Biochemistry: Dna Structure, Replication And Repair

Front 1

Which eukryotic DNA polymerase contains primase and initiates DNA synthesis?

Back 1

Pol alpha

Front 2

Which eukryotic DNA polymerase functions in repair but has no proofreading ability?

Back 2

Pol Beta

Front 3

Which eukryotic DNA polymerase replicates mitochondrial DNA?

Back 3

Pol Gamma

Front 4

Which eukryotic DNA polymerase elongates the leading strand and okazaki fragments?

Back 4

pol delta

Front 5

Which eukryotic DNA polymerase functions in repair and has proofreading ability?

Back 5

Pol Sigma

Front 6

______ _______ is RNA directed DNA polymerase that is seen in transposons and some viruses.

Back 6

Reverse Transcriptase

Front 7

_______ maintains telomeric length in cells.

Back 7

Telomerase

Front 8

Eukaryotic DNA is associated with tightly bound basic proteins called what?

Back 8

Histones

Front 9

Histones are positively charged at physiologic pH as a result of their high content of which two amino acids?

Back 9

lysine and arginine

Front 10

The ________ ends of histones can be acetylated, methylated, or phosphorylated and these modifications serve what purpose?

Back 10

N-terminal ends: they influence how tightly the histones bind DNA and thereby affect transcription of genes.

Front 11

___ _______ can fuse two pyrimidines (usually thymines) adjacent to each other in the DNA, producing a dimer.

Back 11

UV radiation

Front 12

This DNA damaging agent can cause double stranded breaks:

Back 12

High energy ionizing radiation.

Front 13

proteins associated with mismatch repair is associated with which condition?

Back 13

Hereditary nonpolyposis colorectal cancer (HNPCC)

Front 14

This process allows more than one protein to be made from a single gene:

Back 14

alternative splicing

Front 15

Many genes occur in ______ representing structually related proteins.

Back 15

Families

Front 16

This is the largest human gene and links muscle contractile elements to the cell membrane:

Back 16

Dystrophin

Front 17

What process is responsible for the fact that the proteome is significantly larger than the genome?

Back 17

alternative splicing

Front 18

Most SNPs are ______ the protein coding regions.

Back 18

Outside

Front 19

The most common type of polymorphism:

Back 19

SNP (Single Nucleotide Polymorphisms)

Front 20

_______ is a different form of a particular gene- SNPs contribute to this difference.

Back 20

Allele

Front 21

This SNP results in a change in amino acid in a protein:

Back 21

Nonsynonymous.

Front 22

How can SNPs outside the coding region can be associated with phenotypes?

Back 22

If they affect the process of gene expression (transcription, splicing, etc.)

Front 23

Mitochondrial DNA contains information about some proteins, all other mitochondrial proteins are encoded where?

Back 23

In the nuclear genome- they're then translated in the cytoplasm and imported into the mitochondria.

Front 24

Several genetic diseases of strict maternal inheritance are caused by mutations in ______ ______.

Back 24

Mitochondrial DNA

Front 25

Name the three components of nucleotides:

Back 25

1. 5 carbon sugar
2. Organic base
3. Phosphate

Front 26

_______ bases contain a 9 atom ring. What are the two types?

Back 26

Purines - Adenine and Guanine

Front 27

______ bases contain a six atom ring. What are the three types?

Back 27

Pyrimidine - Cytosine, uracil and Thymine

Front 28

A purine or pyrimidine base linked to a sugar:

Back 28

Nucleoside

Front 29

The first sugar is linked to a phosphate in a nucleotide by a ________ bond.

Back 29

Phosphoester

Front 30

The second and third phosphates are linked to the nucleotide by ________ bonds.

Back 30

Phosphoanhydride

Front 31

Why can a nucleoside enter a cell more easily than a nucleotide?

Back 31

Because the phosphate group on the nucleotides is negatively charged and cannot go into and out of cells easily.

Front 32

The drug 5-flurouracil is converted to its active form _______ in the body.

Back 32

5-FdUMP

Front 33

How does 5-FdUMP inihibit tumor cell replication?

Back 33

Through inhibition of thymidylate synthase (TS) which is needed for de novo synthesis of pyrmidines (C, T and U)

Front 34

Approximately 85% of an intravenous dose of 5-FU is inactivated in the liver by _________.

Back 34

Dihydropyrimidine dehydrogenase (DPYD).

Front 35

DNA is linked by _______ bonds between which two ends?

Back 35

phosphodiester bonds between the 3' and 5' ends of adjoining residues.

Front 36

Which base pairs are more themally stable?

Back 36

G-C base pairs.

Front 37

Each turn of the DNA helix contains on avg. _____ base pairs.

Back 37

10.5

Front 38

The major form of DNA is called ______.

Back 38

B DNA

Front 39

Generally, ______ is single stranded nucleic acid.

Back 39

RNA

Front 40

Unlike DNA, the base pairing in RNA is _________.

Back 40

intramolecular

Front 41

The temperature at which 50% of DNA is melted.

Back 41

Melting temperature (Tm)

Front 42

The ________ effect is related to base stacking interactions in double standed DNAm which decreases the absorption of light.

Back 42

Hypochomic Effect

Front 43

The peak of absorbance of DNA is _______.

Back 43

260 nm

Front 44

The amount of absorbed light for ______ _______ DNA is about 50% less than that for _________ ________ DNA.

Back 44

Double stranded absorbs about 50% less light than single stranded.

Front 45

A highly ordered complex of DNA and protein.

