DNA replication

Where do PTM of histone tails take place 

On the N-Terminal ends of the histones 

Where are topoisomerase inhibitors used in 

chemotherapy regimens to cause cell death of cancer cells 

When both strands are used for DNA synthesis and two copies of the daughter DNA have one old strand and one newly synthesized strand, this shows that DNA is

Semi-conservative 

When a histone is acetlyated, where is the addition of the acetyl group going?

On the lysine amino acids of the hsitone tails 

What seals the nicks and fills in the gaps on the DNA 

DNA ligase

What makes a nucleosome bead 

When the DNA wraps twice around the histone octamer

What is Single strand binfing protein important in DNA replication?

If the template strand has hairpins, DNA polymerase will skip some sequence, causing deletion mutations

What histone binds linker DNA 

Histone H1

What enzyme removes the RNA annealed to the DNA 

RNAse 

What does acetylation do?

Neutralizies the positive charges and loosens the interactions between the histones and the DNA, increasing the likihood of transcription 

What do HATs and HDACs do? 

HATs add acetyl groups the the histone 
HDACs remove or repress the acetyl groups from attatching to histones 

What controls the checkbpoints in the cell cycle to make sure that events of one phase are completed properly before the next pahse begins 

Tumor Suppressors 

Uses its own RNA template to extend the parental strand of DNA

Telomerase 

unwinds the DNA helix to move the replication fork forward 

Helicase (Mcm)

Transcriptionally active DNA (euchromatin) tends to be replicated early in 

S phase 

The nucleoli are dense areas that contain the acrocentric chromosomes which encode ______ , and this is where _______are made

rRNA 
Ribosomes 

The combination of DNA and proteins is called 

Chromatin 

The _________ (aka the 30 nm fiber) is the form of DNA that is the template for most processes

Nucleofilament 

synthesizes a short RNA primer to provide the first 3’OH in a DNA polymerase reaction of replication 

Primase 

Small positively charges proteins are called 

histones 

Short stature, photosensitivity, multiple health problems and increased risk of cancer.

High degree of genomic instability

Bloom Syndrome 

Send positive signals for continuation of the cell cycle 

Proto-oncogenes 

Replicated discontinuously in a series of Okasaki fragments

DNA synthesis starts at the replication fork and moves toward the origin

Many primers (one for each Okasaki fragment)

Lagging strand 

Replicated continuously

New DNA synthesis moves away from the origin, in the same direction as the replication fork

Few primers required

Leading strand 

relieve supercoiling and tangling of the DNA ahead of the replication fork 

Topoisomerases 

recruit Mcm helicase in G1 = “matchmaker proteins”, only available in G1

Cdc6 and Cdt1

reactivation of telomerase in somatic cells makes them

immortal 

Rare disorder caused by mutation of a helicase needed for DNA replication during repair and recombination

Bloom Syndrome 

Protect ends of chromosomes from degradation and fusion

Distinguish ends of intact chromosomes from broken ones

Telomeres ( the ends of chromosomes )

Phosphorylation of Mcm activates its

helicase activity 

– it separates the strands to create the replication bubble, and moves away from the origin with the replication forks

ORC + Mcm = 

Pre-RC ( pre- replicative complex ) which means liscenced orgin at the end of G1

Nucleosomes are seperated by approx. 50 bp called 

linker DNA 

Multiple redundant mechanisms ensure that the pre-RC can’t form again until the next G... why?

