Chapter 5 book

you should checkout slide 49

what is a mutation rate

frequency at which new DNA mutations occur

what does a deleterious mutation refer to

mutation that reduces orangism’s ability to survive and reproduce

It is estimated that the limit of essential genes is 30,000 because

more genes provide more chances for harmful mutations

what is an essential gene

gene responsible for survival and reproduction

Germ cells refer to

cells involved in transmission of genetic information from parent to offspring

somatic cells refer to

body cells

What kind of cells mainly affect the individual and not generations

somatic

Local natural selection refers to the

rapid proliferation of a cell causing competition within a tissue for resources

Cancer is a result of

Accumulation of somatic cell mutations giving them a growth advantage.

What are the purple circles + what forms them + what do they give rise to

Zygote cell,

formed by fusion of two gametes

germ line and somatic

Why must the DNA helix separate before replication

expose bases to allow pairing

The 3’ OH end on a new strand is important as it

allows next nucleotide to be added

What is a nucleotide triphosphate

nucleotide with a

base

deoxyribose sugar

3 phosphates

why are the 3 phosphates important in a nucleotide triphosphate

provide energy needed to add nucleotide to growing dna strand

What is the fate of the phosphates in a nucleotide triphosphate

1 becomes DNA backbone by forming a phosphodiester bond

2 leave as pyrophosphate (PPi) to drive reaction forward

DNA synthesis proceeds in the ___ direction

5-3

If a complementary strand is made in the 5-3 direction, the template strand is in the __ direction

3-5

DNA Polymerase role

hold template and complementary in correct position

check exposed bases on template

brings correct nucleotide

catalyzes phosphodiester bond

Why is DNA replication considered semiconservative

each dna molecule builds 1 new and keeps old 1

What does this figure reveal

semiconservative replication

each daughter DNA molecule contains one older strand and one newly made strand

Which strand has continuous synthesis

Leading

Which strand has discontinuous synthesis

Lagging

What causes the looping on the lagging strand

Okazaki fragments must be synthesized in 5-3

It is estimated there is 1 mistake per ___ nucleotides copied

10^10

How does polymerase proofread bases

DNA POL changes shape around active site (conformational change)

allows base with correct geometry to pair and catalyze phosphodiester bond

What is the second proofread DNA polymerase is responsible for

Exonucleolytic proofreading

Exonucleolytic proofreading only occurs after

DNA Polymerase added the wrong nucleotide

How does exonucleolytic proofreading work

incorrect nucleotide cut off

Why does RNA polymerase not require such an efficient exonucleolytic proofreading

