Session 8: Gene expression Flashcards by Emily Wilson

A polynucleotide is..

DNA or RNA

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A polypeptide is…

A protein

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Making a polynucleotide or a polypeptide requires what 3 things?

Enzymes
Active substrates
A template

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What three stages are involved in making a polynucleotide or a polypeptide?

Initiation
Elongation
Termination

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What are the enzyme, activated substrates and template needed to make DNA (DNA replication)?

Enzyme: DNA polymerase
Activated substrates: deoxynucleoside triphosphates (dNTPs)
Template: DNA

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What are the enzyme, activated substrates and template needed to make RNA (Transcription)?

Enzyme: RNA polymerase
Activated substrates: nucleoside triphosphate (NTPs)
Template: DNA

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What are the enzyme, activated substrates and template needed to make a polypeptide (Translation)?

Enzyme: Ribose
Activated substrates: Amino acids
Template: mRNA

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What is involved at each stage of DNA replication?

Initiation: recognition of origin of replication initiation proteins and binding of DNA polymerase
Elongation: 5’ to 3’ chain growth
Termination: Replication forks meet

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What is the process called that converts DNA into mRNA?

Transcription

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What is the process called that converts mRNA into protein?

Translation

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What is involved at each stage of Transcription?

Initiation: promoter recognition, transcription of initiation factors binding of RNA polymerase
Elongation: DNA strands unwind and RNA reads the nucleotide sequence and inserts and links together complementary RNA nucleotides (forming pre-mRNA)
Termination: RNA polymerase stops adding nucleotides when a 3’ termination sequence is reached

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What happens to the pre-mRNA once it has been made in the nucleus form mature mRNA?

They are processed to remove introns, and the remaining exons are then spliced together to form mature mRNA

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What are added to the 5’ and the 3’ ends of the mRNA following its transcription?

5’ end: nucleotide cap

3’ end: poly- A tail

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Once the ends have been capped what happened to the mature, processed mRNA?

It leaves the nucleus through a nuclear pore and enters the cytoplasm for translation

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During translation what two other forms of RNA interact with mRNA?

ribosomal RNA (rRNA) and transfer RNA (tRNA)

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What bond is formed between amino acids?

Peptide bond

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What strand is the DNA coding strand?

Is this strand used in transcription?

The strand that is complementary to mRNA (besides the Ts and Us)
No it is not used in transcription

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What strand is the DNA template strand?

Is this strand used in transcription?

The template strand is the “non-coding” but this is the strand that is being used to make the mRNA
The mRNA carries the code
Yes this strand is used in transcription

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Does transcription proceed from left to right or from right to left on the chromosome?

Neither!!! It proceeds from 5’ end to 3’ end in either direction

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What is the purpose of the 5’ cap and the 3’ polyA tail that are added to the pre-mRNA?

To protect against degradation

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An unusual attachment provides protection from degradation. The cap is attached by its ______ end to the ______ end of the mRNA.

5’

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What happens during polyadenylation and at what end of the RNA does this happen?

At the 3’ end
A sequence is recognised by a specific endonuclease
polyA polymerase adds a poly A tail to the 3’ end

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True or false: Ribosomes exist in Prokaryotes and Eukaryotes

True

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What are the differences between ribosomes between prokaryotes and eukaryotes?

Prokaryotes:
3 rRNAs and 56 proteins
30S and 50S subunits
70S ribosome

Eukaryotes:
4 rRNAs and 82 proteins
40S and 60S subunits
80S ribosome

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What is the clinical importance and relevance of these differences in ribosomes between prokaryotes and eukaryotes?

Can target specific prokaryotic subunits in antibiotics, for example

Ribosomal RNA (rRNA) is made with which polymerase?

RNA polymerase I

Messenger RNA (mRNA) is made with which polymerase?

RNA polymerase II

Transfer RNA (tRNA) is made with which polymerase?

