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biosci > Gene to Protein > Flashcards

Gene to Protein Flashcards

1
Q

What is gene expression?

A

The process of going from DNA to functional protein

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2
Q

What is the central dogma

A

DNA–> RNA –> Protein

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3
Q

What is DNA

A

The heritable material used to store and transmit information from generation to generation

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4
Q

What is RNA

A

Acts as a messenger to allow the information stored in the DNA to be used to make proteins

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5
Q

What is the function of proteins

A

To carry out cellular functions

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6
Q

What are the three main steps of gene expression?

A
  • Transcription (of RNA to DNA)
  • Processing (of the pre-mRNA transcript)
  • Translation (of the mRNA transcript to a protein
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7
Q

Where does transcription occur

A

Nucleus

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8
Q

Where does processing occur

A

Nucleus

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9
Q

Where does translation occur

A

Cytoplasm

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10
Q

What are the three steps of transcription

A

Initiation, elongation, termination

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11
Q

What is a transcription factor?

A

A protein that binds to the promoter region

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12
Q

What is the promoter region?

A

The start of a gene (upstream)

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13
Q

What is the template strand?

A

The strand that is transcribed

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14
Q

What is the coding strand?

A

The strand that contains the base sequence for a particular protein 5’/3’ end

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15
Q

What happens in transcription

A
  1. Polymerase binds to promoter
  2. moves downstream through gene, transcribing RNA
  3. Detatches after terminator reached
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16
Q

Why is it important for DNA to be stable but not for RNA

A

DNA holds genetic information so it needs to have limited change to last the lifetime of a cell.
For RNA, they are short-lived so can make another one

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17
Q

What are the three steps in initiation of transcription

A
  • A eukaryotic promoter: A TATA box typically 25 nucleotides upstream from a eukaryotic promoter
  • Several transcription factors bind to DNA: several transcription factors (including the TATA box binding protein) assemble
  • Transcription initiation complex forms: RNA polymerase II can now bind along with more transcription factors to form the transcription initiation complex
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18
Q

Transcription - Initiation defintion

A

Assembly of multiple proteins required before transcription can commence

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19
Q

how many nucleotides are exposed at a time when DNA is unwound?

A

10-20

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20
Q

What happens in elongation of transcription (1)

A

Complementary RNA molecules are added to the 3’ end of the growing transcript. 3’ OH of transcript binds with 5’ phosphate of the incoming nucleotide to form a phosphodiester bond.

Double helix reforms as transcript leaves the template strand

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21
Q

What happens in termination of transcription

A

After transcription of the polyadenylation signal (AAUAAA) nuclear enzymes release the pre-mRNA and RNA polymerase then dissociates from the DNA.

pre-mRNA is now ready for further processing

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22
Q

what is the polyadenylation signal in transcription termination?

A

AAUAAA

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23
Q

What are the three elements of mRNA processing

A

Capping, tailing and splicing

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24
Q

What happens in capping of pre-mRNA processing

A

A modified guanine nucleotide is added to the 5’ end

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25
Q

What happens in tailing of pre-mRNA processing

A

50-250 adenine nucleotides (polyA) are added to the 3’ end

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26
Q

What happens in splicing of pre-mRNA processing

A

Introns are removed from the transcipt and exonsare rejoined to form mature mRNA

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27
Q

Why are capping and splicing carried out?

A

Capping and Tailing are thought to facilitate export, confer stability and facilitate ribisome binding in cytoplasm

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28
Q

What are exons

A

Coding regions (inc UTR’s)

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29
Q

What are introns

A

Non-coding regions in intervening exons

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30
Q

What is a UTR

A

Untranslated regions at 5’ and 3’ ends. Part of the exon but doesn’t code

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31
Q

Where does splicing occur (mRNA processing)

A

The spliceosomes in the nucleus

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32
Q

What are spliceosomes?

A

A large complex of proteins and small RNAs

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33
Q

What is alternative splicing

A

A process by which different combinations of exons are joined together. This results in the production of multiple forms of mRNA from a single pre-mRNA.

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34
Q

What does alternative splicing allow for

A

Multiple gene products from the same gene, approximately 20,000 genes.

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35
Q

What does the mature mRNA transcript bind to?

A

Once it leaves the nucleus, the mature mRNA transcript binds to a ribosome

36
Q

What are the three main steps of translation

A

Initiation, elogation and termination

37
Q

Translation - defintion

A

Mature mRNA transcript exits the nucleus and is bound by the ribosome

38
Q

What happens in translation

A
  • Codons are translated into amino acids
  • tRNA molecules within the cytosol with specific anticodons carry corresponding amino acids
  • H bonds form between mRNA and anticodon of the appropriate tRNA
  • The amino acids are added via peptide bonds to the growing polypeptide chain
39
Q

What does the tRNA and mRNA held within the ribosome enable

A

Ribosomes allow mRNA and tRNA to be held together closely, allowing formation of the polypeptide chain

40
Q

Ribosome has binding sites for mRNA and tRNA, true or false

A

True

41
Q

What is the ‘A site’

A

(amino site)
holds ‘next-in-line’ tRNA

42
Q

What is the P site

A

(peptidol)
Holds tRNA carrying the growing polypeptide

43
Q

What is the E site

A

(exit)
tRNA’s exit from here

44
Q

What end of the mRNA does the small ribosomal subunit bind to?

