Chapter 15 - The Genetic Code & Translation Flashcards
Which of the following is considered a secondary structure of proteins? A. Hairpin loops B. Helix-turn-helix domains C. Stem-loops D. Alpha helix E. Zinc fingers
D. Alpha helix
If instead of 20 amino acids there were 200 amino acids, what would you predict would be the minimum number of bases per codon?
4 bases per codon
4^4 = 256 (base = possible nucleotides; exponent = number of bases per codon)
AGG (tRNA) / UCC (mRNA): What is the first nucleotide at the 5’end of the anticodon if mRNA is 5’ - 3’?
G
Any given mRNA sequence has __ possible reading frames, and the correct one is determined by a(n) __ codon.
Any given DNA sequence has __ possible reading frames.
3; start / initiation codon (almost always AUG)
6 (3 per strand until the template strand is determined).
Suppose you have identified a segment of genomic DNA that contains the YFG locus.
How many possible reading frames are there for the ORF of the mRNA?
Six.
Initially, you do not know which strand is the sense strand for the YFG gene. Each strand has 3 possible reading frames. Therefore, there are 6 possible reading frames until the sense strand is established.
Poly(U) is translated into a polypeptide consisting of all phenylalanine. Poly(C) is translated into a polypeptide consisting of all proline. When a random co-polymer of U and C is made, a protein consisting of the four amino acids—leucine, phenylalanine, proline, and serine—is made even though there are eight possible codons. From this finding, it is possible to conclude that:
A. some of these four amino acids are specified by more than one codon.
B. the genetic code must be a triplet code.
C. there is only one codon each for phenylalanine and proline.
D. there are three different codons for both serine and leucine.
A. some of these four amino acids are specified by more than one codon.
Might be D, but you can’t assert that without proof!
Which statement is true regarding the binding of an amino acid to a tRNA?
A. Amino acids bind to the 5’ end of the tRNA.
B. The binding of amino acids to tRNAs requires GTP.
C. There is one aminoacyl tRNA synthetase for each of the 20 amino acids.
D. Each aminoacyl tRNA synthetase recognizes a different tRNA.
C. There is one aminoacyl tRNA synthetase for each of the 20 amino acids.
The one gene, one enzyme hypothesis evolved to the one gene, one ___; then to one gene, two or more related polypeptides called ___ or ___.
polypeptide; isoforms or variants
What roles to proteins fill? (CREDS)
communication; regulation; enzymes, defense (immunity); structure
All amino acids have 4 parts to their basic structure: a ___ _ atom, a ___ atom, an ___ group; a ___ group; and an _ group
central C; hydrogen; amino; carboxyl; R
There are __ major categories/groups of amino acids; therefore, if one is switched within the __ group, the overall effect will likely be __. Exceptions include __ (because they’re rare and designate the starting point); __ (due to disulfide bonds that are critical to proteins and their structure); and __ (they often cause bends in polypeptides).
5; same; minimal
Met (methionine); Cys (cysteine); Pro (proline)
__ (an AA) is fairly rare, often plays a role in __ activity, is one of 2 AA’s with a _ atom; has only one codon which is the ‘start’ codon (___).
Met (M); enzymatic; sulphur; AUG
T or F: R groups with aromatic rings are hydrophilic
false; benzene and other hydrocarbon rings (think crude oil) is hydrophobic
__ is one of two AAs that have a __ atom, and are important because they form __ bonds.
Cys (C); sulphur; disulfide
__ is an amino acid that often leads to bends in a __. In addition, it has no free __ group.
Pro; polypeptide
amino
These two AAs are prominent in histones.
Lys (K); Arg (R)
__ is an AA that is usually positive, but small changes in pH can change it to ___.
His (H); neutral
Peptide bonds of AAs form between the __ group of one AA and the ___ group of the next AA. These bonds form due to a __ reaction.
The peptides that are formed have ___ with the __ group being positively charged (corresponding to the _’ end of the mRNA) and the __ being negatively charged (corresponding to the _’ end).
carboxyl; amino
condensation
polarity; amino; 5’; carboxyl; 3’
Polypeptides are linear __ of AAs; proteins are several subunits of ___.
polymers; polypeptides
Protein structure: the primary structure is the __ __; the secondary structure includes 2 sub-structures: β __ __ and 𝜶 __ (both form as a result of __ bonding between __ and an __ atom); tertiary structure is the overall __-__ shape (most __ stable form); and quaternary structure includes __ between 2 or more ___. Single polypeptide structure ends with the __ structure.
AA sequence
pleated sheet; helix; hydrogen; H; electronegative
three-dimensional; thermodynamically
interactions; polypeptides
tertiary
In general, what are codons, and what do they specify?
group of 3 nucleotides that specify an AA or a “stop production” signal.
There are __ possible codons, however, __ code for AAs (called __ codons). The other 3 are __ codons. Since there are only __ major AAs, the genetic code is said to be a __ code meaning that one AA can be coded by __ or __ codons (most have __, some as many as __; but __ and __ have only __).
64; 61; sense.
stop
20; degenerative; 2 or more; 4; 6; Met (M) and Trp (W); 1
__ codons code for the same AA. ___ tRNAs can be charged with the same AA - they differ in their ___ which presents a problem: most organisms have __ tRNAs than codons. __ solves this by enabling __ tRNAs to pair with __ codons that differ in the __ position (this position is a little “__” with its pairing).
