Biology 211 Exam 2 Study Guide

Front 1

LECTURE 7

Back 1

LECTURE 7

Front 2

During mitosis, chromatin is ? packed

Back 2

tightly

Front 3

when packed tightly, the chromatin ? in length, but ? in width

Back 3

Decrease
Increases

Front 4

10nm fiber is the

Back 4

smallest

Front 5

30nm fiber is the

Back 5

largest

Front 6

DNA is packed into

Back 6

nucleosomes

Front 7

what makes up a nucleosome

Back 7

DNA+histone core

Front 8

Core DNA is

Back 8

the DNA wrapped around the histone

Front 9

Linker DNA is

Back 9

the DNA between histones

Front 10

The Histone core is composed of 4 proteins named

Back 10

H2A
H2B
H3
H4

Front 11

The four proteins are ? charged

Back 11

+

Front 12

There is one other Histone and it is called

Back 12

H1

Front 13

What does H1 do?

Back 13

It binds to the linker DNA

Front 14

What does it do once bound to the linker DNA

Back 14

It can help condense the histones

Front 15

What makes the DNA stick to the Histones

Back 15

The DNA is - and the Histone core is + charged

Front 16

First step in forming a histone

Back 16

H3 and H4 come together to form a tetramer

Front 17

After the H3-H4 teramer is formed, what happens?

Back 17

H2A and H2B come together to form a dimer and they join the tetramer

Front 18

3 things make up a total Histone core

Back 18

2 H2A H2B dimers
1 H3 H4 tetramer

Front 19

Complete histone core assembles ONLY when

Back 19

DNA is present

Front 20

Two models for nucleosome compaction are

Back 20

solenoid
zig zag

Front 21

The solenoid model has its nucleosomesstacked on

Back 21

the edge

Front 22

Where is the linker DNA in the solenoid model

Back 22

burried in the middle of the superhelix, but never passes through the center

Front 23

The zig zag model has it nucleosomes stacked in

Back 23

a zig zag array

Front 24

The linker DNA must ? in a zigzag model

Back 24

pass straight through the central axis of the fiber

Front 25

What are the N-Terminal tails crucial for

Back 25

forming the 30nm fiber

Front 26

Two ways that the N-terminal tails are modified to regulate Histone function

Back 26

Acetylation
Methylation

Front 27

What is the first step in Histone Acetylation

Back 27

Histone acetyl transferase adds acetyl groups to the N terminal tails

Front 28

What happens after these tails have been acetylated

Back 28

Bromodomain proteins associate with the acetylated tails

Front 29

Histone acetylation means

Back 29

transcriptionally ACTIVE

Front 30

What associates with acetylated histone tails?

Back 30

Bromodomain proteins

Front 31

What is the first step to Hoistone Methlyation

Back 31

histone methyl transferase adds methyl groups to the N terminal tails

Front 32

Once the N terminal tails are methlyated, what happen

Back 32

Chromodomain proteins recognize the methlyated histones and associate

Front 33

Histone methlyation means

Back 33

Transcriptionally REPRESSED

Front 34

What associates with methlyation?

Back 34

Chromodomain proteins

Front 35

After DNA replication, new nucleosome inheritance follows two rules. The rule for the H3 H4 tetramer is

Back 35

the old H3 H4 tetramer will associate with one of the daughter starnd and the other daughter strand will get a new H3 H4 tetramer

Front 36

The rule for the H2A H2B dimer

Back 36

The old H2A H2B dimer is released, so the daughter starnd can get either an old or new H2a H2B dimer

Front 37

LECTURE 8

Back 37

LECTURE 8

Front 38

First two things needed for DNA synthesis

Back 38

-dNTPs
-Primer template junction

Front 39

what does the template strand do

Back 39

provides the ssDNA that will direct the addition of nucleotides

Front 40

What does the primer do

Back 40

it is complemntary to the template strand but shorter and it is where you start from

Front 41

The RNA primer must have ? on its end

Back 41

3'-OH group

Front 42

What does this 3'-OH group do

Back 42

it is extended by the additional of other nucleotides

Front 43

How is DNA replication powered?

