Functional Genomics/dna Replication

Front 1

Define 5-meC and its role in the regulation of gene expression.

Back 1

cytosines in the CKG islands of DNA are methylated to form 5-methylcytosine. Proteins (MBPs) can bind to this and block gene expression.

Front 2

What is the class of antibiotics that inhibits DNA gyrase?

Back 2

AMINOCOUMARINs: (ex. nalidixic acid, novobiocin) bind to ATPase active site of DNA gyrase and block its energy source. QUINOLONES: (nalidixic acid) bind DNA gyrase and keeps it from decatenating DNA

Front 3

5'-mCpG mutation hot spots in DNA, fxn

Back 3

deamination of cytosine can be repaired, but deamination of 5-methylcytosine cannot be repaired. Therefore genetic disease often occurs at 5'-mCpG mutation "hot spots" in DNA.

Front 4

steps of synthesis and replacement of RNA primers?

Back 4

1 DNA primase synthesizes RNA primer, 2 primer extended, 3 DNA filled in after primer, 4 DNAp1 replaces RNA primer replaces RNA primer with DNA nucleotides, 5 DNA ligase closes gaps

Front 5

Name the enzyme that is responsible for each of the following: 1 synthesis of RNA primers,2 adding nucleotides to 3' end of DNA, 3 relieving supercoiling, 4 proofreading, 5 connecting Okazaki fragments

Back 5

1 DNA primase synthesizes RNA primers, 2 DNA polymerase (usually DNApIII) adds nucleotides to 3' end of DNA, 3 DNA gyrase (or topoisomerase) relieves supercoiling of DNA, 4 DNA polymerase I proofreads, 5 DNA ligase forms phosphoanhydride bonds (?) between Okazaki fragments

Front 6

nick vs. gap, def

Back 6

A nick is a interruption in the phosphoanhydride bonds, a gap is a place where whole nucleotides are missing

Front 7

Name the enzyme that is responsible for each of the following: 1 removing the RNA primer from the lagging strand close to the replication fork, 2 adding nucleotides to the place where the primer used to be

Back 7

1 RNAase removes primer from lagging strand, 2 telomerase lengthens newly synthesized lagging strand on 5' end

Front 8

What do DNA polymerases require in order to work?

Back 8

a primer with a free 3' OH group

Front 9

DNA gyrase, fxn

Back 9

alleviates supercoiling created by DNA helicase

Front 10

Define the following: transition mutation, transversion mutation, nonsense mutation, silent mutation, missense mutation

Back 10

transition mutation: pur for pur, pyr for pyr. Transversion mutation: pyr for pur, pur for pyr. Nonsense: forms a stop codon. Silient mutation: no change in aa. Missense mutation: base substitution changes resulting aa.

Front 11

Define the following: genome mutation, chromosome mutation, gene mutation. Give the rates that each occurs.

Back 11

GENOME MUTATION: chromosome missegregation (ex. aneuploidy) occurs 10^(-2) per division. CHROMOSOME MUTATION: (ex. translocation) occurs 6x10^(-4) per division. GENE MUTATION: base pair mutation (ex. point mutation) occurs 10^(-10) per base pair per division or 10^(-6) per locus per generation

Front 12

Give the effect on DNA for reach of the following mutagenic processes or chemicals: acid and heat depurination, ionizing radiation, alkylating agents, spontaneous deaminations

Back 12

acid and heat depurination (missing base), ionizing radiation (altered base), alkylating agents (altered base), spontaneous deaminations (incorrect base)

Front 13

Give the effect on DNA for reach of the following mutagenic processes or chemicals: intercalating reagents (acridines), UV irradiation, ionizing radiation, psoralen derivatives, mitomycin C

Back 13

intercalating reagents (deletion-insertion), UV irradiation (dimer formation), ionizing radiation (strand breaks), psoralen derivatives (interstrand cross-links), mitomycin C (interstrand cross-links)

Front 14

Describe the basic types of DNA repair. (3)

Back 14

1 PROOFREADING by DNA polymerases for mutations that occur during DNA replication, 2 MISMATCH for mutations that pass proofreading, 3 EXCISION REPAIR for mutations that occur spontaneously

Front 15

What is the significance of high fidelity DNA replication?

Back 15

Correlates with increased life span. People have greater DNA repair activity than shrews and we live longer.

Front 16

How are defects in DNA repair mechanisms related to cellular function and human disease?

Back 16

result in a high frequency of chromosome and gene (base pair) mutations, predisposing affected individuals to cancer (ex. leukemia)

Front 17

What is the orientation of the template strand, 3'->5' or 5'->3'

Back 17

5'->3' (nucleotides are added to the 3' end)

Front 18

Give a general description of bacterial DNA replication

Back 18

bidirectional or θ replication

Front 19

oriC: acronym, def, components (2)

Back 19

origin of Chromosomal replication; signal for the start of replication; contains 1 AT-rich region, 2 DnaA boxes

Front 20

What initiates replication of DNA? Describe the mechanism.

Back 20

binding of DnaA proteins to the DnaA box sequence; causes region to wrap around DnaA proteins and separates AT-rich region

Front 21

DNA helicase, fxn

Back 21

separates DNA strands

Front 22

SSB: acronym, fxn

Back 22

single-strand binding proteins; bind to separated DNA strands to hold them apart

Front 23

What is the eukaryotic equivalent of DNA gyrase?

Back 23

topoisomerase

Front 24

RNA primers: name of enz that synthesizes, average length of sequence

Back 24

synthesized by DNA primase; average length is 10-12 nucleotides

Front 25

telomerase: composition, fxn

Back 25

composed of protein and RNA, binds to 3' overhang of DNA and adds a repeating sequence. DNA primase later adds a primer and allows synthesis to occur as normal on the strand with a 5' end.

Front 26

most common types of polymerase errors? (2)

Back 26

frameshift, base substitution

Front 27

Substituting A for G would be an example of what kind of base substitution?

Back 27

transition

Front 28

Substituting T for G would be an example of what kind of base substitution?

Back 28

transversion

Front 29

Describe the functions of DNA polymerases I, II, and III.

Back 29

III: main replicating enz. I: fills in gaps, excises primers on lagging strand.

Front 30

DNA polymerases only read in the 5' to 3' direction, unless they are doing what?

Back 30

proofreading 3' to 5'

Front 31

polymorphism, def

Back 31

the presence of two or more distinct phenotypes in a population due to the expression of different alleles of a given gene (ex. blood types)

Front 32

SNP, acronym

Back 32

single nucleotide polymorphism

Front 33

What is the tautomeric form of adenine and cytosine vs. guanine and thymine

Back 33

adenine and cytosine form amino->imino tautomers, while guanine and thymine form keto->enol isomers

Front 34

C normally pairs with G. What does the tautomeric form pair with?

Back 34

A

Front 35

What will spontaneous deamination convert each of the following to? cytosine, adenine

Back 35

cytosine to uracil, adenine to hypoxanthine

Front 36

Describe the mechanism of mismatch repair

Back 36

some adenines of parental DNA strands are methylated, child DNA strands are reviewed for mismatches before methylation

Front 37

MBP, acronym

Back 37

5-meC binding protein, blocks gene expression on methylated strands of DNA

Front 38

"catenate", def

Back 38

arrange in a series of chains (ex. spores)