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Bio 2 & 3 > Block 2. Lecture 9. From gene to protein > Flashcards

Block 2. Lecture 9. From gene to protein Flashcards

1
Q

Three main steps of gene expression

A

Transcription of RNA from DNA
Processing of the pre-mRNA transcript
Translation of the mRNA transcript to a protein

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2
Q

RNA

A

RNA (ribonucleic acid) acts as a messenger to allow the information stored in the DNA to be used to make proteins

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3
Q

Multiple control points in gene expression

A
  1. Transcription. Controls whether it happens in the first place.
  2. capping, extent of polyadenylation, alternate splicing, producing an mRNA able to be translated
  3. specific proteins assist in nuclear export of mRNA
  4. regulatory proteins can block translation, variable mRNA life-spans. In the ribosome. ( short-lived or long-lived)
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4
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

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5
Q

Three steps of transcription

A

Three steps:

  1. Initiation. Polymerase binds to promoter.
  2. Elongation. moves downstream through the gene, transcribing RNA.
  3. Termination. Detaches after terminator reached
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6
Q

Pairs of bases DNA to mRNA

A

A-U
T-A
G-C
C-G

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7
Q

RNA vs DNA structure

A

RNA uses the nitrogenous base Uracil, in place of Thymine and it is single stranded, while DNA is double stranded.

Thiamine is more stable than uracil. It is more important for DNA to be stable and protect the heritable information

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8
Q

Initiation phase of transcription

A

Assembly of multiple proteins required before transcription can commence

  1. A eukaryotic promoter. A sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter. TATA box typically ~25nt upstream
  2. Several transcription factors bind to DNA. Assembly of several transcription factors including the TATA box binding protein (TBP)
  3. Transcription initiation complex forms. RNA Polymerase II can now bind along with more transcription factors to form the transcription initiation complex
    transcription begins..…
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9
Q

Transcription- elongation & termination

A

10-20 nucleotides exposed at a time when DNA unwound

Elongation: Complementary RNA nucleotides added to 3’ end of growing transcript (3’OH of transcript binds with 5’ phosphate of
incoming nucleotide)
Double helix reforms as transcript leave the template strand. IT FORMS A PHOSPHODIESTER BOND BETWEEN RNA MOLECULES/NUCLEOTIDES

Termination: 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

The pre-mRNA transcript is now ready for further processing

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10
Q

BONDS in transcription( elongation and termination)

A
  • When the DNA strands separate the Hydrogen bonds break
  • Hydrogen bonds form between RNA nucleotides and the bases on the template strand of the DNA
  • Phosphodiester bonds form between the RNA nucleotides. Stronger than H-bonds. Once they are formed the H-bonds dissociate.
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11
Q

mRNA processing- capping, tailing, and splicing

A

Capping: a modified guanine nucleotide is added to the 5’ end

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

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

Splicing: introns are removed from the transcript

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12
Q

EXONS

A

coding regions( inc. UTRs) become parts of the protein APART FROM UTRs

the regions that get spliced together

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13
Q

INTRONS

A

non-coding regions intervening exons

get spliced out and removed from the RNA to create mRNA

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14
Q

UTR

A

untranslated regions at 5’ and 3’ ends. Do not become part of protein.

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15
Q

Where and how does splicing occur?

A

At the spliceosome within the nucleus. Within the spliceosome there are small RNAs

Spliceosome: a large complex of proteins and small RNAs

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

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16
Q

Alternative splicing

A

Alternative splicing is a process by which different combinations of exons are joined together. ( different introns removed). This results in the production of multiple forms of mRNA from a single pre-mRNA

Gene–> multiple different proteins produced

Alternative splicing allows for multiple gene products from the same gene
~20,000 genes, there could be many times that number of proteins!!

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17
Q

Translation

A

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

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18
Q

Three main steps of translation

A

initiation, elongation, termination

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19
Q

Binding sites within the ribosome

A

mRNA binding site on small subunit

A site( aminoacyl-tRNA binding site): holds “next-in-line” tRNA

P site(peptidyl-tRNA binding site): holds tRNA carrying the 
growing polypeptide

E site: tRNAs exit from here

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20
Q

Translation- elongation

A

Codon recognition:
tRNA 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)

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21
Q

Translation-termination

A

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

Release factor promotes hydrolysis
Bond between p-site tRNA and last amino acid is hydrolysed, releasing polypeptide

Ribosomal subunits and other components dissociate
Hydrolysis of two GTP molecules required
Ribosome components can be recycled

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22
Q

how many standard( coded for) amino acids are there?