Back 43

pyrophosphate hydrolysis

Front 44

The structur and function of the DNA polymerase can be visualized using three strucutres

Back 44

Palm
Fingers
Thumb

Front 45

The Palm does 2 things

Back 45

-Binds metal ions at the catalytic site (where the magic happens)
- Monitors the accuracy of base pairing

Front 46

The Fingers do three things

Back 46

- Bind incoming dNTPs
-Then they close and form the bonds once proper dNTPs have been bound
- It bends the template strand to make sure only one dNTP will be added to the next available base

Front 47

The Thumb does two things

Back 47

- Maintains the correct position of the Primer:Template junction
- Maintains a strong interaction between the Polymerase and the template strand

Front 48

What does this strong interaction between the enzyme and substrate do for the RNA polymerase

Back 48

it allows the polymerase to slide along the template strand and continually bind new dNTPs processivly

Front 49

What does the proofreading exonuclease do and where does it do it

Back 49

It removes incorrectly paired bases from the 3' DNA end

Front 50

Which strand of DNA is replicated?

Back 50

BOTH

Front 51

DNA Polymerase functions ONLY in the

Back 51

5'-3' direction

Front 52

What does the Primase do

Back 52

it adds small RNA primers to the template strand

Front 53

How many primers does the leading strand need?

Back 53

1

Front 54

How many primers does the lagging strand need?

Back 54

many

Front 55

Okazaki fragments are

Back 55

the stretches of DNA replicated between RNA primers on the lagging strand

Front 56

How are RNA primers removed?

Back 56

By RNAse H

Front 57

What does RNAse H do

Back 57

It cleaves the bonds between the ribonucleotides

Front 58

this makes RNAse a ?

Back 58

Exonuclease because it can only cleave at the end where there is not bond between DNA and RNA at the primer

Front 59

What happens after the primer is removed?

Back 59

DNA polymerase binds the free 3'OH end of the DNA and fills the gap

Front 60

What seals the nick left behind by DNA polymerase?

Back 60

DNA ligase

Front 61

How does DNA ligase seal this nick?

Back 61

By forming phosphodiester bonds between the 3' OH end and 5' P end

Front 62

What does the unwinding of the DNA?

Back 62

DNA helicase

Front 63

Once the Helicase goes through and unwinds the DNA and there is only ssDNA left, what happens

Back 63

The DNA must remain free of base pairing

Front 64

How is the DNA reamin free of base pairing?

Back 64

Single stranded DNA binding proteins bind the bases and dont allow other proteins to bind

Front 65

These SSBs bind, how

Back 65

cooperatively - once one binds it helps another and another and another

Front 66

What helps to releave the tension created by unwinding the DNA?

Back 66

Topo II bc it cuts both strands

Front 67

LECTURE 9

Back 67

LECTURE 9

Front 68

What is an apoenzyme

Back 68

and enzyme that require a co -factor, but does not have one

Front 69

An example of an apoenzyme is

Back 69

just the DNA polymerase core enzyme

Front 70

what is a holoenzyme

Back 70

an apoenzyme with all it's co-factors that

Front 71

what do these co-factors do?

Back 71

enhance its productivity

Front 72

What is an example of a holo enzyme

Back 72

DNA Polo III

Front 73

The main goal of DNA Pol I is

Back 73

to remove the RNA primers

Front 74

Is DNA Pol I processive?

Back 74

No

Front 75

Is DNA Pol III processive?

Back 75

yes

Front 76

What helps to increase the processitivity

Back 76

The DNA sliding Clamp

Front 77

How does the sliding clamp increase the processtivity

Back 77

by encircling dsDNA and holding the DNA polymerase onto the DNA primer:Template junction

Front 78

On the lagging strand, how does the sliding clamp opperate

Back 78

Once DNA Pol reaches the end of an Okazaki fragment the clamp is released

Front 79

First step in loading the sliding clamp

Back 79

The sliding clamp loader starts off closed

Front 80

Why does it matter that thesliding clamp loader is closed, and what happens

Back 80

If it is closed it cannot bind the sliding clamp. ATP binds the loader and it opens

Front 81

what do these co-factors do?

Back 81

enhance its productivity

Front 82

What is an example of a holo enzyme

Back 82

DNA Polo III

Front 83

The main goal of DNA Pol I is

Back 83

to remove the RNA primers

Front 84

Is DNA Pol I processive?

Back 84

No

Front 85

Is DNA Pol III processive?