RNA polymerase III

Relative to the other main types of RNA, rRNA has how many kinds and how many copies of each kind?

rRNA has only 4 kinds, very few | But it has many copies of each kind

Relative to the other main types of RNA, mRNA has how many kinds and how many copies of each kind?

mRNA has many kinds: 100,000s | But only a few copies of each

Relative to other main types of RNA, tRNA has how many kinds and how many copies of each kind?

tRNA has around 100 kinds (more than rRNA but less than mRNA) It has very many copies of each kind

In an isolated cell how much of the RNA is rRNA?

>80%

In an isolated cell, how much of the RNA is mRNA?

Around 2%

In an isolated cell, how much of the RNA is tRNA?

Around 15%

What is the adaptor molecule required for translation?

Transfer RNA (tRNA)

The genetic code is a __________ code and is ___________

triplet | degenerate

What do we mean when we say the genetic code is degenerate?

A single amino acid can be coded for by more than one codon

The genetic code results in 5' to 3' template read-through, producing _____ terminus to ______ terminus polypeptide chain extension

N | C

tRNA forms _____ _____ which contribute to its clover shape

Stem loops

How are "stem loops" formed?

The formation of Hydrogen Bonds between anti-parallel, complementary sequences

The amino acid binds to where on the tRNA molecule?

The 3' OH of the last base that is bound

The name of the tRNA depends on the what?

Amino acid bound to it

What does the tRNA "anticodon" do?

It recognises different "codons" in the mRNA

Methionyl tRNA has anticodon 5'CAU, what mRNA codon does this recognise?

5'AUG

What is the "wobble" base position and what does it infer?

The 5'base of anticodon/3'base of codon | It allows more flexibility in the recognition which gives the genetic code its degeneracy

What happens at the three stages of translation?

Initiation: recognition of AUG start codon by 'special' methionyl tRNA ribosome Elongation: addition of aminoacyl tRNAs which promote N to C chain growth Termination: stop codons

The 'special' methionyl tRNA recognises what on the mRNA strand?

The 5' 5' cap

Which subunit of the ribosome can then bind?

The 40S, smaller subunit can bind

Does the process of translation initiation use energy?

Yes

Once the tRNA comes across an AUG codon on the mRNA what is able to attach to the complex? Does this use energy?

The larger ribosome subunit (60S) | Yes this uses energy

Once the fully functional ribosome is found during initiation of translation, elongation can commence. What are the two sites that we find inside of the ribosomes?

P site | A site

There is enough space to recognise ____ codons in the ribosome

The growing amino acid chain is moved from the ____ site to the _____ site

P | A

Does elongation during translation take energy?

Yes

What is the enzyme responsible for moving the amino acid from the P site to the A site and forming a peptide bond?

Peptidyl transferase

During termination of translation, a stop codon in the mRNA will be present in which ribosomal site?

A site

Do tRNA molecules have anticodons for stop codons?

What molecule binds to the Stop codon on mRNA?

Release Factor

Following binding of release factor to the stop codon on mRNA, what happens?

The complex dissociates. mRNA, tRNA and polypeptide are released from the ribosome §

What molecule breaks the bond between tRNA and peptide during termination of translation?

Water

Which codon specifies the first amino acid in any protein?

AUG

A eukaryotic gene encoding a protein might be ten times longer than the theoretical minimum length. Explain

A eukaryotic gene contains introns (non-coding regions) as well as exons (coding regions) and therefore the will make the gene longer than the minimum length of the protein

Why are there only a few kinds of rRNA and 100,000s of kinds of mRNAs?

rRNAs are not specific and code for ribosomal subunits only, many different mRNAs are needed to code for many different proteins

Why are DNA polymerases capable of editing and error correction (proof-reading), whereas the capacity for error correction in RNA polymerases appears quite limited?

A single base error in RNA isn't going to have much of an impact downstream as it will most probably be degraded, and won't be passed onto progeny and there are many other 'normal' copies of RNA. DNA mutation will impact all of the cells as the error is passed onto the progeny through cel divisions.

The addition of what to which carbon of the nucleotides that make up DNA/RNA denotes whether it is doxy- or oxy-?

``` Hydroxyl group (-OH) The 2' Carbon ```