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Principles: Biochemistry > Gene regulation and Protein synthesis > Flashcards

Gene regulation and Protein synthesis Flashcards

1
Q

True or false: RNA is a single chain

A

False- RNA is single stranded but not a single chain

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2
Q

What are the 3 main classes of RNA?

A
  1. Ribosomal RNA (rRNA) - combines with proteins to form ribosomes where protein synthesis takes place
  2. Transfer RNA (tRNA) - carries amino acids to be incorporated into the protein. Acts as adapters between nucleic acid code and amino acid code
  3. Messenger RNA (mRNA) - carries genetic information for protein synthesis
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3
Q

What kind of structures do RNA form?

A

RNA forms stem-loop structures

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4
Q

What are the base pairing rules in RNA?

A

Adenine pairs with uracil (replaces thymine) and cytosine pairs with guanine

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5
Q

What is the purpose of RNA polymerase?

A

RNA polymerase synthesises RNA by using one DNA strand as a template to copy the nucleotide sequence into RNA. Prokaryotic cells have one type of RNA polymerase where as eukaryotic cells have 3 types (Pol I, Pol II, Pol III). Pol II is used to synthesise all mRNA

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6
Q

Compared to eukaryotes, how does the location of transcription/translation/protein synthesis etc differ in prokaryotes

A

In eukaryotes, DNA replication, transcription/translation and processing all takes place in the nucleus then mRNA is transported to the cytoplasm for protein synthesis. However in prokaryotes, all these processes occur in the same place

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7
Q

Explain the steps of transcription

A
  1. RNA polymerase binding - detection of initiation sites (promotors) on DNA. This also requires transcription factors
  2. DNA chain separates and unwinds
  3. Transcription initiation - adding of the first nucleotide of the growing RNA
  4. Elongation - addition of more nucleotides to RNA chain
  5. Termination - release of the finished RNA and RNA polymerase dissociates and is recycled
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8
Q

Which strand is being read and which strand is not being transcribed/read?

A

The template strand is the one being read and the coding strand is not being read

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9
Q

What is a TATA box?

A

A TATA box is part of a promoter sequence. The TATA box is usually present about 25 nucleotides upstream of many genes transcribed by RNA polymerase II (Pol II)

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10
Q

What is the TBP (TATA box binding protein)?

A

This is the protein that recognises the TATA box. It is part of TFIID which is a general transcription factor and is required for all Pol II transcribed genes. It also induces kinks to DNA. TBP also provides a landing platform for further transcription factors and for RNA polymerase

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11
Q

What are transcription factors?

A

Transcription factors are proteins that control the rate of transcription

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12
Q

What is meant by “specific” transcription factors?

A

These are DNA binding proteins which contain 2 domains that can be physically separated:
1. DNA-binding domain
2. Transcriptional activation/depression domain
These transcription factors bind to specific DNA sequences called enhancers, which are in the vicinity of a promoter so they can regulate transcription positively or negatively

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13
Q

How can an activator protein on a strand of DNA be brought into contact with the transcription complex?

A

DNA can bend to bring these 2 things closer together

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14
Q

How does coordinated gene expression work?

A

This is in response to specific stimuli (e.g hormones, steroids)

  1. A stressor activates transcription of a regulatory protein through a specific sensitive transcription factor
  2. Binding of the regulatory protein to the stress response element (SRE) stimulates transcription of genes
  3. This produces different proteins participating in the stress response
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15
Q

How are the ends of mRNA processed?

A
  1. Splicing
  2. Addition of poly (A) tail
  3. Addition of a 5’ cap
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16
Q

During translation, what part of tRNA molecules binds with mRNA?

A

The anti-codons of tRNA molecules form base pairs with the codons of mRNA. This binds in triplets

17
Q

What is the meaning of degenerate?

A

This means many amino acids have more than one codon (e.g there are 4 codons that code for serine)

18
Q

What is the meaning of unambiguous?