Back 85

yes

Front 86

What helps to increase the processitivity

Back 86

The DNA sliding Clamp

Front 87

How does the sliding clamp increase the processtivity

Back 87

by encircling dsDNA and holding the DNA polymerase onto the DNA primer:Template junction

Front 88

On the lagging strand, how does the sliding clamp opperate

Back 88

Once DNA Pol reaches the end of an Okazaki fragment the clamp is released

Front 89

First step in loading the sliding clamp

Back 89

The sliding clamp loader starts off closed

Front 90

Why does it matter that thesliding clamp loader is closed, and what happens

Back 90

If it is closed it cannot bind the sliding clamp. ATP binds the loader and it opens

Front 91

Once the loader is opened what happens

Back 91

It binds the sliding clamp

Front 92

Once the loader has bound the sliding clap what happens

Back 92

The sliding clamp will open

Front 93

Pnce the sliding clamp is open what happens

Back 93

the sliding clamp binds around the DNA q

Front 94

once the open Sliding clamp has bound the DNA what happens

Back 94

The clamp loader hydrolyzes ATP and the loader closes, causing the Clamp to close around the DNA as well

Front 95

LECTURE 10

Back 95

LECTURE 10

Front 96

The Polymerase chain reaction is

Back 96

a powerful way to amplify DNA sequences

Front 97

First step of the PCR

Back 97

the template DNA strands must be denatured into ssDNA

Front 98

Once the ssDNA is made, what happens

Back 98

Primers are added

Front 99

why are the Primers added?

Back 99

PCR cant start without Primers

Front 100

After the Primers are added, what happens

Back 100

DNA Pol is added to extend the Primers

Front 101

This process is then..

Back 101

repeated over and over

Front 102

How many times are eukaryotic chromosomes replicated per cell divison

Back 102

once

Front 103

Chromosome replication occurs only during the ? Phase

Back 103

S

Front 104

Once an origin has been copied, it must..

Back 104

remain inactive until the cell divides

Front 105

Eukaryotic DNA replication is initiated by

Back 105

Pre-Replicative Complex (Pre-RC)

Front 106

Where is the Pre-RC formed

Back 106

G1 phase

Front 107

When is the Pre-RC activated?

Back 107

S phase

Front 108

What activates the Pre-RC

Back 108

CDKs and DDKs

Front 109

What happens after the Pre-RC is activated by the CDKs and DDKs

Back 109

DNA helicase begins to unwind the the dsDNA

Front 110

After the helicase unwinds the dsDNA what happens

Back 110

a DNA Pol/Primase complex comes in

Front 111

What does the DNA Pol/Primase complex do

Back 111

adds a primer and extends and breifly entends it with a short stretch of DNA

Front 112

Then what happens

Back 112

The primase exits breifly

Front 113

Once the Primase exits, what happens

Back 113

The sliding clamp loader and sliding clamp come in and assemble at the primer template junction and begin synthesizing the lagging and leading strand

Front 114

Will the DNA Pol/Primase come back?

Back 114

yes to help synthesize the lagging strand

Front 115

What are the CDK levels like in G1

Back 115

Low

Front 116

If the CDK levels are low in G1, what does this mean

Back 116

allows Pre-RC to form, but not enough to activate it

Front 117

How are CDK levels in S phase

Back 117

high

Front 118

If the CDK levels are high is S phase, what does this mean

Back 118

Signals for DNA replication to begin at existing pre-RC complexes

Front 119

High CDK levels also prevent

Back 119

the formation of new pre-RCs

Front 120

CDK remains high until

Back 120

the cell divides into and enters G1 phase again

Front 121

When the last RNA primer is removed in the lagging strand, how can DNA Pol fill the gap?

Back 121

IT CANT

Front 122

this means that since it cant fill the gap at the end of every single round of replication

Back 122

linear chromosomes gets shorter and shorter

Front 123

Some cells have ? that are used to ?

Back 123

Proteins that are used as primer to synthesize the last okazaki fragment

Front 124

Another way to get around this problem is by utilizing

Back 124

Telomeres and Telomerases

Front 125

At the very end the ? end extends farther then the ? end

Back 125

3' end extends farther than the 5' end

Front 126

What extends the 3'

