Chapter 14: Translation Flashcards
Which region of a tRNA molecule binds to amino acids?
3′ end
The 3′ end of a tRNA molecule contains the amino acid binding site.
A tRNA molecule has a cloverleaf structure that is dictated by base pairing.
The anticodon loop recognizes a complementary mRNA codon.
A tRNA molecule does not contain a codon loop.
Although tRNA molecules contain a variable loop, they do not bind amino acids in this region.
Which of the following statements best describes the function of aminoacyl tRNA synthetase?
It attaches a specific amino acid to a tRNA molecule.
Aminoacyl tRNA synthetase catalyzes the charging reaction that links a specific amino acid to a tRNA molecule.
Aminoacyl tRNA synthetase is an enzyme.
ATP is the energy source in the tRNA charging reaction.
Aminoacyl tRNA synthetase does not synthesize tRNA molecules.
tRNA molecules by themselves do not synthesize proteins.
TRUE or FALSE?
Each aminoacyl tRNA synthetase is specific for one amino acid and a small number of tRNAs.
True
Think about the mechanisms underlying the charging process.
Each aminoacyl tRNA synthetase enzyme recognizes only one amino acid, but each enzyme can often recognize several tRNAs because there is usually more than one codon for each amino acid.
All of the following are involved in the process of tRNA “charging”:
ATP
Amino acids
Aminoacyl tRNA synthetase
Ribosomal RNA and ribosomes form the site of protein translation. Transfer RNAs work to bring amino acids to the ribosome. After a tRNA contributes its amino acid to the growing polypeptide chain, it must be “recharged” with a new amino acid. This is done independently of rRNA.
Is rRNA involved in the process of tRNA “charging?”
NO
The ribonucleic acid components known to exist in eukaryotic ribosomes are the following: ___, ___, ___, and ___ .
5.8S, 18S, 28S, and 5S.
aminoacyl tRNA
A covalently linked combination of an amino acid and a tRNA molecule.
Also referred to as a charged tRNA.
The central paradigm of biochemistry holds that information flows from DNA to RNA to protein. The process of making protein from the mRNA is called translation. Translation is carried out by the ribosome, which binds to the mRNA and binds tRNA, which recognizes the codons on the mRNA and brings the appropriate amino acid with it. The ribosome forms the peptide bond between the new amino acid and the growing peptide chain.
The process of translation, or protein synthesis, is a crucial part of the maintenance of living organisms. Proteins are constantly in use and will break down eventually, so new ones must always be available. If protein synthesis breaks down or stops, then the organism dies.
Once elongation is underway, tRNAs involved in the process occupy a series of sites on the complexed ribosome.
The occupation of sites occurs in the following order:
A Site, P Site, E Site
tRNAs associate with sites on the ribosome in the order listed.
When a peptide bond is formed between two amino acids, one is attached to the tRNA occupying the P site and the other _______.
is attached to the tRNA occupying the A site
The following statement concerns peptide bond formation:
It is catalyzed by peptidyl transferase.
It does not use water, nor does it require GTP.
In prokaryotes, the methionine that initiates the formation of a polypeptide chain differs from subsequently added methionines in that _______.
a formyl group is attached to the initiating methionine
This modification is not present on methionine residues added during elongation.
Translation is directly dependent on all of the following associations:
association of the 30S and the 50S ribosomal subunits
complementary base pairing between mRNA and rRNA
complementary base pairing between mRNA and tRNA
Translation is NOT directly dependent on the following association:
complementary base pairing between mRNA and DNA
Transcription, not translation, is dependent on this association.
Which of the following best describes the first step in the formation of the translation initiation complex?
The small ribosomal subunit binds to an mRNA sequence near the 5’ end of the transcript
At which site does the charged initiator tRNA bind during protein synthesis?
P site
The initiator tRNAfmet binds to the mRNA codon in the P site of the ribosome. The initiator tRNA is the only one that binds in the P site; all other tRNAs bind the ribosome in the A site.
TRUE or FALSE?
The enzyme EF‑Tu catalyzes the formation of a peptide bond between the amino acid held by the tRNA in the A site and the elongating amino acid chain held by the tRNA in the P site.
FALSE
Peptidyl transferase is the enzyme that catalyzes the formation of peptide bonds during translation. EF‑Tu is an elongation factor that facilitates the entry of charged tRNAs into the A site.
What event occurs during translocation?
mRNA shifts in the 5’ direction along the ribosome.