A

It binds to the 5’ cap of the mRNA

45
Q

How do new amino acids arrive

A

via tRNA’s

46
Q

What is the function of the tRNAs

A

It is the physical link between the mRNA and the amino acid sequence of proteins

47
Q

What way does the small ribosomal subunit scan?

A

Downstream

48
Q

What amino acid does the initiator tRNA carry

A

Methionine (Met)

49
Q

What bonds form between initiator anti-codon and mRNA

A

Hydrogen bonds

50
Q

How is the initiation complex completed

A

When the large ribosomal subunit then binds

51
Q

What is required for translation initiation assembly

A

Energy (GTP - guanosine triphosphate)

52
Q

What are the three main steps of translation elongation

A

Codon recoginition, peptide bond formation and translocation

53
Q

What is codon recognition (translation elongation)

A
  • Base pairs with complementary anticodon.
  • GTP invested to increase accuracy/inefficiency
54
Q

What happens in peptide bond formation (translation elongation)

A
  • A large subunit of rRNA catalyses peptide bond formation.
  • Removes it from tRNA in P site
55
Q

What happens in translocation (translation elongation)

A
  • Moves tRNA from A to P site
  • tRNA in P site moves to E and is released
  • Energy is required (GTP)
56
Q

What happens to the empty tRNA’s in translation elongation

A

They are ‘reloaded’ in the cytoplasm using aminoacyl-tRNA synthetases

57
Q

What are three main steps in translation termination

A
  1. Ribosome reaches a stop codon on mRNA
  2. Releases factor that promotes hydrolysis
  3. Ribosomal subunits and other components dissociate
58
Q

What happens when the ribosome reaches a stop codon on mRNA in translation termination (1)

A

mRNA stop codon in the A site is bound by a release factor

59
Q

What happens when release factor promotes hydrolysis in translation termination (2)

A

Bond between p-site tRNA and last amino acid is hydrolysed, releasing polypeptide

60
Q

What happens when ribosomal subunits and other components dissociate in translation termination (3)

A
  • Hydrolysis of two GTP molecules required.
  • Ribosomal components can be recycled.
61
Q

What does translation termination require?

A

2 GTP

62
Q

Why is gene expression regulated

A

It is regulated to allow the cell to express a specific protein to carry out a specific function at a particular time and place (spatial and temporal control)

63
Q

What can regulatory proteins do

A

Block translation, variable mRNA life-spans

64
Q

What are the control points in gene expression

A
  • transcription factors need to assemble, DNA needs to be accessible
  • capping, polyadenation, alternate splicing, producing an mRNA need translating
  • specific proteins assit in nuclear export of mRNA
  • regulatory proteins block translation, varible mRNA life spans
65
Q

Why is control of gene expression important

A

To achieve the right thing at the right time in the right place (also known as temporal and spatial control)

66
Q

What are ‘house-keeping’ proteins

A
  • Proteins that are continuosly produced as they are always needed in the cell.
  • typically have longer half-life than cells
67
Q

What is an example of a ‘housekeeping’ protein?

A

Tubulin for microtubules

68
Q

How can a short-lived protein be produced as a result of cell signalling

A
  • Cell signalling (e.g ligand binding a cell surface receptor, or activating an intracellular receptor)
  • Signal transduced and may enter nucleus to activate transcription
  • Results in production of short-lived protein to carry out required function
69
Q

What do the side chains (R groups) determine

A

The properties of each amino acid

70
Q

Are electrically charged side chains hydrophobic or hydrophilic

A

Hydrophilic

71
Q

Is 5’ side of transcript the N-terminus or the C-terminus

A

N-terminus

72
Q

What bonds hold amino acid sequences together

A

Covalent bonds

73
Q

What does the polypeptide start to do as soon as it leaves the ribosome

A

Forms secondary structure

74
Q

How do secondary structures form?

A

Form due to relatively weak hydrogen bonding between oxygen on the carbonyl group and hydrogen on the amine group

75
Q

What are teritiary structures

A

3D shape stabilised by side chain interactions

76
Q

What are quartenary structures

A
  • Multiple proteins associate together to form a funtional protein
  • Not all proteins form a quatenary structure
77
Q

Where do proteins destined to function in the cytosol complete translation

A

Free ribosomes in the cytoplasm

78
Q

Where do proteins that go through the endomembrane system complete translation

A

They complete translation at fixed ribosomes on the RER

79
Q

What happens in the golgi for protein processing and sorting

A

Many proteins are processed and sorted through the RER and Golgi (but not all)

80
Q

Where are signal peptides found

A

At N-terminus of the protein (~20aa)

81
Q

What is an SRP

A

Signal recognition particle

82
Q

What are the 6 steps in how signal peptides direct ribosomes to RER

A
  1. Polypeptide synthesis begins
  2. SRP binds to signal molecule
  3. SRP binds to receptor protein
  4. SRP detatches and polypeptide synthesis resumes
  5. Signal-cleaving enzyme cuts off signal peptide
  6. Completed polypeptide folds into final conformation
83
Q

What happens to secretory and membrane proteins at step 6 (when completed polypeptide folds into final conformation)

A
  • A secretory protein such as insulin is solubilised in lumen
  • A membrane protein remains anchored to the membrane
    Both then go to Golgi via vesicles for further maturation
84
Q

Why do post-translation modifications occur

A

Translation may be complete, but the protein may not yet be functional

85
Q

Where are two places in the cell that post-translation modifications can occur

A

Within the Golgi or the cytosol

86
Q

What do post-translation modifications do?

A

They can confer activity, ability to interact with other molecules, or direct to particular locations

biosci (28 decks)

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