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124 Cards in this Set
- Front
- Back
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Define translation
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protein synth from mRNA template
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What is being translated?
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GENETIC INFORMATION encoded by the mRNA template
Genetic code is being translated 5' --> 3' direction into a chain of AAs (protein) |
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What brings the AAs to the mRNA in the ribosome
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tRNA
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What is the product of translation?
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protein
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How does translation proceed?
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from N-terminus(amino) to the C-terminus(carboxy)
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Where does translation occur
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Predominantly in the cytoplasm. Some happens in the mitoch. Possibly, some in the nucleus
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What structure mediates translation
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ribosomes
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In terms of the genetic code, define universal
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same genetic code is used in all organisms except for a few exceptions, including mito. and some algae
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In terms of the genetic code, define triplet
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a set of three nucleotide bases on mRNA code for one AA
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In terms of the genetic code, define degenerate
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Single AA may have more than one triplet code. Usually a sequential relationship btw degenerate codes
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In terms of the genetic code, define non-overlapping
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a set of three adjacent bases is treated as a complete group. The set of bases, called the CODON, is used once for each translation step.
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Describe the role of tRNA in translation
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tRNAs are able to match the right AA to the codon specified in the mRNA b/c they have both:
1) AA binding site (CCA end); esther bond at the CCA end 2) codon binding site (anticodon) |
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Outline the rxn catalyzed by aminoacyl synthetases
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the attachment of AA to tRNA via ester bonds at the CCA (3') end
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what is a polyribosome
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a cluster of ribosomes simultaneously translating an mRNA molecule
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describe the P-site
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One of two aminoacyl tRNA binding sites for AAs. Site where peptidyl transferase creates peptide bonds btw a new AA and the growing chain
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describe the A-site
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One of two aminoacyl tRNA binding sites for AAs. Site where incoming aminoacyl tRNA binds to the ribosomes
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What is a missense mutation
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a point mutation in which a single nucleotide is changed, resulting in a codon that codes for a different AA.
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What is a nonsense mutation
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a point mutation that results in a translation stop codon; premature termination of polypeptide.
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What is a frameshift mutation
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An insertion or deletion of a base; shifts the way ALL codons are read from that point
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Describe where translation occurs and what organelle mediates translation.
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Translation predominantly occurs in the cytoplasm. Some occurs in the mito. and possibly some in the nucleus
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Describe the initiation step of translation
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1. 30S subunit binds to mRNA. Initiation factors help in binding. Energy is req'd via ATP
-the two aminoacyl tRNA binding sites (P and A) of 30S are placed over the first 2 codons on mRNA 2. The anticodon of the first tRNA with attached AA binds the AUG start codon of the mRNA at the P site 3. GTP is needed to bind the large subunit (50S) to the small subunit 4. Many protein initiation factors req'd for initiation; more for eukary. |
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What is an initiation factor?
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protein molecules that help start the protein synth process
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Which AA(s) is(are) the first to bind to the small subunit?
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1. formylmethionine tRNA (prokary)
2. methionine tRNA (eukary) |
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What is the combined form of the small are large subunit named?
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Prokary: 30S + 50S = 70S initiation complex. This is comprised of ~55 proteins + rRNA
Eukary: 40S + 60S = 80S initiation complex; make up of ~80 proteins + rRNA |
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How does the formation of small/large subunit occur?
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by a conformational change
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How does the elongation step of translate happen?
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Elongation is the actual formation of the polypeptide
1. A second AA-tRNA binds to the A site of the ribosome; this requires elongation factors 2. Peptide bond formation is catalyzed by peptidyl transferase (ribozyme) 3. tRNA w/o its AA now leaves the P site and the tRNA with the 2 AA at the A site is TRANSLOCATED to the P site, leaving the A site empty. GTP is required 4. As the next codon enters the A site, the next AA-tRNA enters the A site and the peptidyl transferase rxn occurs again (GTP required). This continues until a stop codon on the mRNA reaches the A site of the ribosome. |
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Describe the peptidyl transferase rxn
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alpha-amino group of the A site AA attacks the carbonyl group of the P site AA.
Both AAs are now attached to the A site |
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In what direction does translocation occur?
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from the P site to the A site
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What are the products of the peptidyl transferase reaction?
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dipeptidly-tRNA (located at A site)
+ deacylated tRNA-fMet (at the P site) |
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Describe the termination step of translation?
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1) a stop codon on mRNA in the A site CANNOT bind an AA-tRNA
2) protein-releasing factors bind to the A site 3) peptidyl transferase hydrolyzes the bond btw the polypeptide and the tRNA at the P site 4) Polypeptide released from the ribosome 5) Ribosome subunits dissociate |
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What are functions of the ribosome?
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1) move along the mRNA template deciphering the code for conversion from nucleotide to AA seq
2) bind the proper tRNA adaptor molecule containing an AA 3) catalyze formation of peptide bonds btw AAs using energy from ATP or GTP |
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What components are involved in the biochem rxns of ribosomes?
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1) many protein subunits within ribosome
2) all 3 major forms of RNA 3) AAs 4) cytosolic enzs 5) cytosolic factors 6) ATP, GTP |
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T/F
The three stop codons are UGA, UAC and UAG |
False
UGA, UAA, UAG |
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T/F
The first two bases of an codon of the tRNA confers the most specificity for the AA and provide the strongest binding affinity |
False
anti-codon; not codon |
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How do antibiotics inhibit growth of microorganisms?