RNA is temporary

Why is 3-5 synthesis bad for proofreadinbg

Provides no energy to replace bad nucleotide

RNA primer function

Provide free OH group for polymerase

Sequence of nucleic acid building

Primase

rna primer

dna polymerase

ribonucleotide triphosphate is built from

ATP

GTP

CTP

UTP

nucleotide triphosphate is built from

dATP

dGTP

dCTP

dTTP

How is RNA primer started

base pairing of two ribonucleotide triphosphates through a phosphodiester bond

Why is the RNA primer removed from an okazaki fragment

Allows for continuous full DNA

What seals neighboring okazaki fragments together

dna ligase

what bond does dna ligase use

phosphodiester bond

Ligase acts upon a strand ___ an RNA primer has been removed

after

What are the advantages to an erasable RNA primer

errors made during primer synthesis are easily recognized and removable

DNA helicase role

separate two DNA strands ahead of replication fork

Single Strand DNA binding proteins role

bind exposed single strands to hold them open

What sliding clamp do eukaryotes use

PCNA

PCNA role

keep dna pol attached

clamp loader role

attach clamp to dna

Where is a clamp placed on the lagging strand

primer-template junction

Polymerase epsilon is used on a __ to

leading strand

bind sliding clamp

synthesize dna continuously

Polymerase alpha is used on a __ to

lagging strand

start an Okazaki fragment with included primase

Polymerase delta is used on a __ to

lagging strand

bind with sliding clamp and extend fragment

Two wayseukaryotic DNA replication more complex than bacterial replicatoin

SSB uses 3 subunits instead of 1

Eukaryotes divide polymerase into alpha delta epsilon

mutator gene refers to a gene that

when mutated, increases overall mutation rate

3 Consequences of adding RNA instead of DNA to a backbone

break

distort

mutations

__ Nucleotides are more abundant than __ nucleotides in a cell

RNA

DNA

Topoisomerase function

relieve twisting strain

the winding problem refers to

untwisting of DNA causing further DNA ahead of fork to twist tighter

Topoisomerase relieves supercoiling through

temporary cut of phosphodiester bond

Which Topoisomerase method requires ATP

Top 2

Top 2 differs from top 1 as it

cuts both strands

What creates the first opening in a replication fork

initiator protein

Replication origin refers to a location in which

DNA Double helix is first opened

Replication origins usually contain

dna sequence that allow initiator proteins to recognize and bind

regions that are easily separated

what is this

dna replication of ecoli

How does E coli stop an initiator protein

Hydrolysis of ATP to ADP

Why do eukaryotes require many origins and slow forks

DNA is larger + wrapped in chromatin

Unlike bacteria cells, eukaryotic cells can only replicate DNA during

s phase

Two identical sister chromatids only become separated during the

M phase

What increases the chance of ORC in humans

local open chromatin

When are 2 inactive helicases loaded

G1

During 2 phase, what activates incomplete helicases

Kinase

Two roles of kinase during S phase

activate loaded helicase

phsphorylate ORC

Why is important to prevent ORC from loading new helicases

prevent re-replication

Beyond DNA replication, eukaryotic chromosome replication requires large amounts of

histones and nucleosomes

What does it mean when histone synthesis is coupled to s phase

Cell makes the right amount of histones for newly replciated DNA

What makes it hard to access DNA

histones

What helps remove / loose histones

Chromatin remodel proteins

histone chaperones

What signals the termination of DNA replication in a eukaryotic cell

Meeting of two replication forks in which CMG helicases are tagged with ubiquitin

What is the problem with the last RNA primer on the lagging strand

no 3 oh from dna polymerase to extend

Telomere ends are placed on template strands to allow which enzyme to act upon it

Telomerase

How does telomerase help with the end replication issue

Extend 3’ end of parental DNA with telomere repeats

How does Polymerase alpha help with the end replication issue

synthesizes RNA primer + short DNA stretch

How does Polymerase delta help with the end replication issue

synthesizes RNA into DNA strand

Double role of telomeres

Protect degradation

Indicate normal chromosome end rather than DNA Damage

Overhang refers to

the trimming of a 5’ end of a DNA strand leaving an exposed 3’ end

Overhang is achieved by the enzyme

nuclease

3’ Overhang and a telomere repeat sequence attracts

shelterin

shelterin role

cap chromosome end to prevent dna repair system from treating telomere as a break

DNA replication has what effect on telomere length?

Shortens telomeres

Telomerase has what effect on telomere length?

Extends and helps maintain telomeres

How does replicative senescence occur?

Telomeres become critically short, the cell senses the chromosome ends as DNA damage, and permanently exits the cell cycle

Why is too little telomerase a problem?

It causes excessive telomere shortening, which can reduce cell division and contribute to tissue dysfunction and premature-aging effects

What is depurination?

Loss of adenine or guanine when the bond between the purine base and deoxyribose breaks

What is deamination?

Removal of an amino group (nh2)

How does UV light damage DNA?

It causes adjacent pyrimidine bases to form covalent bonds, creating pyrimidine dimers such as thymine dimers

What is the role of DNA glycosylase in base excision repair?

It recognizes a specific damaged base and removes that base from its sugar

How does DNA glycosylase differ from AP endonuclease?

DNA glycosylase removes the damaged base, while AP endonuclease cuts the phosphodiester backbone at the resulting AP site

What DNA repair method does not require excision of the damaged nucleotide?

Direct reversal

What is direct reversal?

A repair process that chemically reverses DNA damage without removing the damaged nucleotide