Gene to Protein Flashcards
1
Q
What is gene expression?
A
The process of going from DNA to functional protein
2
Q
What is the central dogma
A
DNA–> RNA –> Protein
3
Q
What is DNA
A
The heritable material used to store and transmit information from generation to generation
4
Q
What is RNA
A
Acts as a messenger to allow the information stored in the DNA to be used to make proteins
5
Q
What is the function of proteins
A
To carry out cellular functions
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
7
Q
Where does transcription occur
A
Nucleus
8
Q
Where does processing occur
A
Nucleus
9
Q
Where does translation occur
A
Cytoplasm
10
Q
What are the three steps of transcription
A
Initiation, elongation, termination
11
Q
What is a transcription factor?
A
A protein that binds to the promoter region
12
Q
What is the promoter region?
A
The start of a gene (upstream)
13
Q
What is the template strand?
A
The strand that is transcribed
14
Q
What is the coding strand?
A
The strand that contains the base sequence for a particular protein 5’/3’ end
15
Q
What happens in transcription
A
- Polymerase binds to promoter
- moves downstream through gene, transcribing RNA
- Detatches after terminator reached
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
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
18
Q
Transcription - Initiation defintion
A
Assembly of multiple proteins required before transcription can commence
19
Q
how many nucleotides are exposed at a time when DNA is unwound?
A
10-20
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
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
22
Q
what is the polyadenylation signal in transcription termination?
A
AAUAAA
23
Q
What are the three elements of mRNA processing
A
Capping, tailing and splicing
24
Q
What happens in capping of pre-mRNA processing
A
A modified guanine nucleotide is added to the 5’ end
25
What happens in tailing of pre-mRNA processing
50-250 adenine nucleotides (polyA) are added to the 3' end
26
What happens in splicing of pre-mRNA processing
Introns are removed from the transcipt and exonsare rejoined to form mature mRNA
27
Why are capping and splicing carried out?
Capping and Tailing are thought to facilitate export, confer stability and facilitate ribisome binding in cytoplasm
28
What are exons
Coding regions (inc UTR's)
29
What are introns
Non-coding regions in intervening exons
30
What is a UTR
Untranslated regions at 5' and 3' ends. Part of the exon but doesn't code
31
Where does splicing occur (mRNA processing)
The spliceosomes in the nucleus
32
What are spliceosomes?
A large complex of proteins and small RNAs
33
What is alternative splicing
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.
34
What does alternative splicing allow for
Multiple gene products from the same gene, approximately 20,000 genes.
35
What does the mature mRNA transcript bind to?
Once it leaves the nucleus, the mature mRNA transcript binds to a ribosome
36
What are the three main steps of translation
Initiation, elogation and termination
37
Translation - defintion
Mature mRNA transcript exits the nucleus and is bound by the ribosome
38
What happens in translation
* 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
What does the tRNA and mRNA held within the ribosome enable
Ribosomes allow mRNA and tRNA to be held together closely, allowing formation of the polypeptide chain
40
Ribosome has binding sites for mRNA and tRNA, true or false
True
41
What is the 'A site'
(amino site)
holds 'next-in-line' tRNA
42
What is the P site
(peptidol)
Holds tRNA carrying the growing polypeptide
43
What is the E site
(exit)
tRNA's exit from here
44
What end of the mRNA does the small ribosomal subunit bind to?
It binds to the 5' cap of the mRNA
45
How do new amino acids arrive
via tRNA's
46
What is the function of the tRNAs
It is the physical link between the mRNA and the amino acid sequence of proteins
47
What way does the small ribosomal subunit scan?
Downstream
48
What amino acid does the initiator tRNA carry
Methionine (Met)
49
What bonds form between initiator anti-codon and mRNA
Hydrogen bonds
50
How is the initiation complex completed
When the large ribosomal subunit then binds
51
What is required for translation initiation assembly
Energy (GTP - guanosine triphosphate)
52
What are the three main steps of translation elongation
Codon recoginition, peptide bond formation and translocation
53
What is codon recognition (translation elongation)
* Base pairs with complementary anticodon.
* GTP invested to increase accuracy/inefficiency
54
What happens in peptide bond formation (translation elongation)
* A large subunit of rRNA catalyses peptide bond formation.
* Removes it from tRNA in P site
55
What happens in translocation (translation elongation)
* Moves tRNA from A to P site
* tRNA in P site moves to E and is released
* Energy is required (GTP)
56
What happens to the empty tRNA's in translation elongation
They are 'reloaded' in the cytoplasm using aminoacyl-tRNA synthetases
57
What are three main steps in translation termination
1. Ribosome reaches a stop codon on mRNA
2. Releases factor that promotes hydrolysis
3. Ribosomal subunits and other components dissociate
58
What happens when the ribosome reaches a stop codon on mRNA in translation termination (1)
mRNA stop codon in the A site is bound by a release factor
59
What happens when release factor promotes hydrolysis in translation termination (2)
Bond between p-site tRNA and last amino acid is hydrolysed, releasing polypeptide
60
What happens when ribosomal subunits and other components dissociate in translation termination (3)
* Hydrolysis of two GTP molecules required.
* Ribosomal components can be recycled.
61
What does translation termination require?
2 GTP
62
Why is gene expression regulated
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
What can regulatory proteins do
Block translation, variable mRNA life-spans
64
What are the control points in gene expression
* 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
Why is control of gene expression important
To achieve the right thing at the right time in the right place (also known as temporal and spatial control)
66
What are 'house-keeping' proteins
* Proteins that are continuosly produced as they are always needed in the cell.
* typically have longer half-life than cells
67
What is an example of a 'housekeeping' protein?
Tubulin for microtubules
68
How can a short-lived protein be produced as a result of cell signalling
* 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
What do the side chains (R groups) determine
The properties of each amino acid
70
Are electrically charged side chains hydrophobic or hydrophilic
Hydrophilic
71
Is 5' side of transcript the N-terminus or the C-terminus
N-terminus
72
What bonds hold amino acid sequences together
Covalent bonds
73
What does the polypeptide start to do as soon as it leaves the ribosome
Forms secondary structure
74
How do secondary structures form?
Form due to relatively weak hydrogen bonding between oxygen on the carbonyl group and hydrogen on the amine group
75
What are teritiary structures
3D shape stabilised by side chain interactions
76
What are quartenary structures
* Multiple proteins associate together to form a funtional protein
* Not all proteins form a quatenary structure
77
Where do proteins destined to function in the cytosol complete translation
Free ribosomes in the cytoplasm
78
Where do proteins that go through the endomembrane system complete translation
They complete translation at fixed ribosomes on the RER
79
What happens in the golgi for protein processing and sorting
Many proteins are processed and sorted through the RER and Golgi (but not all)
80
Where are signal peptides found
At N-terminus of the protein (~20aa)
81
What is an SRP
Signal recognition particle
82
What are the 6 steps in how signal peptides direct ribosomes to RER
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
What happens to secretory and membrane proteins at step 6 (when completed polypeptide folds into final conformation)
* 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
Why do post-translation modifications occur
Translation may be complete, but the protein may not yet be functional
85
Where are two places in the cell that post-translation modifications can occur
Within the Golgi or the cytosol
86
What do post-translation modifications do?
They can confer activity, ability to interact with other molecules, or direct to particular locations
