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Cell Structure & Function > From gene to protein > Flashcards

From gene to protein Flashcards

1
Q

What is gene expression?

A

The process of going from DNA to a functional product

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2
Q

Gene expression diagram

A

Cytoplasm with nuclear envelope and nucleus.
Inside the nucleus; During transcription, DNA turns into Pre-RNA DUring RNA processing to mRNA; translation occurs; ribosome & polypeptide

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3
Q

DNA (deoxyribonucleic acid) is the heritable material
that is ….

A

used to store and transmit information from
generation to generation

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4
Q

RNA (ribonucleic acid) acts as a messenger to…

A

allow the information stored in the DNA to be used to
make proteins

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5
Q

Proteins carry out …

A

cellular functions

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6
Q

What are the 3 main steps in gene expression ?

A

Transcription of RNA from DNA
Processing of the Pre-mRNA script
Translation of the mRNA to a protein

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7
Q

What occurs during Transcription?

A

1- Polymearase binds to promoter
2- moves downstream through the gene, transcribing rna
3-detaches after terminator reached

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8
Q

RNA uses what diff base?

A

RNA uses nitrogenous base uracil instead of DNA which uses thymine

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9
Q

Is RNA double stranded like DNA

A

No- it is single stranded

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10
Q

3 main steps in transcription?

A

Initiation
Elongation
Termination

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11
Q

initiation is..

A

Assembly of multiple proteins required before transcription can commence

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12
Q

is 5-3 coding (non-template) or non coding (template) strand

A

5-3 is non-template strand
3-5 is template strand

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13
Q

WHich EUkaroytic promoter is used?

A

TATA box 25nt upstream

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14
Q

what are the 3 steps of initation

A

1- a eukaroytic promoter
2- several transcription factors bind to DNA- Assembly of several transcription factors including
the TATA box binding protein (TBP)
3- transcription intitation complex forms- RNA Pol II can now bind along with more transcription
factors to form the transcription initiation complex

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15
Q

How many nucleotides are exposed at a time when DNA unwound?

A

10-20 nucleotides exposed at a time when DNA unwound

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16
Q

What happens during Elongation:

A

Complementary RNA nucleotides added to 3’ end of
growing transcript (3’OH of transcript binds with 5’ phosphate of
incoming nucleotide)

it forms a phosphodiester bond
Double helix reforms as transcript leaves the template strand

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17
Q

WHat happens during termination

A

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

Fidelity (proofreading) is less than for DNA replication

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18
Q

WHat are the 3 steps in mRNA processing

A

capping, tailing, splicing

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19
Q

Capping:

A

a modified guanine nucleotide is
added to the 5’ end

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20
Q

Tailing:

A

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

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21
Q

Why do capping & tailing occur

A

Capping and tailing are thought to facilitate export,
confer stability and facilitate ribosome binding in cytoplasm)

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22
Q

splicing?

A

Introns are removed from the transcript

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23
Q

Exons:

A

regions that remain in mature RNA (includes UTR)

24
Q

UTR:

