2C: protein structure and translational and post-translational gene regulation Flashcards
define translation
the assembly of amino acids into polypeptides on ribosomes
what is the general structure of amino acids?
central C atom attached to amino group (-NH2), carboxyl group (-COOH), an H atom, and an R group
how are amino acids joined together?
through covalent peptide bonds between the amino group and carboxyl group by a dehydration reaction.
what is a polypeptide?
linear chain of amino acids linked by peptide bonds
how can nonpolar amino acids be identified?
the R group never has any O and has no charged groups
how can uncharged polar amino acids be identified?
their R groups contain one O but have no charges anywhere.
how can negatively charged polar amino acids be identified?
their R groups contains two Os and have a negative charge on one of the Os.
how can positively charged polar amino acids be identified?
their R groups contain no O, but have a positively charged NH3+, H2N+, or NH+ in the upper left/top
what are aromatic amino acids?
amino acids whose R group contains a carbon ring with alternating single and double bonds
which amino acid is always the first one in a polypeptide?
methionine
which amino acid causes kinks in polypeptide chains?
proline
which amino acid causes disulfide bridges?
cysteine
what is methionine?
the first amino acid in a polypeptide (coded by the start codon)
what is proline?
the amino acid that causes kinks in polypeptide chains
what is cysteine?
the amino acid that causes disulfide bridges, contributing to the structure of polypeptides
what is the primary level of protein structure?
the amino acid sequence
what is the 2° level of protein structure?
alpha-helix/beta-sheet. depends on H bonding in polypeptide backbone
what is the 3° level of protein structure?
the 3D structure of a single polypeptide
what is the 4° level of protein structure?
interactions between two or more polypeptides, forming a mutlisubunit protein
what are two things that can disrupt protein folding?
denaturation (through heat or chemicals) or mutations that change amino acid sequence
what are chaperones? (protein structure)
helping groups that function by temporarily binding to newly synthesized proteins, helping them to fold correctly
what are 3 diseases associated with misfolded proteins?
➝ Alzheimer’s
➝ Parkinson’s
➝ Creutzfeldt-Jakob
what is the function of tRNAs?
to bring amino acids to the ribosome for addition to the polypeptide chain
what is the N-terminal end?
the end of a polypeptide where assembly started (the beginning of the polypeptide)
what is the C-terminal end?
the end of a polypeptide where assembly ended
what is an anticodon?
a 3-nucleotide segment that base-pairs with codons in mRNA. (binds antiparallel to the codon, like usual)
what is the structure of tRNA?
tRNA base-pair w/ themselves and wind into a four double-helical segments. at the tip of one segment is the anticodon. opposite to the anticodon is a free 3’ end (the accepter stem) that links to the amino acid corresponding to the anticodon.
what is a sense codon?
a codon in mRNA that codes for an amino acid and corresponds to an anticodon in tRNA
what is the wobble hypothesis?
the 61 sense codons can be read by less than 61 anticodons because the pairing between the anticodon and the codon is flexible for the last base (the one at the 3’ end of the codon). therefore, several codons with the same first two bases but different third bases can bind to the same anticodon (depending on the 5’ base of the anticodon).
what is inosine?
a purine base present in tRNA that can bind to any base in mRNA except for G when at the 5’ end of the tRNA.
what is aminoacylation/charging?
the process of adding an amino acid to tRNA
what is aminoacyl-tRNA?
tRNA linked to its corresponding amino acid
what are aminoacyl-tRNA synthetases?
a collection of different enzymes that catalyze aminoacylation
what is the aminoacylation/charging reaction?
amino acid ＋ tRNA ＋ ATP ➞ aminoacyl-tRNA ＋ AMP ＋ PPi
what are the steps of aminoacylation?
① ATP and the amino acid bind to the aminoacyl-tRNA synthetase. the enzyme catalyzes the joining of the amino acid to AMP with the release of two phosphates
② the correct tRNA binds to the enzyme
③ the enzyme transfers the amino acid from amino acid AMP (AA-AMP) to the tRNA, forming AA-tRNA. AMP is released.
④ AA-tRNA is released from the enzyme, and the enzyme is ready to go to step 1 again
what is the start sense codon? what does it code for?
AUG. codes for methionine
what are the stop codons? what do they code for?
UAA, UAG, and UGA. do not code for amino acids
define ribosome
ribonucleoprotein particles that carry out protein synthesis by translating mRNA into chains of amino acids
what is the large subunit (ribosome)?
made up of rRNA and proteins (more than the small subunit), contains the peptidyl-transferase centre for formation of peptide bonds
what is the small subunit (ribosome)?
made up of rRNA and proteins (less than the large subunit), contains the decoding centre where charged tRNAs read and decode the codon of mRNA. determines which amino acid is to be attached
what is the svedberg unit?
(symbol: S)
measure of sedimentation velocity and, therefore, mass. used to measure the size of the subunits of the ribosome
are the two subunits that make up the ribosome always together?
no. they’re separate when in the cytoplasm, but join together on the mRNA molecule
are ribosomes the same in bacteria and in eukaryotes?
no. the structures differ slightly and eukaryotic ribosomes are slightly bigger
what are the 3 binding sites in ribosomes?
