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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
Q

Introns:

A

intervening regions that do not remain in mature RNA

26
Q

Where does splicing occur?

A

At the spliceosome, within the nucleus

27
Q

What is the spliceosome

A

Spliceosome: a large complex of proteins and small RNAs

28
Q

What happens durinf splicing

A

Introns are removed from the transcript and exons
are rejoined to form mature mRNA

29
Q

ALternative splicing

A

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
Q

protein sequence determines ….

A

its final structure

31
Q

structure determines..

A

function

32
Q

DNA mutations can affect …

A

ability of the protein to function

33
Q

What happens in translation overview

A

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
Q

Ribosome has binding sites ….

A

for mRNA and tRNA

35
Q

Is the mrna binding site on the ribosomes small or large subunit

A

small

36
Q

Ribosome

A

A site: holds “next-in-line” tRNA
P site: holds tRNA carrying the
growing polypeptide
E site: tRNAs exit from here

37
Q

RNA is the physical link between …

A

the mRNA and the amino acid sequence of proteins
Transfer RNA (tRNAs) – the translatorObjective

38
Q

Translation - initiation – a closer look

A

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
Q

translation - elongation – a closer look

A

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
Q

translation - termination – a closer look

A

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
Q

Gene expression is tightly..

A

regulated

42
Q

Multiple control points of gene expression..

A

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
Q

Why is control of gene expression important?

A

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
Q

Amino acid properties

A

The side chains (R groups) determine
the properties of each amino acid

There are twenty standard (coded for) amino acids

45
Q

WHich is N terminus & C terminus

A

N- 5
C-3

46
Q

Primary strcuture

A

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
Q

Secondary structure

A

Held by weak hydrogen bonds to
form alpha helix and beta sheets

48
Q

Tertiary structure

A

3D shape stabilized by
side chain interactions

49
Q

Quatenary structure

A

Multiple proteins associate
together to form a functional
protein
Not all proteins form
quaternary structures

50
Q

Protein processing and sorting

A

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
Q

Signal peptides direct ribosomes..

A

to RER

52
Q

Signal peptide

A

at N terminus of the protein (~20aa)

53
Q

SRP

A

signal recognition particle

54
Q

A secretory protein such as insulin
is solubilized in lumen, while a..

A

membrane protein remains
anchored to the membrane
Both then go to the Golgi via
vesicles for further maturation

55
Q

Post‐translational modifications

A

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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