Synonymous
isoaccepting
anticodon
fewer
Wobble; isoaccepting; synonymous; 3rd; “sloppy”
Any RNA sequence has 3 potential __ __; they are defined by __ which designates not only the __ point but also all subsequent ___.
reading frames
AUG; start; frames
The ___ codon (aka start codon) is nearly always ___; but GUG and UUG are two exceptions that have been found. The __ codon codes for __ in bacteria and __ in eukaryotes (in bacteria, the __ group or the whole AA is often removed).
initiation; AUG
initiation; f-Met; Met; formyl
The 3 codons that signal the end of polypeptide synthesis are U–, U–, and U–. They are called __ codons, __ codons, or __ codons. __ don’t react with these codons; instead, __ factors interact with them.
UAA, UAG, UGA
Stop; termination; nonsense
tRNAs; release
If codons were only 2 nucleotides per frame, how many possible aa’s could it code for?
4^2 = 16 (4 nucleotides, 2 per frame)
The genetic code is almost universal; are there any exceptions? Where are most exceptions found?
Yes, stop codons are usually the exception, but there are very few sense codons that are an exception as well.
Most exceptions are found in mitochondria.
What are the 4 major steps of translation?
(1) tRNA charging; (2) initiation; (3) elongation; (4) termination
tRNA charging: __-__ __ is the enzyme that adds aa to the proper tRNA. There are __ of these enzymes altogether: __ per __; so if there are 4 ___ tRNAs, there will be __ enzyme(s).
aminoacyl-tRNA synthetases
20; 1; AA
isoaccepting; 1
Binding AA to tRNA requires __. The AA is always attached to the _’ end of tRNA where there is always a _ _ _ codon. The AA is attached to __ by its __ group. The anticodon is located at the _’ end.
ATP
3’; CCA
adenine; carboxyl
5’
Bacteria initiate translation when the \_\_ ribosomal subunit and IF-_ bind to mRNA (directed by the \_\_-\_\_ sequence on mRNA). IF- prevents the \_\_ ribosomal subunit from binding. Next, IF-_ binds to the \_\_ ribosomal subunit, and IF-_, \_\_\_, and _-_-tRNA complex before binding to the AUG start codon. Hydrolyzed \_\_ (now \_\_\_) and all 3 \_\_ factors dissociate, then finally the \_\_ ribosomal subunit attaches.
small; IF-3; Shine-Delgarno
IF-3; large
IF-1; small; IF-2; GTP; f-MET-tRNA;
GTP; GDP, initiation factors (IF-#); large
Initiation of translation in eukaryotic cells includes several things: (1) __ ribosomal subunit; (2) __ factors; (3) the initiator tRNA (__-tRNA); (4) the _‘__; and (5) __-binding proteins (translation can’t happen without these proteins).
Factors bound to the __ tail interact with the __-binding proteins to facilitate transcription.
The complex scans until it finds the start codon (surrounded by a consensus seq. called the __ sequence).
small; initiation; Met; 5’ cap; cap
poly(A); cap
Kozak
The elongation step of transcription includes three sites on the ribosome: __ (A) site; __ (P) site; and __ (E) cite. The __ tRNA begins at the __ site. EF-__ (which is tugging along __), and the next __ tRNA combine and enter the __ site. __ (hydrolyzed __) and EF-__ are released. EF-__ regenerates EF-__ and __ (now __). A __ bond forms between the two AAs, then the ribosome __ to the next codon (requires EF-G and hydrolysis of __). tRNA that was at the __ site moves to the __ site and leaves, the __ site moves to the __ site, and the __ site is free to accept the next __ tRNA.
aminoacyl; peptidyl; exit. initiation; P; EF-Tu; GTP; charged; A GDP; GTP; EF-Tu EF-Ts; EF-Tu; GDP (GTP) peptide; translocates; GTP P; E; A; P; A; charged
During transcription, formation of the peptide bond requires __ __. This enzyme couldn’t be found in early experiments because it is part of 28S (one of the large subunits of ribosome) making it a __.
peptidyl transferase; ribozyme
__ factors recognize the 3 __ codons, and, along with other factors, promote three things: __ of the tRNA in the __ site, release of the mRNA from the __, and __ of the two ribosomal subunits.
Release; stop; cleavage; P; ribosome; dissociation
How long does mRNA last in prokaryotes v. eukaryotes?
prokaryotes = a few minutes
eukaryotes = a few hours to days
Antibiotics exploit differences in __ proteins and -RNAs between prokaryotes and eukaryotes.
ribosomal; rRNAs
What are polyribosomes? Are they specific to prokaryotes or eukaryotes?
They’re mRNA with multiple ribosomes attached. They are not specific to either; but they exist in prokaryotes before transcription is ever completed (no organelles).
T or F: polypeptides are modified after synthesis in eukaryotes, but not prokaryotes
False: they’re modified post-synthesis in both eukaryotes and prokaryotes.
The “__” form of a proteins is inactive; modifications to make it active include: __, __, __ and __ (MPGA). Additionally, some amino acids might be __ or __. Proper function requires __ of the proteins (secondary structure) which can be done independently or might require molecular __ (an example are __ __ proteins).
“pro”; methylation; phosphorylation; glycosylation; acetylation.
added; removed.
folding; chaperones; heat shock
Antibiotics:
__ blocks entry of tRNA into the A site.
__ binds to the large subunit and blocks peptide bond formation (28S ribozyme activity).
__ binds to the small subunit and blocks initiation.
__ blocks translocation of the ribosome to the next codons.
(Tetras Aren’t Chloroformed with Pepsi; and the Spleen Initiates Erythrocytic Transport).
Tetracycline
Chloramphenicol
Streptomycin
Erythromycin