A

This means that each codon codes for only one amino acid (e.g AUG = start codon)

19
Q

True or False: Reading frames on RNA molecules can be different depending on where translation starts

A

True

20
Q

Name 7 components that are required for translation

A
  1. tRNA molecules
  2. ATP + GTP for energy source
  3. Amino acids
  4. Specific sets of protein factors for different steps
  5. Ribosomes
  6. mRNA
  7. aminoacyl-tRNA synthetase (tRNA-ligase)
21
Q

What is aminoacyl-tRNA synthetases?

A

This binds amino acids to their corresponding tRNA molecule. They are highly specific and ATP provides the energy for the formation of covalent bond

22
Q

Where does translation occur?

A

Translation occurs in the ribosome

23
Q

What does ribosomes contain?

A

Contain 4 different rRNA molecules and they also contain protein components. There are 2 different sub-units in ribosomes - one small and one large

24
Q

How many tRNA binding sites do ribosomes have and what are they called?

A

Ribosomes have 3 tRNA binding sites:

  1. E = Exit
  2. P = peptidyl
  3. A = aminoacyl acceptor
25
Q

Explain how the ribosome is a multi-step assembly line for protein synthesis

A

The first tRNA starts at the P site. The A site is where a donor tRNA molecule, which is carrying the appropriate amino acid, is positioned before that amino acid is incorporated into the protein. These then form a peptide bond to create a chain and everything moves along by one codon so that the A site is free to accept another tRNA molecule with a new amino acid so that this can repeat and the chain can continue to grow. This peptide bond formation is catalysed by peptidyl transferase. Once a polypeptide chain has formed it moves along to the E site where it will soon be exiting the ribosome. The polypeptide chain is finished when the A site encounters a STOP codon

26
Q

What are the 3 steps called in translation?

A
  1. Initiation - the ribosome gets together with the mRNA and the first tRNA so translation can begin.
  2. Elongation - amino acids are brought to the ribosome by tRNAs and linked together to form a chain
  3. Termination - the finished polypeptide is released to go and do its job in the cell
27
Q

Name 4 types of chromosomal mutations

A
  1. T - Translocations
  2. I - Inversions
  3. D - Duplications
  4. D - Deletions
28
Q

Name 3 types of point mutations

A
  1. S - Substitution
  2. I - Insertion
  3. D - Deletion
29
Q

What is meant by missense mutation?

A

Missense mutation is when a mutation results in a change in the amino acid so can alter the function of a protein

30
Q

What is meant by nonsense mutation?

A

Nonsense mutation is when a mutation results in a new STOP codon so can shorten the chain, usually causing the protein to not work

31
Q

What is meant by silent mutation?

A

Silent mutation is when there may have been a base change however this didn’t result in a change of amino acid so no effect on protein function

32
Q

What is meant by frameshift mutation?

A

Frameshift mutation is when there is an insertion or deletion of bases which causes the reading frame to change so can effect all amino acids after the mutation

33
Q

What 3 things may need to be done to a protein to completely finish it?

A
  1. Targeting - moving a protein to final destination. This depends on the specific amino acid sequence within the translated protein
  2. Modification - adding of further chemical groups or cleavage
  3. Degradation - unwanted or damaged proteins have to be removed
34
Q

When does post-translational modification occur and name some examples of post-translational modifications?

A

Post-translational modification can occur at any time during the “life cycle” of a protein however, it most commonly occurs after translation has been completed. Examples of post-translational modifications include:
• Phosphorylation - addition of phosphate by kinase
• Proteolysis - cleaving polypeptide
• Glycosylation - Addition of carbohydrates

35
Q

What is the difference between “free” and “bound” ribosomes?

A

“Free” ribosomes are in the cytosol and makes proteins for the cytosol, nucleus, mitochondria. These are translocated post-translationally

“Bound” ribosomes are on the RER and make proteins for the plasma membrane, ER, golgi apparatus, secretion. These are translocated co-translationally

36
Q

What are 2 destinations of newly synthesised proteins?

A
  1. Go to the organelles or cytosol

2. Go to the rough endoplasmic reticulum

Principles: Biochemistry (9 decks)

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