human genetics exam 3 module SGs

S phase

where does DNA replication take place?

existing (parental strand) and new (daughter strand) after replication

Why is DNA semi-conservative?

Origin of replication

What is a site where DNA replication is initiated?

Bi-directionally

DNA replication takes place _______ from an origin of replication.

Origin specification is determined by factors other than DNA sequence.

Is the origin of replication defined by a specific sequence or other factors?

DNA topoisomerase

prevents tangling og the DNA ahead of the replication fork.

SIngle strand binding proteins

_____ bind to a single stranded DNA to protect the DNA from degradation and to prevent the single strands reforming a double helix before replication.

DNA helicase

separates the 2 DNA strands at the replication fork

DNA primase

lays down an RNA primer to primer

DNA polymerase delta (δ)

adds incoming nucleotides to the 3’ nd of lagging strand sections by forming a phosphodiester bond.

DNA polymerase epsilon ε

adds incoming nucleotides to the 3’ end of the leading strand sections by forming a phosphodiester bond.

DNA polymerase alpha (α)

begins DNA replication from a primer (DNA polymerase delta or epsilon then take overf rom DNA polymerase alpha)

DNA ligase

forms the final covalent bond to link the 5’ nucleotide of one okazaki fragment to the 3’ nucleotide of the upstream okazaki fragment following the removal of a primer.

Flap endonuclease

removes RNA primers by cleaving RNA nucleotides from the 5’ end until all nucleotides have been removed.

Telomerase

adds telomere repeats to the 3’ end of a parental (template) DNA strand (telomere repeats then get added to the 5’ end of the complementary daughter strand by DNA primase and DNA polymerase)

In G1 by sequential binding of several different proteins to the origin of replication to form the pre-replication complex. In the S phase the pre-replication complex is activated to form the pre-initiation complex by the recruitment of additional factors including DNA polymerase and proteins that form the helicase complex.

How is DNA replication initiated?

a short RNA sequence that is necessary to prime DNA replication

WHat is an RNA primer?

DNA polymerase cannot add a nucleotide to a bare strand; it needs a 3’ end on which to add an incoming nucleotide.

Why is an RNA primer needed?

3’

Does DNA polymerase add nucleotides to the 5’ end of the new strand or the 3’ end of the new strand?

5’—-3’

Is the new DNA strand synthesized in the 5’—-3’ direction or the 3’——-5’ direction?

cleavage of pyrophosphate from an incoming nucleotide supplies the energy for phosphodiester bond formation

Where does DNA polymerase get the energy for the formation of a phosphodiester bond to add an incoming nucleotide?

okazaki fragments

the lagging strand is made up of?

Towards the replication fork

When synthesizing the leading strand, does DNA polymerase move toward the replication fork or away?

continueous segment

IS the leading strand made up of okazaki fragments or made continuously?

DNA polymerase moves away from the replication fork o.e., it moved in the opposite direction along the DNA strand.

when synthesizing the lagging strand, does DNA polymerase move toward the replication fork or away from it?

On the lagging strand, DNA polymerase must synthesize the new strand in the 5’-3’ direction, but the replication fork is moving in the opposite direction along the strand. DNA polymerase must therefore make a short Okazaki fragment, then move back towards the fork to make the next Okazaki fragment once more template DNA has been separated.

Why is it necessary to make okazaki fragments on one strand?

Once a primer has been removed, the 5’ DNA nucleotide that was linked to the primer only has one phosphate group (the pyrophosphate group was cleaved off when the nucleotide was added to the primer), so there is no pyrophosphate to provide energy for DNA polymerase to form a phosphodiester bond to link it to the 3’ nucleotide of the upstream DNA fragment that replaced the primer. DNA ligase can make that phosphodiester bond to connect two adjacent DNA fragments.

Why is DNA ligase needed to form the final phosphodiester bond to link DNA fragments following removal of primers?

 From right to left because the new strand is made going from 5’-3’ (i.e., incoming nucleotides added to the 3’ end), which is moving toward the left of the page.

If the DNA strand below acts as a template during DNA replication, which way will DNA polymerase slide along the strand- from left to right or from right to left?

