Important Information Flashcards by Aífe Hayden

What are phosphodiester bonds?

Covalent bonds that link adjacent nucleotides together in both DNA and RNA

Formed between the OH group on the 3’ C of one nucleotide and phosphate on the 5’ C of the next nucleotide

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What are hydrogen bonds between nucleotides?

They join nitrogen bases of nucleotides together in complementary base pairs in the centre of DNA

This holds the 2 antiparallel strands together

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What is a replication “bubble” in DNA replication?

Where the two separate strands open up from the origin of replication

A replication fork is found at either end of the bubble

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DNA replication is semi-conservative, what does this mean?

Each of the 2 daughter molecule will have one of the old parent strands and 1 newly made strand

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What is a replication fork?

A Y-shaped region found at each end of a replication bubble

This is where the new strands of DNA are elongating

They move away from the origin of replication

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What is the Origin of Replication?

The position in DNA where the helix is first opened

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What is the leading strand?

The new strand that can be synthesised continuously

The new strand in the 5’ to 3’ direction strand (complementary to the 3’ to 5’ parent strand)

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What are okazaki fragments

Short sequences of DNA nucleotides which are synthesized discontinuously and later linked together by DNA ligase to create the lagging strand during DNA replication

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What is an exonuclease?

An enzyme which removes successive nucleotides from the end of a polynucleotide molecule

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What happens if DNA pol finds out the previous nt is incorrect?
(3)

DNA pol removes the incorrect nt by cutting the phosphodiester bond

This releases the nt

DNA pol tries again to add the correct nt

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What four proteins cooperate to form the replication machine?

Helicase

Topoisomerase

Sliding clamp

Single strand binding proteins

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How does helicase work?

Uses energy of ATP hydrolysis to speed along DNA and separate the strands of parental DNA ahead of polymerase

It breaks the hydrogen bonds between base pairs

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How does ligase work?

Joins 5’ phosphate end of one DNA fragment to 3’ OH end of the next (ATP required for ligase activity)

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How does topoisomerase work?

Prevents DNA helix upstream from becoming supercoiled by relaxing it

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How does the sliding clamp work?

Keeps DNA polymerase firmly attached to DNA template

On the lagging strand it releases polymerase from the DNA each time an Okazaki fragment is completed

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What are the four key players in DNA replication?

Ligase

Helicase

Primase

DNA polymerase

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What does nuclease do?

Removes any incorrect nucleotides - by cleavage of phosphodiester bonds

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Classify DNA damage.

Single strand

Double strand

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What causes single strand damage?

Endogenous replication errors

Oxidative chemicals

Non-ionising radiation e.g. UV

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What are the two classifications of agents that can damage DNA?

Exogenous

Endogenous agents

Give three examples of exogenous agents

Toxins

Chemicals

UV radiation

What causes double strand damage?

Antitumor agents e.g. Cisplatin

Ionising radiation e.g. Gamma rays

Define DNA damage

Any alteration to DNA that distorts its geometry

What are the five types of single strand damage?

Base Mismatch

Depurination

Deamination

Thymine dimers

Bulky adducts

What does DNA pol I primarily do? | 2

Exonuclease activity (nuclease activity at end of chain) Nick translation

What does DNA pol II primarily do?

DNA repair

What does DNA pol III primarily do?

DNA synthesis

What is a mutation?

Randomly produced permanent change in a sequence of DNA

What are the three repair processes for SSD?

Mismatch repair (MMR) for repairing Base excision repair (BER) Nucleotide excision repair (NER)

What is meant by 5' and 3'? | 2

The 5' and 3' indicate the carbon numbers in the DNA's sugar backbone. The 5' carbon has a phosphate group attached to it and the 3' carbon a hydroxyl (-OH) group

How do you draw deoxyribose? | 7

Draw a pentagon - O at the top with four carbons Label each carbon in a clockwise direction 1' to 4' ``` 1' = OH on top and H on bottom 2' = H on top and H on bottom 3' = H on top and OH on bottom 4' = 5' on top and H on bottom 5' = (HOCH2) ```

What is the structural difference between deoxyribose and ribose?

2' and 3' of ribose have a H on top and an OH on bottom

To which C of ribose is the nitrogenous base attached?

To which C of ribose is the phosphate attached?

Define transcription

A portion of DNA nucleotide sequence (gene) is copied into a RNA nucleotide sequence

Define translation | 2

The synthesis of polypeptide under direction of RNA Formation of amino acid chains - proteins

What are transcription factors?

A collection of proteins that mediate the binding of RNA pol II to promoter in eukaryotes

What is RNA polymerase called when it is comprised of all five of it's subunits?

Haloenzyme

What are the three main steps in transcription in prokaryotes?

Binding and initiation Elongation Termination

How does initiation of transcription work in eukaryotes? | 4

A collection of proteins called transcription factors are needed They mediate the binding of RNA pol II to promoter A promoter DNA sequence (TATA box) is crucial for forming the transcription initiation complex Complex then moves Pol II to start site of gene and begins to polymerise

What is the spliceosome? | 2

Small nuclear RNAs (snRNA) Combined with proteins (snRNP)

What does mRNA need to be bound to in order to be transported? (3)

Poly-A-binding protein Cap-binding complex Nuclear transport receptor

What is an operon?

A set of adjacent genes in a bacterial genome, transcribed from a single promoter into a single mRNA

Write a note on the trytophan operon | 4

5 genes which encode for enzyme which manufacture trytophan These genes are arranged in a cluster on the genome (form an operon) Genes transcribed from one promoter as 1 long mRNA molecule from which 5 proteins are translated This operon isn't needed if bacteria can get trytophan from their environment so it's shut off

Define a repressor protein.

A protein that switches genes off or represses them

Define an activator protein

A protein that switches genes on or activates them

Write a note on the lac operon | 4

Operon that encodes proteins required to import and digest lactose Consists of 3 genes: lacZ, lacY and lacA All genes under control of 1 promoter Allolactose - lactose digestion intermediate - binds to repressor to inactivate it

What is the genetic code?

The rules by which nucleotide sequence of a gene is translated into an amino acid sequence of a protein

What do ribosomes do in translation?

They add each amino acid brought to it by tRNA to the growing end of a polypeptide chain