand is produced discontinuously

what are short, discontinuously synthesized DNA sequences (100-200 nucleotides in eukaryotes, 1000-2000 in bacteria) that form the lagging strand during DNA replication?

okazaki fragments

what corrects errors that occur during replication?

proofreading

what polymerases possess 3'-->5' exonuclease activity to remove mismatched bases?

DNA polymerase I and III

what are the three possible models for DNA replication?

conservative, semi-conservative, dispersive

how did we find the 3 models of DNA replication?

grow bacteria with a heavy and light isotope, centrifuge, and see how samples align by density (2 rounds of replication)

what is the concluded model for DNA replication?

semiconservative

what kind of replication is when both parent strands are used to generate a daughter strand, and each cell gets a copy of the parental strand?

semiconservative replication

significance of semiconservative replication

during DNA repair, if parental strand is still intact it will use the parent strand to correct the error

DNA at the tips of chromosomes

telomeres

which kinds of cells have telomeres?

eukaryotes, bacteria are circular so they don't have ends

what is responsible for completing synthesis of dsDNA at the telomeres?

telomerase

what enzyme is only active in germ cells?

telomerase