A

untranslated regions at 5’ and 3’ ends of mRNA

25
Introns:
intervening regions that do not remain in mature RNA
26
Where does splicing occur?
At the spliceosome, within the nucleus
27
What is the spliceosome
Spliceosome: a large complex of proteins and small RNAs
28
What happens durinf splicing
Introns are removed from the transcript and exons are rejoined to form mature mRNA
29
ALternative splicing
is a process by which different combinations of exons are joined together. This results in the production of multiple forms of mRNA from the same pre-mRNA population. Alternative splicing allows for multiple gene products from the same gene ~20,000 genes, there could be many times that number of proteins!!
30
protein sequence determines ....
its final structure
31
structure determines..
function
32
DNA mutations can affect ...
ability of the protein to function
33
What happens in translation overview
Mature mRNA transcript exits nucleus and is bound by the ribosome Codons are translated into amino acids tRNA molecules within the cytosol with specific anticodons carry corresponding amino acids Hydrogen bonds form between mRNA and anticodon of the appropriate tRNA The amino acid is added via peptide bonds to the growing polypeptide chain
34
Ribosome has binding sites ....
for mRNA and tRNA
35
Is the mrna binding site on the ribosomes small or large subunit
small
36
Ribosome
A site: holds “next-in-line” tRNA P site: holds tRNA carrying the growing polypeptide E site: tRNAs exit from here
37
RNA is the physical link between ...
the mRNA and the amino acid sequence of proteins Transfer RNA (tRNAs) – the translatorObjective
38
Translation - initiation – a closer look
Initiator tRNA = tRNA carrying methionine (Met) Small ribosomal subunit with initiator tRNA already bound binds 5’ cap of mRNA Small ribosomal subunit scans downstream to find translation start site (AUG) Large ribosomal subunit then binds – completing the initiation complex Energy (GTP- Guanosine triphosphate) is required for assembly Initiator tRNA = tRNA carrying methionine (Met) Hydrogen bonds form between initiator anticodon and mRNA
39
translation - elongation – a closer look
Codon recognition: base pairs with complementary anticodon GTP invested to increase accuracy / efficiency Peptide bond formation: A large subunit rRNA catalyses peptide bond formation Removes it from tRNA in P site Translocation: moves tRNA from A to P site tRNA in P site moves to E and is released Energy is required (GTP) Empty tRNAs are ‘reloaded’ in the cytoplasm using aminoacyl-tRNA synthetases
40
translation - termination – a closer look
1- ribosome reaches a stop codon on mRNA mRNA stop codon in the A site is bound by a release factor 2- release factor promotes hydrolysis Bond between p-site tRNA and last amino acid is hydrolysed, releasing polypeptide 3- ribosomal subunits and other components disssacoaite Hydrolysis of two GTP molecules required Ribosome components can be recycled
41
Gene expression is tightly..
regulated
42
Multiple control points of gene expression..
Transcription factors need to assemble, and DNA needs to be accessible capping, extent of polyadenylation, alternate splicing, producing an mRNA able to be translated specific proteins assist in nuclear export of mRNA regulatory proteins can block translation, variable mRNA life-spans
43
Why is control of gene expression important?
to achieve the right thing at the right time in the right place!! (this is temporal and spatial control) Housekeeping (commonly used) proteins are continuously produced * protein and mRNA are present in large quantities (e.g. Tubulin) * typically, have longer “half life” in cells Other proteins are produced in response to stimuli as required * cell signaling (e.g. ligand binding a cell surface receptor, or activating an intracellular receptor) * signal transduced and may enter nucleus to activate transcription * results in the production of a short-lived protein to carry out the required function
44
Amino acid properties
The side chains (R groups) determine the properties of each amino acid There are twenty standard (coded for) amino acids
45
WHich is N terminus & C terminus
N- 5 C-3
46
Primary strcuture
Protein sequence (primary structure) is determined by DNA sequence Held by covalent bonds between amino acids (relatively strong) The polypeptide starts to form secondary structures as soon as it leaves the ribosome
47
Secondary structure
Held by weak hydrogen bonds to form alpha helix and beta sheets
48
Tertiary structure
3D shape stabilized by side chain interactions
49
Quatenary structure
Multiple proteins associate together to form a functional protein Not all proteins form quaternary structures
50
Protein processing and sorting
All translation commences on free ribosomes Many proteins are processed and sorted through the RER and Golgi – but not all Proteins destined to function in the cytosol – complete translation on free ribosomes Proteins that go through the endomembrane system - complete translation at fixed ribosomes on the RER
51
Signal peptides direct ribosomes..
to RER
52
Signal peptide
at N terminus of the protein (~20aa)
53
SRP
signal recognition particle
54
A secretory protein such as insulin is solubilized in lumen, while a..
membrane protein remains anchored to the membrane Both then go to the Golgi via vesicles for further maturation
55
Post‐translational modifications
Translation is now complete, but the protein may not yet be functional Common (there are 100s) post‐translational modifications include Phosphorylation (addition of a phosphate group) * Methylation (addition of a methyl group) * Acetylation (addition of an acetyl group) * Biotinylation (addition of biotin) * Carboxylation (addition of a carboxylic acid group) * Carbohydrate addition (particularly for membrane bound proteins, eg. glycoproteins) * Cleavage * Ubiquitination Can confer activity – eg. via phosphorylation or enzyme cleavage or ability to interact with other molecules – eg. biotinylation, methylation of histones or direct to particular locations – eg. ubiquitination for proteasome degradation Some occur within the Golgi, others in the cytosol modification errors could lead to non-functional proteins

Cell Structure & Function (6 decks)

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