Translocation is the process by which mRNA shifts by 3 bases in the 5’ direction along the ribosome to bring another codon into the A site.
translocation
A chromosomal mutation associated with the reciprocal or nonreciprocal transfer of a chromosomal segment from one chromosome to another. Also denotes the movement of mRNA through the ribosome during translation.
The term peptidyl transferase relates to ________.
peptide bond formation during protein synthesis
TRUE or FALSE?
Prokaryotic and eukaryotic ribosomes are structurally and chemically identical.
FALSE
The following statement is true of translation in eukaryotes:
In eukaryotes, a given mRNA produces only one type of polypeptide chain.
Because the eukaryotic ribosome binds to the cap and not a ribosome-binding sequence, the ribosome cannot bind at any other site on the mRNA and begin translation at an internal site. Some viruses have evolved novel strategies to allow exception to this rule.
Consider the more complex nature of the eukaryotic ribosome and the translational process.
In eukaryotes, transcription takes place in the nucleus and translation takes place in the cytoplasm, after the mature mRNA has been processed.
Protein chains in eukaryotes start with methionine. Only prokaryotes use the formyl derivative.
In eukaryotes, ribosomes bind to the 7-methyl guanosine cap at the 5’ end of the mRNA, not to a ribosome binding sequence.
RANDOM FACTS:
The charged initiator tRNA forms part of the initiation complex and carries methionine.
E site is the exit site at which an uncharged tRNA is ejected from the ribosome.
There is no T site in the ribosome.
A Site is the site at which charged tRNAs complementary to the mRNA codon in the A site enter the ribosome.
RANDOM FACTS:
The two ribosomal subunits join together to form a complex during translation initiation.
Amino acids are added to the polypeptide chain during elongation.
The polypeptide is cleaved from the terminal tRNA as part of the translation termination.
The Beadle and Tatum experiments were based on all of the following assumptions:
X-irradiation can induce mutations.
auxotrophs fail to grow on minimal media
supplemented media permit growth of auxotrophic strains of Neurospora
The Beadle and Tatum experiments were NOT based on the following assumption:
two strains of auxotrophic Neurospora that grow on minimal medium supplemented with biotin have mutations in the same gene
Since biosynthetic pathways have multiple steps, each catalyzed by a separate enzyme, these two strains would not necessarily have the same mutation.
In their first round of screening, Beadle and Tatum plated spores on minimal medium. The purpose of this screen was to _______.
determine whether any auxotrophic mutants had been generated
Specific deficiencies were tested in subsequent rounds of screening.
Which of the following can be inferred from the Beadle and Tatum experiments?
For a mutation resulting in the production of a defective enzyme involved in a biosynthetic pathway, the compound preceding the corresponding step will accumulate.
The defective enzyme is unable to convert the precursor to the next compound in the pathway. Therefore, the precursor accumulates.
Which of the following statements is true of a Neurospora valine auxotroph?
The cells can grow on minimal medium + valine.
The cells can grow if the nutrient it cannot produce itself (i.e., valine) is supplied in the medium.
The one-gene:one-enzyme hypothesis emerged from work on which two organisms?
Neurospora and Drosophila
By their experimentation using the Neurospora fungus, Beadle and Tatum were able to propose the far-reaching hypothesis that ________.
the role of a specific gene is to produce a specific enzyme
TRUE or FALSE?
Different sets of human hemoglobins are found at different times in development.
True
During embryonic and fetal development, the set of polypeptides found in hemoglobin is completely different from that found in the hemoglobin of adults.
The primary structure of a protein is determined by ________.
the sequence of amino acids
One form of posttranslational modification of a protein includes ________.
removal or modification of terminal amino acids
All of the following statements may apply to a protein domain:
Each protein contains at least one domain, but may contain several domains.
Domains may have resulted from exons of different genes, which were reshuffled during evolution.
Within a single protein, different domains may serve different functions, such as ligand-binding or catalysis.
The following statements does NOT apply to a protein domain:
A domain consists of a single type of secondary structure.
TRUTH: A domain may contain more than one type of secondary structure.
Assuming that an amino acid sequence is 250 amino acids long, how many different molecules, each with a unique sequence, could be formed?
20^250
Studies of Neurospora led to the one gene : one ________ statement, whereas studies of human hemoglobin led to the one gene: one ________ statement .
Studies of Neurospora led to the [one gene : one enzyme] statement, whereas studies of human hemoglobin led to the [one gene: one polypeptide] statement .
electrophoresis
A technique that separates a mixture of molecules by their differential migration through a stationary medium (such as a gel) under the influence of an electrical field.