Back 45

Chromatin

Front 46

_______is not part of a core nucleosome but a linker histone associated with the linker region between nucleosomes.

Back 46

Histone H1

Front 47

The presence of this histone causes the nucleosomes to assmeble into a 30nm fiber.

Back 47

Histone H1

Front 48

NH2 groups of ______residues in the terminal tails of the core histones can be modified.

Back 48

Lysine

Front 49

Name two common histone modifications:

Back 49

acetylation and methylation

Front 50

________ of histones decreases the net positive charge in the region. What is the effect of this?

Back 50

Acetylation. DNA is less ithgtly bound to histones, may be accessible to transcription machinery.

Front 51

Which two enzymes are associated with histone acetylation?

Back 51

Histone Acetyl Transferases (HAT) and Histone deacetylases (HDAC)

Front 52

Highly condensed form of chromatin, transcriptionally inactive:

Back 52

heterochromatin

Front 53

Less condensed form of chromatin, transcriptionally active:

Back 53

Euchromatin

Front 54

The physcial ends of the chromosome that have highly repetetive DNA sequences and are devoid of genes:

Back 54

Telomeres

Front 55

This structure in telomeres stabilizes the chromosome by allowing the cell to distinguish it from ends of DNA broken due to damage:

Back 55

G-quartet

Front 56

Difference in DNA sequence between individuals:

Back 56

Polymorphism

Front 57

phenotype associated with quantitative loss of function, loss of one allele results in phenotype, production of both alleles needed for normal function.

Back 57

Haploinsufficiency

Front 58

The proportion of individuals carying a mutant allele that have an associated phenotype:

Back 58

penetrance

Front 59

Point mutation that does not affect the amino acid sequence of the protein:

Back 59

synonymous SNP

Front 60

A point mutation that changes one amino acid for another:

Back 60

Missense mutation (non-synonymous SNP)

Front 61

When an amino acid is changed to one of three termination codons:

Back 61

nonsense mutation

Front 62

What are the three termination codons?

Back 62

UGA, UAA, UAG

Front 63

Short, repetetive sequences of 1, 2, or 3 amino acids that can be unstable and undergo expansion that increases the number of repeats:

Back 63

Microsatellite sequences (aka VNTR)

Front 64

The number of ______ among individuals is highly polymorphic and can be used in DNA fingerprinting:

Back 64

VNTR's

Front 65

Term for increased severity of symptoms and/or earlier age of onset within subsequent generations in a pedigree.

Back 65

Genetic anticipation

Front 66

What are the two common retro-transposons in humans?

Back 66

Alu and L1

Front 67

What is the major human LINE element capable of transposition and possibly of disrupting gene function?

Back 67

L1

Front 68

What is the major human SINE element that is capable of transposition?

Back 68

Alu

Front 69

________ recognizes Uracil as a foreign base in DNA and cleaves the glycosidic bond.

Back 69

DNA Glycosylase

Front 70

Covalently linked cyclobutane pyrimidine dimers (thymine dimers) are caused by what?

Back 70

UV light

Front 71

Pyrimidine Dimers are repaired by __________.

Back 71

Nucleotide Excision Repair (NER)

Front 72

These are important detoxifying enzymes in the body that make drugs and other foreign chemicals in the body into more water soluble compounds that can be excreted:

Back 72

Cytochrome p450

Front 73

This enzyme converts a pro-carcinogen in cigarettes into a carcinogen by generating epoxides and other reactive oxygen species that covalently attach to DNA

Back 73

Cytochrome p450

Front 74

Recombination of free ends is used to repair what kind of DNA damage?

Back 74

Double stranded breaks

Front 75

What are the two ways to repair double stranded DNA breaks? Which is more error prone?

Back 75

1) Homologous Recombination
2) Non-Homologous End joining
Non homologous end joining is more error prone

Front 76

Recognizes DNA that doesn't contain telomeres and realigns them:

Back 76

Non-Homologous End Joining (NHEJ)

Front 77

How is the parent strand identified for DNA mismatch repair?

Back 77

Because DNA is methylated at specific sites (hemi-methylation)

Front 78

In DNA mismatch repair, the hemi-methylated site is recognized by the protein _____ and the mismatched base is recognized by ______.

Back 78

Mut H and Mut S

Front 79

In DNA replication, chain growth is in which direction?

Back 79

5' --> 3'

Front 80

Replication of DNA initiates at _________ and proceeds in both directions from there:

Back 80

Origin of Replication

Front 81

DNA synthesis is initiated with what kind of primer? What synthesizes this primer?

Back 81

RNA primer
Primase

Front 82

Which two polymerases play a role in normal DNA replication in bacteria?

Back 82

Pol I and Pol III

Front 83

Which bacterial DNA polymerase removes RNA primers and replaces them with DNA (has both 5'-3' exonuclease and polymerase activity)?

Back 83

Pol I

Front 84

What is the major replicating enzyme of bacterial DNA?

Back 84

Pol III

Front 85

What carries out primer synthesis in eukaryotes?

Back 85

Pol alpha

Front 86

Unwinds the DNA double helix:

Back 86

DNA helicase

Front 87

Relieves the torsional strain in DNA from the unwinding:

Back 87

Topoisomerase

Front 88

Type of reaction involved in topoisomerase relieving the torsional strain:

Back 88

transesterfication

Front 89

Name the two enzymes (one in bacteria, one in eukaryotes) that remove RNA primers

Back 89

DNA Pol I (bacteria)
Fen I (eukaryotes)

Front 90

What acts as the sliding clamp in DNA replication in eukaryotes? In bacteria?

Back 90

PCNA (eukaryotes)
Beta subunit of DNA Pol III (bacteria)