MOLBIO LEC MIXED TOPICS RATIONALE

1

How many origins of replication do prokaryotes have?

Multiple (to speed up replication)

How many origins of replication do Eukaryotic chromosomes have?

DNA polymerase I

What fills in the gap after primer removal?

DNA polymerase I

Removes RNA primers and fills in the gap with DNA

S (synthesis)

DNA Replication happens during the ____________ phase of interphase

before

DNA replication occurs ____before/during/after___mitosis/meiosis

DNA polymerase

Proofreading during replication is done by

DNA polymerase

- Has proofreading capability via 3' to 5' exonuclease activity.

3'-TAGC-5'

What is the complementary DNA strand of 5'-ATCG-3'?

3'-TAGC-5'

Complementary strand that runs in the opposite direction with matching bases

Primer

What molecule is synthesized as a short RNA sequence?

Primer

Synthesized as a short RNA sequence to initiate replication

One old and one new strand per molecule

Why is DNA replication considered semiconservative?

Secure polymerase to DNA

What is the role of sliding clamp proteins?

sliding clamp

helps keep DNA polymerase attached for efficient synthesis

Cytosine

Which base pairs with guanine

three hydrogen bonds

Guanine pairs with cytosine via

replication bubble

Area where DNA is uncoiled for replication

replication bubble

area where replication begins

lagging strand

Which strand requires more primers

discontinuous synthesis

More primers are needed for the lagging strand due to

Telomeres

Unique to eukaryotes, these protect chromosome ends

3' to 5' exonuclease

Which enzyme activity is needed for proofreading?

3' to 5' exonuclease

- This activity allows for proofreading

Single-strand binding proteins

What stabilizes the unwound DNA strands

Single-strand binding proteins

These stabilize unwound DNA.

Ligase

Which enzyme catalyzes phosphodiester bond formation?

Ligase

Catalyzes the formation of phosphodiester bonds to join DNA fragments.

Nucleotides

What are the building blocks of DNA?

Nucleotides

The basic building blocks of DNA

RNA polymerase

Which enzyme is not directly involved in DNA synthesis?

RNA polymerase

Involved in transcription, not DNA replication

5' to 3'.

Synthesis direction of new DNA strands`

Done via 3' to 5' exonuclease activity

DNA polymerase proofreading function

Sliding clamp

Keeps DNA polymerase attached to DNA

replicon

Unit of DNA replicated from a single origin

Replication proceeds in both directions from origin

Characteristic of bidirectional replication

eukaryotic replication

Replication with multiple origins in linear chromosomes

prokaryotic DNA replication.

Involves circular chromosomes with one origin

Antiparallel nature of DNA strands

Strands run in opposite 5' to 3' orientations

deoxyribose

Sugar found in DNA nucleotides

T

A pairs with

C

G pairs with

DNA polymerase

Replaces RNA primers with DNA nucleotides

DNA polymerase III

Main enzyme adding nucleotides on both strands in bacteria

Ligase

Joins DNA fragments by forming phosphodiester bonds

Helicase

Unwinds the DNA duplex ahead of the fork

primase

synthesizes short RNA primers

Topoisomerase

Relieves supercoiling by cutting and rejoining DNA

RNA primer

short RNA segment required to initiate synthesis

lagging strand

Discontinuously synthesized strand composed of Okazaki fragments

leading strand

Continuously synthesized strand moving toward the fork

RNA primer

Short RNA segment required to initiate synthesis

RNA polymerase II

Which polymerase transcribes mRNA in eukaryotes

TBP (part of TFIID)

What binds to the TATA box first?

Pol II and general transcription factors

The pre-initiation complex includes:

TFIIH

What unwinds DNA in eukaryotic transcription?

TFIIH

has helicase activity that unwinds DNA during initiation

The carboxyl-terminal domain

The CTD of RNA Pol II is:

CTD

The ________of RNA Pol II is a tail-like structure that regulates transcription and RNA processing.

Pol II leaves the promoter

Promoter escape occurs when

initiation, elongation

Promoter escape happens when RNA Pol II transitions from __________ to __________

NELF and DSIF

RNA Pol II pauses shortly after initiation due to:

NELF and DSIF

These factors cause RNA Pol II to pause shortly after transcription begins.

Early during elongation

RNA capping happens:

5' cap

added shortly after transcription starts, during early elongation.

Guanylyltransferase

What adds the 5' cap?

Guanylyltransferase

This enzyme adds the 5' cap to mRNA.

5' cap

Protect RNA and aid in translation

5' cap

protects mRNA from degradation and facilitates ribosome binding for translation

Polyadenylation signal

What signals transcription termination in Pol II?

polyadenylation sequence (AAUAAA).

Transcription termination in Pol II is signaled by a

Allosteric and torpedo

Which model describes eukaryotic termination?

Allosteric and torpedo

These models describe how transcription termination occurs in eukaryotes.

CPSF

Which factor cleaves the RNA for termination?

CPSF

cleaves pre-mRNA near the poly(A) site.

XRN2

After cleavage, which exonuclease degrades RNA?

XRN2

a 5' to 3' exonuclease that degrades the RNA downstream of the cleavage site.

Poly(A) polymerase

Adds adenine residues to 3' end

Poly(A) polymerase

adds a poly(A) tail to the cleaved pre-mRNA.

AATAAA

The polyadenylation signal is typically:

AATAAA

This is the most common polyadenylation signal sequence in eukaryotic pre-mRNA

PABP

What stabilizes the poly(A) tail?

PABP

stabilizes the poly(A) tail and aids in translation initiation.

Proceed 5' to 3'

Transcription in prokaryotes and eukaryotes both

Proceed 5' to 3' direction

In both prokaryotes and eukaryotes, transcription proceeds in the

General transcription factor

Which is unique to eukaryotic transcription?

General transcription factor

Eukaryotic transcription uniquely requires multiple _______________ to initiate transcription

Transcription initiation

Transcription factors regulate

Transcription factors

regulates Transcription initiation

Transcription factors

bind DNA to regulate when and where transcription starts

transcription

In prokaryotes, translation can begin: During

Prokaryotic mRNA

The Shine-Dalgarno sequence is found in:

: The Shine-Dalgarno sequence

aligns the ribosome with the start codon in prokaryotes.

80S

Eukaryotic ribosomes are

Kozak sequence

The ribosome-binding site in eukaryotic mRNA includes:

Kozak sequence

Eukaryotic mRNAs have a _____________ around the start codon to facilitate translation initiation.

cytoplasm

In prokaryotes, translation and transcription occur in:

cytoplasm

In prokaryotes, transcription and translation are coupled in the

release factors

Terminate translation