Theme 2C Flashcards by Daddy Longlegs

What are the three steps of translational regulation of gene expression?

Initiation
Elongation
Termination

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What is Translation?

assembly of amino acids into polypeptides

aa contain amino & carboxyl group bonded to central carbon (a) with a hydrogen and R group

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Two amino acids are joined together by a covalent ________ bond between the ______ and ________ by a ____________

peptide; amino; carboxyl; dehydration reaction

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Polypwptides are

linear chains of amino acids linked by peptide bonds

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Type of Amino Acid

Non-polar Amino Acid

R groups usually contain -CH2 or -CH3

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Type of Amino Acid

Uncharged polar amino acid

R groups usually contain oxygen (-OH)

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Type of Amino Acid

Charged amino acid

R groups that contain acids or bases that can ionize

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Type of Amino Acid

Aromatic amino acid

R groups contain a carbon ring with alternating single and double bonds

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Special Functional amino acid

Methionine

first amino acid in polypeptide

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Special Functional amino acid

Proline

causes kink in polypeptide chains

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Special Functional amino acid

Cysteine (S-S)

What does the S-S contribute to?

disulfide bridge contributes to structure of polypeptides

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Levels of protein structure

Primary amino acid sequence

what does it determine?

protein folding and 3-D structure which is critical for proper function

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Levels of protein structure

2º Structure

what does it depend on?

hydrogen bonding in polypeptide backbone (a-helices & b-sheets)

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Levels of protein structure

3 structure

3-D structure of a single polypeptide and is composed of interactions between amino acid side chains

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Levels of protein structure

4 structure

are interactions between more than one polypeptide to form a multisubunit protein

(ie. hemoglobin)

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Levels of protein structure

Protein folding is disrupted by ______ or ________

denaturation or mutations that change amino acid sequence

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Levels of protein structure

Chaperones function to

protect slow-folding or denatured proteins by preventing their aggregation

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tRNAs

adaptors between codons (mRNA) and amino acids

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slide 6 - tRNA

2-D cloverleaf and 3-D L-shaped folded RNA molecule from

self complementarity

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tRNA

Acceptor stem is

where the amino acid is attached and contains the sequence 5’-CCA-3’ at the 3’ end of the tRNA

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tRNA

The anti-codon is the ________ loop of the cloverleaf and contains three nucleotide sequence that recognize the ___________ by _______________ with mRNA

bottom; codon; base pairing

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What type of base pairing?

____________ base pairing between codon and anticodon in tRNA

antiparallel

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Aminoacyl-tRNA charging

Aminoacyl-tRNA synthease adds

(charging) adding the amino acid to the tRNA

the amino acid to the acceptor stem of the correct tRNA

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Aminoacyl-tRNA (Charging)

Charging Reaction (Aminoacylation)

What is the equation?

amino acid + tRNA + ATP –> aminoacyl-tRNA + AMP + PPi

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The genetic code consists of | 2 things

61 "sense" codons and amino acids specified by them

# Genetic code The codons are written | in what direction?

5'-3', as they appear on mRNA

# Genetic Code AUG (Methionine) | What is it?

initiation (start) codon

# Genetic code UAA, UAG, UGA | are what type of codons?

termination (stop) codons

# Genetic Code The genetic code shows _________ in which an amino acid can be specified by _____________

degeneracy; more than one codon

# Rules of the Genetic Code In what direction are codons on mRNA read?

5'-3' direction

# Rules of Genetic Code Codons are ______________________ and the message contains no __________

non-overlapping; gaps

# Rules of Genetic Code The message is translated in a ________________ by the start codon

fixed reading frame

# Frames Is it neccessary that translation always start at the start codon?

What are the three reading frames

1+, 2+, 3+

Why are there only three and not four frames?

Because 4+ would be the same as 1+

What is the most likely frame that encodes for polypeptide

Are there 61 different tRNAs that bind to the 61 mRNA codons?

There are less than 61 tRNAs because

tRNAs can read more than one codon

Why can tRNAs read more than one codon?

Because base at 5' end of anticodon can form H-bonds with more than one type of base located at the 3' end of a codon "wobble"

Is there wobble during pairing of the other two nucleotides in the anti codon with the codon | not the nucleotide at 5' end

Ribosome | (prokaryotes)

protein synthesis machinery

Ribosome is composed of ___________________ made of a complex of ______________ and ________________

two subunits; proteins; rRNA

# Ribosomes (prokaryotes) The large subunit (50S) is made of ________________ and contains _________________________ for _________________.

5S and 23S rRNA + 34 proteins; peptidyltransferase center; formation of peptide bonds

# Ribosomes (prokaryotes) Small subunit (30S) is made of ________________ and contains ____________ where ____________________ & ________________.