Back 126

Telomerases

Front 127

Telomerase is actually called a

Back 127

riverse transcriptase

Front 128

It is called reverse transcriptase because

Back 128

it uses an RNA strand to synthesis a DNA strand

Front 129

Once the Telomerase synthesizes the DNA from the RNA

Back 129

it moves 6 nucleotides forward and does the same thing

Front 130

Now normal replication can take place by

Back 130

Primase
DNA Pol
Primer degradation

Front 131

LECTURE 11

Back 131

LECTURE 11

Front 132

What is a Transitions mutation

Back 132

is the change of a pyrimidine-pyrimidine, or purine-purine

Front 133

What is a Transversion mutation

Back 133

pyrimidine-purine , or purine-pyrimidine

Front 134

The mismatch repair system does what

Back 134

Increase the accuracy of DNA synthesis

Front 135

Whats the first step in this process

Back 135

MutS (scans) dimer scans the DNA of kinks produce by mismatch bases

Front 136

What does MutS do once it finds a kink

Back 136

It binds and distorts it even further

Front 137

Once this kink is more distorted, what happens

Back 137

MutL (localizes) localizes to the site

Front 138

Once MutL gets to the site, what does it do

Back 138

it recuirts MutH

Front 139

What does MutH do once it gets to the kink

Back 139

It nicks near the mismatch

Front 140

What happens once MutH nicks near the mismatch

Back 140

UvrD is a helicase and it unwinds the DNA from the nick to the mismatch

Front 141

What is the final step

Back 141

DNA Pol III and ligase close the gap

Front 142

With the help of ? , MutH will know which strand is the newly synthesized one

Back 142

Dam Methlyase

Front 143

What does Dam Methlyase do

Back 143

it adds methyl groups to A with the 5'-GATC-3' sequence of the parent strand

Front 144

how does this relate

Back 144

When DNA is newly synthesized Dam methylase has not methylated it yet

Front 145

So that means MutH binds

Back 145

to the non methlyated strand of the Hemimethylated DNA (Hemi = MutH)

Front 146

LECTURE 12

Back 146

LECTURE 12

Front 147

Three types of CSSR Recombination

Back 147

Insertion
Deletion
Inversion

Front 148

During insertion, what happens

Back 148

DNA is inserted into specific sites

Front 149

During deletion, what happens

Back 149

Deletion of a DNA segment

Front 150

The arrows are point in what direction for deleltion to occur

Back 150

Same way

Front 151

What happens in inversion

Back 151

The DNA segment is inverted, or flipped

Front 152

For inversion to occur the arrows have to be facing

Back 152

towards each other

Front 153

What do Transposons do

Back 153

They move certain genetic elements from one DNA site to another

Front 154

Transposons are present in the genome of

Back 154

All organisms

Front 155

They do/do not require duplication?

Back 155

Do not require duplication

Front 156

Why are Transposons the most common source of new mutations in organisms?

Back 156

They show very little sequence selectivity

Front 157

Three classes of Transposons

Back 157

DNA Transposons
Viral-like retrotransposons/retroviruses
Poly-A retro transposons

Front 158

If the Transposon encodes for Transposase, what happens

Back 158

It is autonomous

Front 159

What does autonomous means

Back 159

on its own

Front 160

If DNA Transposons encode for ? and ? they will be autonomous

Back 160

Transposase
Inverted repeats (Arrows facing the opposite way)

Front 161

If a DNA Transposon does not have Transposase ...

Back 161

It will not be non-autonomous (stuck)

Front 162

Viral-like Retrotransposons/Retroviruses have ? repeats and encode for ?

Back 162

Inverted repeats (like DNA Transposons)
Reverse Transcriptase

Front 163

Poly-A Retrotransposons have ? repeats and encode for

Back 163

DO NOT have inverted repeats (theirs face the same way)
Encode for reverse transcriptiase and endonuclease activity

Front 164

Poly-A Retrotransposons have a distinct ? and they are know as ? and ?

Back 164

Termini
5'UTR & 3'UTR

Front 165

LECTURE 13

Back 165

LECTURE 13

Front 166

The most simple type of DNA Transposition is

Back 166

Cut and Paste transposition

Front 167

First step of Cut and Paste

Back 167

Transposase binds the inverted repeats

Front 168

After Transposase bind the inverted repeats..

Back 168

It brings the ends together

Front 169

bring the end together forms the

Back 169

synaptic complex

Front 170

Once the synaptic complex is formed the transposons are

Back 170

cut out

Front 171

When the transposons are cut out it forms

Back 171

2 free 3'OH groups

Front 172

what do these freed 3'-OH groups do

Back 172

attach the phosphodiester bonds in the middle of the new insertion

Front 173

this new insertion is called the

Back 173

target DNA

Front 174

Once this target DNA is loaded onto the old DNA the 3' ends serve as

Back 174

primers

Front 175

the remaining nicks are

Back 175

ligated