A procedure that is often used to separate molecules by using their molecular charges is called ________.
electrophoresis
The secondary structure of a protein includes ________.
α-helix and β-pleated sheet
Electrophoretic separation of HbA from HbS is based on a difference in their ________.
charges
TRUE or FALSE?
When a metabolic block occurs in a biochemical pathway, it is common for amount of the substance immediately prior to that block to increase.
True
TRUE or FALSE?
Sickle-cell anemia is caused by the absence of the alpha chain of hemoglobin.
False
During translation, which 3 mRNA codons signal chain termination?
UAA, UAG, UGA
Early in the 1900s, Sir Archibald Garrod studied a number of metabolic defects in humans. One particular disorder involved the inability to metabolize homogentisic acid. What is the name of this disorder?
alkaptonuria
The general aspects of translation are similar in all organisms. However, there are some differences between bacterial and eukaryotic translation, especially during the initiation phase.
In bacteria, the start codon lies just downstream of a recognition sequence called the Shine-Dalgarno sequence. In eukaryotes, the start codon is located within a different recognition sequence, the Kozak sequence.
In bacteria, the amino acid on the initiator tRNA is a modified methionine called N-formylmethionine (fMet). In eukaryotes, the amino acid on the initiator tRNA is methionine.
Translation elongation in bacteria
Wild-type strains of E. coli have a tRNA with a 5′-GUA-3′ anticodon that recognizes the UAC codon for tyrosine. We can represent this tRNA as GUA-tRNATyr.
Suppose you isolated a strain of E. coli in which a mutation changed the anticodon in this tRNA to 5′-CUA-3′ (creating CUA-tRNATyr). Answer the following questions about translation elongation in each strain.
During translation elongation, a peptide bond is formed between the amino acid (or polypeptide) covalently attached to the tRNA in the P site and the amino acid on the tRNA in the A site. This process continues until a stop codon is presented in the A site.
In wild-type strains of E. coli, there are no tRNAs with anticodons complementary to stop codons. Instead, release factors recognize the stop codons, bind in the A site, and cause the polypeptide to be released from the ribosome, terminating translation.
In a mutant strain that has charged tRNAs with the anticodon 5′-CUA-3′, those tRNAs will bind to the stop codon 5′-UAG-3′. As a result, translation will continue beyond the stop codon, producing an abnormal polypeptide that is longer than its wild-type equivalent. Such strains are called suppressor strains because they suppress translation termination.
The diagram below shows an mRNA molecule that encodes a protein with 202 amino acids. The start and stop codons are highlighted, and a portion of the nucleotide sequence in the early part of the molecule is shown in detail. At position 35, a single base-pair substitution in the DNA has changed what would have been a uracil (U) in the mRNA to an adenine (A).
a nonsense mutation resulting in early termination of translation
The effect of a single base substitution depends on the new codon formed by the substitution. To identify the new codon, it is first necessary to determine the reading frame for the amino acid sequence. The first codon starts with base 1, the second codon with base 4, the third with base 7, and so on.
In this problem, the codon that contains the single base substitution begins with base 34. The original codon (UUA, which encodes the amino acid leucine) is converted by the single base substitution to UAA, which is a stop codon. This will cause premature termination of translation, also called a nonsense mutation.
For each protein, identify its targeting pathway: the sequence of cellular locations in which the protein is found from when translation is complete until it reaches its final (functional) destination. (Note that if an organelle is listed in a pathway, the location implied is inside the organelle, not in the membrane that surrounds the organelle.)
PFK = Cytoplasm only insulin = ER > Golgi > outside cell
There are two general targeting pathways for nuclear-encoded proteins in eukaryotic cells.
- Proteins that will ultimately function in the cytoplasm (PFK, for example) are translated on free cytoplasmic ribosomes and released directly into the cytoplasm.
- Proteins that are destined for the membranes or compartments of the endomembrane system, as well as proteins that will be secreted from the cell (insulin, for example), are translated on ribosomes that are bound to the rough ER.
For proteins translated on rough ER, the proteins are found in one of two places at the end of translation. If a protein is targeted to a membrane of the endomembrane system, it will be in the ER membrane. If a protein is targeted to the interior of an organelle in the endomembrane system or to the exterior of the cell, it will be in the lumen of the rough ER. From the rough ER (membrane or lumen), these non-cytoplasmic proteins move to the Golgi apparatus for processing and sorting before being sent to their final destinations.