Prevents re-replication of DNA, which could lead to gene amplification and/or genomic instability

Most cells enter a non-proliferative state called 

senescence 

make single-strand nicks in DNA

Topoisomerase Type I

Make reversible nicks in the DNA to relieve supercoiling and release the tension

Topoisomerase 

make double-strand breaks in the DNA during replication

Topoisomerase Type II

Loss of telomeric DNA triggers what

Cellular Senescecne 

Loss of telomeric DNA triggers cell cycle checkpoint mechanisms that prevent what 

proliferation 

keep the two strands of parental DNA from reannealing to each other or forming hairpins

Single Strand Binding Proteins (RPA)

Inhibition of topoisomerase causes what

Cell death/ Apoptosis 

In telemores, what is the purpose of the 3' overhang 

fold back and provide structure for shelterin proteins to bind 

In S phase, _____ becomes active and phosphorylates components of the pre-RC

S-Cdk

In bacteria, DNA Pol I has a subunit with 

RNAse Activity 

In one or a few cells, the genomic rearrangements result in 

reactivation of telomerase 

If the checkpoint fails, cells continue to proliferate without telomeres.  Most cells die because of 

genomic instability 

Helicase requires what kind of energy 

ATP

From each origin, DNA replication is 

bi-directional 

Found in germline cells, stem cells and >85% of cancer cells examined

Telomerase 

Following DNA replication, the duplicated chromosome consists of ___________ joined at the centromere

Two sister chromatids 

Fluoroquinolone antibiotics (ciprofloxacin) inhibit

the bacterial topoisomerase type II (GYRASE) 

Falculative means 

"Sometimes" 
used to regulate gene expression of heterochromatin 

enzyme’s ability to catalyze consecutive reactions without releasing the substrate  

Processivity 

Ensures that each origin is activated only once per cell cycle

Licensing of origins in G1

During mitosis, what two structures form at the centromere to seperate the chromosomes into two daughter cells 

Kinetochores and Spindle microtubules 

Does telomeric DNA encode any proteins? 

NO

DNA synthesis is only synthesized in what direction 

5' to 3' direction 

DNA synthesis is in the 5' to 3' direction, but its moving along the template in what direction

3' to 5'

DNA polymerase processivity is increased by a 

sliding clamp 

DNA polymerase creates what kind of bond between the 5' alpha PO4 and the 3' OH? 
What happens to the other phosphates?

Creates a Phosphodiester Bond 

The other two phosphates on the nucleotide are released as pyrophosphate, and its hydrolysis provides energy for the reaction

DNA is replicated in what phase of the cell cycle 

S phase 

Describe the proofreading activity by DNA polymerase 

If the DNA incorportates the wrong nuclotide into the growing strand, it creats steric hinderance and wont base pair properly 

The 3’ end of the newly synthesized strand is forced into a different site of the enzyme, where the last nucleotide added (the incorrect one) is removed by 3’ to 5’ exonuclease activity.

Constitutive heterochromatin tends to replicate late

S phase 

constituitive means 

"always"
which would be in areas such as centromeres and telomeres 

Consist of many tandem copies of a 6 bp DNA sequence, plus proteins that bind 

Telomeres 

Chromosomes are visible only in _______ of the cell cycle 

Metaphase 

Chromosomes are condensed enough to be seen microscopically only during 

mitosis 

Chromatin that is:

Less condensed

Transcriptionally active 

Euchromatin 

Chromatin that is: 

Inactive

More condensed

Often located at nuclear perifery

Heterochromatin 

Cell cycle events are controlled by what? What is their role?

CDK ( Cyclin Dependent Kinases) 
They phosphorylate proteins to accomplish the goals of each phase in the cell cylce 

Binds to the origin throughout the cell cycle

ORC ( origin recogniztion complex )

An RNA depended DNA polymerase is called

Reverse Transcriptase 

An increased rate of loss of telemeric DNA can be a cause and/or an effect of 

disease 

An enzyme that maintains the length of telomeres, but it’s not found in most somatic cells

Telomerase 

An origin of replication can only be used if 

2 mcm helicases are loaded in G1

Addition and removal of various chemical groups to specific amino acids on the histone tails influences ________ and accessibility to ____________

Chromatin Structure 
Transcription Factors 

A bacterial Topoisomerase II

Gyrase 

 Holds DNA polymerase to the template DNA as long as its moving, but releases it when double-stranded DNA is reached 

A regulated sliding clamp, called PCNA 

 Associated with euchromatin formation and active transcription

Histone Acetylation