16S rRNA + 21 proteins; decoding center; charged tRNAs read and decode the codon of mRNA ## Footnote based on anti-codon codon binding through parallel complimentary base-pairing

# Ribosomes (prokaryotes) S (svedberg unit)

measure of seidmentation velocity, and, therefore, mass

# Ribosomes (prokaryotes) each subunit exists separately in the ___________ but the two join together on the __________ molecule

cytoplasm; mRNA

# tRNA binding sites of ribosomes What are the three tRNA binding sites of ribosomes?

1. Aminoacyl (A) 2. Peptidyl (P) 3. Exit (E)

# tRNA binding sites of ribosomes P site (peptidyl)

binds to the tRNA attached to the growing peptide chain

# tRNA binding sites of ribosomes A site (aminoacyl)

binds to the tRNA carrying the next amino acid to be added

# tRNA binding sites of ribosomes E site (exit)

binds to the tRNA that carried the previous amino acid added

# Translation Initiation (eukaryotes) An ______________________ containing the ribosome, mRNA, and the initiator tRNA bound to methionine is formed during translation initiation

initiation complex

What are the steps for translation initiation in eukaryotes

- initiator tRNA met is brought to the P-site of the small ribosome subunit (reaction requires GTP) - complex of initiator tRNAmet and small ribosomal subunit is recruited to the capped 5'-end of mRNA & scans along the mRNA in a 5'-3' direction until it reaches the first 5'-AUG-3' start codon - complimentary base pairing occurs between anticodon of initiator tRNAmet and start codon of mRNA - Large ribosomalsubunit binds to small subunit to form the initiation complex, which is now ready to accept the first tRNA in the A-site - GTP is hydrolyzed to GDP and translation begins

# Translation elongation: growth of the polypeptide What are the steps? | 4 steps

1. correct aminoacyl tRNA is loaded to A site by **Elongation Factor-GTP** (tRNA anticodon is compliemntary to mRNA codon in the A-site) 2. Peptidyl transferase in the large subunit forms a peptide bond between carboxyl group of growing polypeptide and the amino group of the amino acid in the A site (tRNA in P site is uncharged) 3. Ribosome translocate in which the tRNA with the polypeptide shifts from A to P site, and uncharged tRNA shifts from P to E site where it is ejected 4. The next codon of the mRNA is now A site and next aminoacyl tRNA can be loaded by EF-GTP

The three stop codons are found at _________________

end of a protein coding sequence ## Footnote UAA, UAG, UGA

Stop codons are recognized by

proteins called release factor

when ribosome reaches the stop codon, the release factor binds the A-site and stimulates __________________________________________ to _______________________________

peptidyl transferase; cleave polypeptide from P-site tRNA

# Part 2 Posttranslational Regulation of Gene Expression | 3 STEPS

1. Phosphorylation 2. Ubiquitination 3. Proteolysis

# Posttranslational regulation of proteins Phosphorylation

addition of phosphate to proteins by kinases, which can activate or inhibit their activity ## Footnote Example: CDK1 phosphorylates and activates MAP to promote spindle assembly and mitotic entry

# Posttranslational regulation of proteins Ubiquitination

addition of ubiquitin molecules to proteins target them for destruction by the proteasome ## Footnote Example: cylclin is destroyed at the end of mitosis to inactivate CDK1

# Posttranslational regulation of proteins Proteolysis

specific cleavage of the protein can induce activity | done by enzyme protease ## Footnote Example: proteolysis of viral envelope glycoprotein triggers maturation of HIV

Epigenetics

posttranslational modification of histones that affect transcription

# Epigenetics Changes in gene transcription occurs ______________________

without changes in DNA sequence

# Epigenetics Modifications to ______________ on ______________________ affect transcription of genes (histone code). This is a translational/posttranslational event.

lysines; histone tails (have + charge); posttranslational

# Epigenetics Histone acetyltransferase (HATs) that add _________________ to histone tails increase gene transcription by losening DNA binding! Why?

acetyl groups (CH3CO-); because histones negative and DNA is negative, so repulsive forces causes DNA to loosen

# Epigenetics ___________________ of histone tails can activate and repress transcription of genes

methylation

# Epigenetics DNA can be _________________________ at ________________ close to promoter repressing transcription

methylated; CpG islands

# Epigenetics ______________________________ displaces nucleosomes from promoter regions (ATP-dependent) activating transcription

Chromatin remodelling complex

# Level of gene regulation Translational regulation

control of protein synthesis (rate of trnaslation initiation or formation of the initiation complex)

# Level of gene regulation Posttranslational regulation

control of protein abundance & activity ## Footnote ie. availability of functional proteins

# Level of gene regulation Abundance of protein depends on its rate of _________________________ (translation initiation) and ____________________ (posttranslational)

synthesis; degradation

# Level of gene regulation Activity of protein depends on ___________________________ and _____________________________ (cleavage)

posttranslational modifications; processing

# Level of gene regulation The expression level of a specific gene depends on the ______________________ & ___________________

abundance of proteins; its activity

# rEVIEW slide 20

# 4 Levels Levels of Eukaryotic Gene Regulation

1. Epigenetics (Chromatin remodelling) 2. Transcriptional (mRNA synthesis) 3. Post-transcriptional (mRNA processing) 4. Translation (protein synthesis) 5. Post-translation (protein processing)

# Levels of Eukaryotic Gene Regulation Changes at any level of gene regulation would potentially _______________

alter protein expression and cause variation in phenotype

Theme 2C Flashcards

Protein Structure & Translational and Posttranslational Gene Regulation (76 cards)