① A site (aminoacyl site)
② P site (peptidyl site)
③ E site (exit site)
what is the function of the A site?
the function of the aminoacyl site is to bind to the tRNA carrying the next amino acid to be added
what is the function of the P site?
the peptidyl site is where tRNA attached to the growing peptide chain binds
what is the function of the E site?
the exit site is where exiting tRNA binds as it leaves the ribosome
what are the three stages of translation?
same as transcription:
① initiation
② elongation
③ termination
define initiation (translation)
the first step where the translation components assemble on the start codon of the mRNA
what are the steps of translation initiation?
① specialized methionine-tRNA with GTP bound to it binds to the P site of the small ribosomal subunit and forms a complex.
② the complex binds to the 5’ cap end of the mRNA and scans along the mRNA in a 5’-3’ direction until the first start codon reaches the P site.
③ base pairing occurs between the start codon and the tRNA.
④ the large ribosomal subunit binds to the small subunit to form the initiation complex.
⑤ the GTP is hydrolyzed to GDP and elongation can begin.
what is the reading frame?
the correct frame for reading codons correctly, 3 bases at a time. determined by the binding of the met-tRNA to the start codon
define elongation (translation)
the assembled complex (ribosome) reads the string of codons in mRNA one at a time while joining the specified amino acids into the polypeptide
what is the EF?
the elongation factor is a protein bound to the aminoacyl-tRNA, which is released once the tRNA binds to the codon
what powers the ribosome along the mRNA?
GTP hydrolysis
what is peptidyl transferase?
enzyme in the large ribosomal subunit that catalyzes the formation of the peptide bond in the amino acid chain
what are the steps of translation elongation?
① an aminoacyl-tRNA binds to the corresponding codon in the A site (facilitated by EF-GTP)
② peptidyl transferase cleaves the amino acid from the tRNA in the P site and forms a peptide bond between it and the amino acid on the tRNA in the A site.
③ the ribosome translocates along the mRNA to the next codon. since the two tRNA remain bound to their respective codons, they are shifted down to the E site and P site.
④ empty tRNA is released from the E site. sites E and A are once again empty, back to step 1.
how does translation elongation compare in bacteria and eukaryotes?
it is very similar, but occurs much faster in bacteria than eukaryotes
define termination (translation)
the final step that completes the translation process when the complex disassembles after the last amino acid specified by the mRNA has been added to the polypeptide
what is the RF?
the release factor (or termination factor) is a protein that binds to the A site and causes the ribosome to disassemble into its subunits. does not base pair w/ the stop codons (bc its a protein, not RNA), just outcompetes the tRNA for the position at the A site because there are no tRNA corresponding to the stop codons.
what are the steps of translation termination?
① a stop codon reaches the A site of the ribosome.
② the RF binds to the A site.
③ the RF stimulates peptidyl transferase to cleave the polypeptide from the tRNA in the P site, and it is released.
④ the empty tRNA and RF are released, and ribosomal subunits separate and leave the mRNA
what is DNA methylation?
addition of methyl groups directly to DNA bases by methylation enzymes, thereby preventing the binding of transcription factors to the area, turning the gene off.
how is eukaryotic DNA organized in chromatin?
DNA is wrapped around a core of two molecules each of histones H2A, H2B, H3, and H4, forming the nucleosome. organized further by histone H1 linking adjacent nucleosomes
what is acetylation of histone tails?
the loosening of histone tails in chromatin to allow trancription to occur
what function does acetylation of histone tails serve?
it converts the chromatin from the normal (inactive) form to the active form
what is the process of acetylation of histone tails?
① regulatory transcription factor binds to a sequence associated with a gene, recruiting protein complexes that include histone acetyltransferase.
② histone acetyltransferase adds acetyl groups to specific amino acids of the histone tails
③ acetylation changes the charge of the histone tails and results in a loosening of the association of the histones with the DNA.
what is histone acetyltransferase?
an enzyme that adds acetyl groups to specific amino acids of the histone tails
what is chromatin remodelling?
change in chromatin structure as a result of acetylation of histone tails or of displacement of nucleosomes in the promoter region from the DNA by multiprotein complexes
what does histone deacetylase do?
catalyzes the removal of acetyl groups from histone tails, causing them to tighten around the DNA again
what does histone methylation do?
inactivates genes (reversible)
what is the histone code?
a regulatory mechanism for altering chromatin structure, thereby affecting gene activity based on signals in histone tails represented by chemical modification patterns.
how do poly(A) tails affect translation?
longer tails mean increased translation, shorter tails mean decreased translation
what are 3 types of post-translational regulation?
① phosphorylation
② ubiquitination
③ proteolysis
what is phosphorylation (relating to regulation)?
addition of phosphate to proteins by kinases. can activate or inhibit the activity of these proteins
what is ubiquitination?
addition of a ubiquitin molecule (“doom tag”) to a protein to mark it for destruction by a proteasome
what is proteolysis?
specific cleavage of a protein that can induce activity (ex: proteolysis of viral envelope trigger maturation of HIV)
what is translational regulation?
control of protein synthesis
what is post-translational regulation?
control of protein abundance and activity (availability of functional proteins)
what does the abundance of protein depend on?
➝ rate of synthesis (translational initiation)
➝ rate of degradation (post-translational regulation)
what does the activity of proteins depend on?
➝ post-translational modifications (like phosphorylation)
➝ processing (like cleavage)
how is expression level of a specific gene defined/determined?
through the abundance of protein from that gene and their activity
define epigenetics
“on top of genetics”: post transcriptional modification of histones that affect transcription