Ribosomes provide the scaffolding on which tRNAs interact with mRNA during translation of an mRNA sequence to a chain of amino acids. A ribosome has three binding sites, each of which has a distinct function in the tRNA-mRNA interactions.
Drag the appropriate tRNAs to the binding sites on the ribosome to show the configuration immediately before a new peptide bond forms. If no tRNA is bound to a site at that time, leave that binding site empty.
E SITE (EMPTY) P SITE (AUA WITH 3 PROTEIN) A SITE (UCC WITH ONLY 1 PROTEIN)
During translation, new amino acids are added one at a time to the growing polypeptide chain. The addition of each new amino acid involves three steps:
Binding of the charged tRNA to the A site. This step requires correct base-pairing between the codon on the mRNA and the anticodon on the tRNA.
Formation of the new peptide bond. In the process, the polypeptide chain is transferred from the tRNA in the P site to the amino acid on the tRNA in the A site.
Movement of the mRNA through the ribosome. In this step, the discharged tRNA shifts to the E site (where it is released) and the tRNA carrying the growing polypeptide shifts to the P site.
Translation initiation in bacteria involves the assembly of a 70S initiation complex from two ribosomal subunits, mRNA, and the initiator tRNA. Three initiation factors (IF1, IF2, and IF3) and GTP are also required. The assembly of these components occurs in a particular order, as follows:
- IF3 binds to the 30S subunit and prevents its association with the 50S subunit, keeping the 30S subunit available for the assembly of the remaining components.
- The 16S rRNA of the 30S subunit base-pairs with the Shine-Dalgarno sequence, which lies just upstream of the start codon in the mRNA. This base pairing positions the mRNA correctly on the 30S subunit.
- The initiator tRNA (tRNAfMet), with IF2 and GTP bound, base-pairs with the start codon in the mRNA. IF1 binds to the A site of the 30S initiation complex.
- The 50S subunit joins the 30S initiation complex.
- The initiation factors are released.
- The resulting 70S initiation complex is now ready for translation elongation.
Translation
Story of the ribosome;
Story of a cellular machine
Machinery: mRNA, tRNA, rRNAs, translation factors
RNA is the catalytic center of the ribosome
Holley’s two-dimensional cloverleaf model of transfer RNA.
Codon: 5’-AUG-3’
Anticodon: 3’-UAC-5’
“Charging” tRNA
tRNA synthetases add amino acid to tRNAs
First, amino acid is converted to activated form, provides energy for transfer to tRNA
Next, amino acid transferred to tRNA
Aminoacyl tRNA snythetases are highly specific, only recognize one amino acid
3 Steps of Translation
Initiation
Elongation
Termination
Initiation
Starts with small ssu rRNA, charged tRNA, GTP, Mg2+, and small initiation factors (IFs)
Small ssu rRNA binds IFs, then binds to mRNA
This “sets” the reading frame
Large subunit rRNA binds
Has a second binding site for charged tRNAs A (aminoacyl) site
Initiation Details Specific to Bacteria
In bacteria, binding site in mRNA is specific site AGGAGG (Shine-Delgarno sequence)
In bacteria, initiation codon AUG calls for modified amino acid f-met (formylmethionine) at the P (peptidyl) site
Elongation
Both subunits bound
2 sites (A & P) available for charged tRNAs
Polypeptide grows by 1 amino acid –> Elongation
mRNA sequence dictates
charged tRNA
Peptidyl transferase makes peptide bond
Complex shifts in direction of P site
tRNAs released from E site
Rate of elongation: 15 amino acids per second in E. coli
Elongation continues until a termination codon is reached
Termination
Termination (stop, nonsense) codons encountered
Signals release of polypeptide chain from terminal tRNA
Eukaryotic Translation
mRNAs generally longer, and longer lasting prior to degradation
5’ ends of mRNA are capped with 7-methylguanosine
Conserved sequence analogous to Shine-Delgarno
AUG is start codon, but for methionine
R=side chain
gives each amino acid its
particular characteristics
20 different side chains
NonPolar Amino Acids
Chemical structures and designations of 8 amino acids found in living organisms that are non-polar and hydrophobic
Polar Amino Acids
Hydrophilic
These are molecules that have a slightly positive part
and a slightly negative part
Chemical structures and designations of 7 amino acids found in living organisms that are polar and hydrophilic.