A

20

23
Q

What determines the properties of each amino acid

A

the side chains(R groups)

Nonpolar(hydrophobic); Polar(hydrophillic); Electrically charged hydrophillic( + -)- Acidic and Basic

24
Q

Which end is N-terminus

A

Amino 5’ mRNA end

25
Q

Which end is C-terminus?

A

Carboxyl end

3’ mRNA

26
Q

What bonds are between amino acids?

A

covalent

27
Q

When do proteins start to form secondary structures?

A

As soon as they leave the ribosome

28
Q

Secondary structure

A

alpha helix
beta pleated sheet
beta strand

29
Q

What bonds are present in the secondary structures

A

hydrogen bonds(weak)

30
Q

Tertiary structure

A

transthyretin polypeptide

3D shape stabilized by side chain interactions

31
Q

Quaternary structure

A

transthyretin protein

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

32
Q

What directs ribosomes to the RER to finish protein synthesis

A

signal recognition particle

33
Q

Common post-translational modifications

A
  • 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
34
Q

Why post-translational modifications occur?

A

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

35
Q

bond between amino acids

A

peptide bond

36
Q

promoter

A

In genetics, a promoter is a sequence of DNA to which proteins bind to initiate transcription of a single RNA transcript from the DNA downstream of the promoter

the promoter has a binding site for the enzyme( polymerase) used to make a messenger RNA (mRNA) molecule.

37
Q

How many nucleotides are exposed at a time when the DNA is unwound

A

10-20

38
Q

polyadenylation signal for termination of transcription

A

AAUAAA

39
Q

Starting codon on the the mRNA where translation begins

A

AUG

40
Q

What is required for the assembly of ribosomal units

A

energy 1 GTP

41
Q

when is energy used (GTP)

A

combining of the ribosomal units

during elongation( formation of the amino acid chain) when new tRNA comes into A. And when tRNA leaves from E

2 GTP is used when all the ribosomal units dissociate. ( hydrolysis of 2 GTP molecules)

42
Q

what amino acid does initiator tRNA carry?

A

methionine(Met)

43
Q

signal peptides

A

Signal peptides (SP) are short peptides located in the N-terminal of proteins, carrying information for protein secretion.

44
Q

release factor

A

binds to the stop codon on mRNA during translation and promotes hydrolysis

The bond between P-site( EPA) t RNA and the last amino acid is hydrolyzed, releasing polypeptide.

45
Q

polypeptide

A

the polymer of amino acids joined together by peptide bonds.

46
Q

nucleotide

A

the basic building block of nucleic acids. RNA and DNA are polymers made of long chains of nucleotides. A nucleotide consists of a sugar molecule (either ribose in RNA or deoxyribose in DNA) attached to a phosphate group and a nitrogen-containing base.

47
Q

What is added to the 5’ end of the mRNA during capping?

A

a modified guanine nucleotide is added to the 5’ end( guanine cap)

protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein.

48
Q

What is added to the 3’ end of mRNA during tailing?

A

50-250 adenine nucleotides (polyA) are added to the 3’ end
The poly-A tail makes the RNA molecule more stable and prevents its degradation. Additionally, the poly-A tail allows the mature messenger RNA molecule to be exported from the nucleus and translated into a protein by ribosomes in the cytoplasm.

49
Q

transcription initiation complex

A

complex of transcription factors and RNA Polymerase 2 bound to the promoter

50
Q

promoter

A

part of the gene that includes the start point and typically extends several dozen of nucleotides upstream from the start point.
TATA box is included in the promoter.

51
Q

Role of transcription factors

A

Transcription factors are required for RNA pol II binding to promoter. TFs are DNA binding proteins, but can also bind other TFs. They assist in bringing RNA pol II in close proximity of the promoter.

51
Q

Role of transcription factors

A

Transcription factors are required for RNA pol II binding to promoter. TFs are DNA binding proteins, but can also bind other TFs. They assist in bringing RNA pol II in close proximity of the promoter.

52
Q

how does splicing occur

A

in the spliceosome

small nuclear RNA recognize the splice sites

53
Q

N and S terminus

A

The N-terminus (also known as the amino-terminus, NH2-terminus, N-terminal end or amine-terminus) is the start of a protein or polypeptide referring to the free amine group (-NH2) located at the end of a polypeptide.

The end with a free carboxyl group is called the C-terminal amino acid residue.

Bio 2 & 3 (8 decks)

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