Genetics- MT 2- Lect 1 (09/18/2026)- LO6.2

Where does DNA Replication start from

Begin at sites called the origin of replications, where specific sequences of DNA are recognized by initiator proteins to start the replication process.

Is DNA replication fast accurate

Yes- The polymerases are faster in bacteria than eukaryotes usually

How are DNA strands separated

By breaking H-Bonds between complementary base pairs.

What does breaking the H-Bonds do

It forms the replication bubble that allows the two strands of DNA to be accessed for replication.

What does forming the replication bubble do

It allows for protein assembly

What is a replication bubble

A replication bubble is a section of DNA that has unzipped (opened up) so that DNA replication can occur.

Is DNA replication bidirectional in prokaryotes and Eukaryotes

Yes

What is the difference in the origins of replication between prokaryotes and eukaryotes

Pro only has one and eu has multiple

Replication bubble Purpose

Copy DNA

Transcription Bubble Purpose

Make RNA from DNA

Enzyme for the Replication Bubble

Helicase opens DNA; DNA polymerase copies it

Enzyme for transcription Bubble

RNA polymerase opens DNA and makes RNA

DNA strands used as templates for Replication Bubble

Both

DNA strands used as templates for Transcription Bubble

Only one

What are the other differences between Replication bubbles and transcription bubbles

Direction	Usually bidirectional	One direction for each transcription event
Forks	Two replication forks	No replication forks
Starting point	Origin of replication	Promoter

DNA Replication Image in eukaryotes

Ends up with two daughter molecule

What does DNA Polymerase 1 do

RNA primers and replaces them with DNA during DNA replication in bacteria

Who won a nobel for purifying all the enzymes and all of the components required for replication in e-coli to have replication outside the cells?

Kornberg

How many chromosomes and what shape do prokaryotes have

1 circular chromosome

How many origins of replication do prokaryotes have

1

Where is the dna in Prokaryotes

Nucleoid Region

How many origins of rep in Eukaryotes

100s-1000s

Do prokaryotes have replication forks doe prokaryotic DNA Replication

Yes

Theta structure

What are the two steps for DNA Replication

Initiation and elongation

Initiation

Replication bubble is formed- RNA primers (5-10) nucleotides are required for DNA synthesis to start

1. Origin is recognized

2. Initiation proteins come in

3. Separation of strands happens with helicase opening up the replication bubble

4. Two replication forks

5. RNA primase lays down the RNA primers for DNA polymerase to start synthesizing DNA

Elongation

New strands of DNA are synthesised- 500 nucleotides per sec in bacteria only 50 per sec in humans- The RNA primers are replaced with DNA by DNA Polymerase I and then ligase seals it

DNA synthesis

the natural or artificial creation of new deoxyribonucleic acid (DNA) molecules by linking nucleotide building blocks together

Which direction is DNA synthesised

5’ phosphase end-3'-OH (hydroxyl) group

Deoxyribose vs ribose

What keeps the strands separated during elongation

Single- strand binding proteins

Does helicase work at one end or both

Both- the proteins etc are on both sides

Initiator Protein function

to recognize and bind to specific DNA sequences at the origin of replication, melt and unwind the double helix, and recruit downstream replication machinery like DNA helicases to start copying the genome

Explain how nucleotides get added

Template strands are read 3’-5’ but Nucleotides are added 5’-3’

DNA polymerase III goes along the template strands 3’-5’ direction and it adds the new nucleotides to the three prime end of the growing strand

Each Nucleotide comes as a tri-phosphate and is very unstable so the nucleotides want to form bonds. The bond between the alpha and beta phosphate is broken and the alpha attaches to the 3’ end of the DNA molecule along with its nucleotide

There are two reactions that are endergonic meaning they require energy, the addition of the 5’P of the dNTP (nucleotide + the triphosphate) to the 3’ OH of the growing strand and the phosphodiester bond formation

Energy is provided by the hydrolysis of the beta and gamma phosphates- exergonic reaction (hydrolysis of P-P)

Synthesis vs polymerization

• DNA synthesis: Making a new DNA strand.

• DNA polymerization: Joining nucleotides together by forming phosphodiester bonds.

Leading Strand

Continuous Polymerization- Grows in the direction of the fork

Lagging Strand

Discontinuous polymerization grows away from the fork in fragments

Initiation Proteins

Initiation proteins identify where to open the DNA, and helicase unzips it- related to origin of replication

Problem in linear chromosomes

The end does not get replicated because the primer can not be laid down on the lagging strand- replication machinery can not complete the 5’ ends of linear DNA

• in most eukaryotic cells the ends become shorter after each round of replication

• Does not happen in prokaryotes

Telomerase

Telomerase adds repetitive DNA sequences (TTAGGG in humans) to the 3′ end of the parental DNA strand- type of polymerase

why cant dna polymerase fill in the gap

DNA polymerase cannot fill the gap left by the last primer because there is no available 3′-OH to extend from- note another enzyme (RNA-ase or smt removes the rna primer)

Telomeres

are protective caps on chromosome ends- active in germ cells inactive in adult/ differentiated cells

Do X and Y chromosomes have the PAR1 and 2 regions

Yes—both the X and Y chromosomes have two shared pseudoautosomal regions, PAR1 and PAR2. They're at the tips and they’re what let X and Y pair and recombine during meiosis

why do we not want telomerase active in somatic cells

We generally don't want telomerase highly active in most somatic cells because it could allow damaged or abnormal cells to keep dividing, increasing the risk of cancer.

How do some cancer cells become immortal

they reactivate the telomerases- that allows them to bypass the signals for apoptosis because the chromosomes do not get short enough to signal it even when they should die

B vs Z form dna

B form= Right handed DNA normal bases

Z from= Left Handed DNA abnormal bases

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Dna-binding proteins recognize the chemical differences derived form the arrangement of the bases in the major or minor grove of the double stranded DNA

Sequence-Specific