Polar, Positively Charged [basic]
Amino Acids
Chemical structures and designations of the 3 amino acids found in living organisms that are polar: positively charged (basic)
Polar, Negatively Charged [acidic]
Amino Acids
Chemical structures and designations of the 2 amino acids found in living organisms that are polar: negatively charged (acidic)
Polar, Negatively Charged [acidic]
Amino Acids
Chemical structures and designations of the 2 amino acids found in living organisms that are polar: negatively charged (acidic)
Primary Protein structure
Sequence of the amino acids in the polypeptide
Secondary Protein structure
The a-helical or ß-pleated-sheet formations in a polypeptide, dependent on hydrogen bonding between certain amino acids.
- Alpha helix
- Beta pleated sheet
ALPHA HELIX
The right-handed a-helix which represents one form of secondary structure of a polypeptide chain.
The ß-pleated-sheet configuration
an alternative form of secondary structure of polypeptide chains
Tertiary structure
- Three-dimensional conformation of protein
Quaternary structure
Conformation of proteins with more than one polypeptide chain
eg. Hemoglobin, 2 alpha and 2 beta chains
Hemoglobin
Four chains (two a and two ß) interact with four heme groups to form the functional molecule.
2 alpha and 2 beta chains
What happens when protein folding goes bad?
Prion diseases: eg., scrapie, kuru, mad cow disease
prion
An infectious pathogenic agent devoid of nucleic acid and composed of a protein, PrP, with a molecular weight of 27,000–30,000 Da.
Prions are known to cause scrapie,a degenerative neurological disease in sheep; bovine spongiform encephalopathy (BSE, or mad cow disease) in cattle; and similar diseases in humans, including kuru and Creutzfeldt–Jakob disease.
What happens in Proteins
Conformational change in protein
Primary amino acid sequence the same
Changed protein is infectious
Changed protein can change normal proteins in healthy individual–> leads to disease phenotype
Protein domains
More than one functional domain in a polypeptide
For example, DNA binding domains, catalytic domains, transmembrane domains
protein domain:
technical definition
Amino acid sequences with specific conformations and functions that are structurally and functionally distinct from other regions on the same protein.
Protein Function:
Structural proteins
collagen & keratin in skin
actin & myosin in muscle
Protein Function:
Enzymes
Catabolic: degradation of larger molecules into smaller molecules
Anabolic: synthesis of molecules, eg. those making up nucleic acids, proteins, lipids, & carbohydrates
Catabolic Enzymes
degradation of larger molecules into smaller molecules
Anabolic Enzymes
synthesis of molecules, eg. those making up nucleic acids, proteins, lipids, & carbohydrates
Protein diversity
The amino acid building blocks and their biochemical characteristics together with structure of proteins leads to vast diversity observed in nature
One Gene-One Enzyme Hypothesis
Beadle & Tatum experiments in Neurospora (model system)
Nutritional mutants
Mutate Neurospora
Isolate mutants that will not grow on minimal media (no amino acids, purines, pyrimidines, or vitamins)
nutritional auxotrophic mutation
Isolate mutants that will only grow with added amino acids
Test the result of the addition of each amino acid to determine what amino acid is required
Determines the pathway that has been affected by mutation
Hypothetical biochemical pathway
Precursor ——(Enzyme A)—-» Ornithine ——(Enzyme B)—-» Citruline ——(Enzyme C)—-» Arginine
How do we determine this pathway?
Grows if given ornithine OR citrulline OR arginine.
Conclusion: Mutation must be “prior” to ornithine, also ornithine and citrulline must be involved in making arginine
Nutritional mutants
Big Deals
Used to determine biochemical pathways
Led to One Gene: One Enzyme hypothesis
One Gene: One Polypeptide
Studies of hemoglobin showed that some proteins could be made of multiple subunits
Each polypeptide is encoded by a separate gene
Example: sickle-cell anemia
sickle-cell anemia
HbA / HbA : homozygous normal
HbA / HbS : heterozygous, carrier
HbS / HbS : homozygous sickle cell
Negatively charged glu–> uncharged valine!!
GAG (glu)—> GTG (valine): single nucleotide change!
phosphodiester bond
In nucleic acids,the system of covalent bonds by which a phosphate group links adjacent nucleotides, extending from the 5’ carbon of one pentose sugar (ribose or deoxyribose) to the 3’carbon of the pentose sugar in the neighboring nucleotide.
Phosphodiester bonds create the backbone of nucleic acid molecules.
The following statements are true about enhancers:
Enhancers contain sequences that are recognized by transcription factors.
Enhancers can differ for each gene in a eukaryotic cell (although overlap is possible).
Enhancers can be located thousands of nucleotides upstream of downstream of the gene they affect.
Enhancers represent control elements located far away from the promoter.