Telomeres are found at the ends of chromosomes and are composed of a short DNA sequence repeated many times (up to thousands of times). They are added to prevent losing germline DNA from the ends of chromosomes during DNA replication.

What are telomeres and why are they added?

Telomerase adds telomere repeats to the 3’ end of a template DNA strands. DNA primase, DNA polymerase, and ligase then synthesize a complementary DNA sequence on the complementary, daughter strands. 

Does telomerase add telomere repeats to the 3’ end or the 5’ end of the template strand? After telomerase has added telomere repeats to the template DNA strand, how are telomere repeats added to the complimentary daughter strand?

Telomerase is active during embryonic and fetal development.

 When is the enzyme telomerase active?

After birth, telomerase ceases to be active in most somatic(body) cells; it only remains active in certain cell types with a high proliferative rate, including germ-line cells,m activated lymphocytes of the adaptive immune system, and some stem cells.

When does the enzyme telomerase cease being active in most somatic cells?

 Telomeres gradually shorten each time cell division occurs in somatic cells. Cells without active telomerase can divide a finite number of times and then reach senescence, which means cell division ceases. Senescence occurs when telomere length becomes critically short; the cell must stop dividing so it doesn’t lose germline DNA from the ends of chromosomes (senescence can occur for other reasons to, such as damaged DNA, for example.)

 What is senescence, and why do cells reach senescence?

Most cancer cells (~80-90%) have mutated to re-activate the telomerase enzyme, which allows them to divide indefinitely without reaching senescence. If telomerase remained active in all somatic cells after birth, the consequence would be much higher rates of cancer. The smaller proportion of cancer cells that do not have an active telomerase enzyme maintain telomere length using homologous recombination.

For cancer cells to become immortal (i.e., they can divide indefinitely without reaching senescence), they must prevent telomere shortening (i.e., otherwise the cell would reach senescence and stop dividing). How do most cancer cells prevent telomere shortening?

Segment of DNA that encodes a functional product.

What is a gene?

A polypeptide of a functional RNA molecule (such as rRNA,tRNA,snRNA,miRNA, for example)

What two types of functional product do genes encode?

The sequence of DNA nucleotides in a gene is copied (transcribed) to a sequence of RNA nucleotides according to complimentary base pairing rules.

 Define transcription (one sentence)

RNA polymerase

what transcribes DNA to RNA?

3 types:

1. RNA pol I: transcribe genes encoding functional RNA molecules

2. RNA pol II: transcribes all polypeptide encoding genes to mRNA

3. RNA pol III:Transcribe genes encoding functional RNA molecules.

What are the types of RNA in humans?

promoter region

What region of a gene does RNA polymerase bind to, to initiate transcription?

All genes transcribed by the SAME RNA polymerase require the same set of GTFs.

Do all genes transcribed by the same RNA polymerase require the same set of GTFs or do different genes transcribed by the same RNA polymerase use different GTFs?

focused: contains sequence (TATA) where GTFs and RNA polymerase bind, then RNA polymerase initiates transcription from a defined transcriptional start site.

Dispersed: promoter does not contain a consensus sequence and contains several potential transcription initiation sites within a range of approx. 100 base pairs.

What is the difference between a focused promoter and dispersed promoter?

Consensus sequence

______ lists the most common nucleotide at each position within the sequence.

mediator complex

_______ interacts with regulatory transcription factors, and regulates phosphorylation of the carboxyl terminal domain (CTD) of RNA pol II, which is the switch between transcription initiation and elongation.

False

T/F: RNA polymerase requires a primer.

5’-3’ direction

RNA polymerase synthesizes a strand of mRNA in the ________.

U

A pairs to

A

T pairs with A

C

G pairs with

G

C pairs with

True
mRNA sequence: 5’ – GGC AUG CAU UAC GGC AUC ACA CUA GGG AUC – 3’

Coding strand: 5’ – GGC ATG CAT TAC GGC ATC ACA CTA GGG ATC – 3’

T/F: the coding and mRNA template are the same other than replacing T for U.

NO; different genes on the same chromosome can use a different DNA strand as the template.

Do all genes on the same chromosome use the same DNA strand as the template strand?

polyA

Transcription ends after RNA polymerase transcribes the ________ signal sequence. After this, RNA polymerase dissociates from the template DNA.