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block protein synth.
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Describe how linezolid inhibits protein synthese.
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blocks formation of 70S initiation complex.
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What is the generic name for Sumycin
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tetracycline
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What two drugs are used as experimental agents? Give their trade names.
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Purmoycin and cyclohexamide.
No trade names |
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What antibiotic(s) is used for TB
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streptomycin. Generic/trade name is the same
Linezolid (Zyvox) |
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Describe how cycloheximide inhibits protein synthesis
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inhibits translocation of eukaryotic peptidyl-tRNA
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What are the trade names of Erythromycin
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E-mycin, Erythrocin, Ethril
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What antibiotic(s) can be used to treat respiratory infections
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tetracycline(Sumycin) and Erythromycin(E-mycin, Erythocin, Ethril)
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Describe how chloramphenicol inhibits protein synthesis.
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binds to 50S subunit and inhibits peptidyl transferase; acts on prokary.
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What is Zyvox used for?
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Linezolid is used to treat skin & soft tissue infections, pnemonia and TB
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Describe how erythromycin inhibits protein synthesis.
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binds to ribsomes and inhibits peptidyl transferase; acts on prokaryotes
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What is Ethril used for?
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Erythromycin is used to treat respiratory and intestinal infections and Legionnaires disease.
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Which antibiotics can be used in eukary?
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Puromycin and cycloheximide. Hint: they are the two experimental agents.
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Describe how tetracycline inhibits protein synthesis.
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binds to A site of ribosomes and blocks entry of AA-tRNAs; prokary only
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What is the generic name of chloromycetin?
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chlororamiphenicol
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What antibiotic(s) is used to treat fungicide?
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cyclohexamide
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What does Sumycin treat?
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tetracylcine treats respiratory infections, acne and skin infections and ulcers
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Describe how streptomycin inhibits protein synthesis
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causes misreading of mRNA and inhibits initiation; prokary only
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What does chloramphenicol treat?
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typhoid fever, Salmonella and chlmydia infections
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Describe how puromycin inhibits protein synthesis.
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cause early termination by mimicking the action of AA-tRNA; acts on BOTH prokary and eukary
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Non-antibiotic inhibitors of protein synthesis are considered ______
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toxins
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List the names of toxins that inhibit protein synthese
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Ricin and Diptheria toxin
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What is Ricin?
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toxic protein from castor bean seeds used as a biological warfare agent
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What is diptheria toxin?
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enz secreted by the pathogenic bacteria Corynebacterium diptheria
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How do DNA mutations cause problems in protein synthesis?
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alter the coding seq of mRNA and the protein that the mRNA codes for
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Describe a chain break.
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When chromosomes become fragmented and segments may be exchanged
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T/F
Coding seq of promoter/enhancer regions may be slightly altered if the chain break occurs at one of these sites |
False
drastically altered |
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T/F
Chain breaks causes mRNAs to often not properly synthesized or degrade before transport to the cell membrane. |
transport to the cytoplasm
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What is a point mutation?
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Single base alteration
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When does a substitution mutation not cause an AA change?
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when the substitution occurs in the 3rd base position of a codon to a base that is also codes for the same AA.
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T/F
All substitution point mutations that cause an AA change alters the function of the protein. |
False;
Some substitutions are acceptable and have no effect on protein function. eg, isoleucine for leucine |
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What are the types of post-translational processing of proteins
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protein folding, biochm modification, targeting and degradation
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Describe protein folding
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1) folding often begins BEFORE synth. is complete
2) begins with the formation of local secondary structures (alpha-helix, beta-conformation) 3) chaperones are enzs made of proteins that couple ATP hydrolysis to protein folding 4) disulfide bonds formed btw cysteine residues help stabilize the conformation of a protein after it is folded |
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What are the types of biochem modifications?
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proteolytic cleavage, AA modification, attachment of carbs and addition of prosthetic groups
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Describe proteolytic cleavage.
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the N-terminal AA is removed by hydrolysis
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Describe AA modification example
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Phosphorylation and hydroxylation are most common modifications.
-OH groups of serine, threonine and tyrosine get phosphorylzed from ATP. Activity of the enz glycogen phosphorylase is reulated by phosphorylation of serine residues Side chains of proline and serine are commonly hydroxlyzed in collagen. |
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Describe the attachment of carbs
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Carb chains of up to 15 residues are CV bonded to proteins at the -OH groups of serine and threonine or on the side chain amide N of asparagine. These are called glycoproteins
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Describe the addition of prosthetic groups
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FAD, biotin, pantothenic acid and heme are examples. Many proteins depend on the presence cofactors or prosthetic groups CV for biological activity
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______ proteins are released from free ribosomes into the cytosol
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soluble
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What type of proteins are directed to the ER while still attached to the ribosome
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secretory, membrane and lysosomal proteins
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What are signal sequences?
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sequences at the N-terminus of some polypeptides that direct it to the ER
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Describe secretory proteins
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proteins that are COMPLETELY translocated across the ER membrane and enter the lumen of teh ER
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Describe lysosomal proteins.
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proteins modified with mannose-6 phosphate residuesH
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Describe plasma membrane proteins
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proteins that are PARTLY translocated across the ER membrane and retained in the membrane
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Give examples of protein targets that are not considered signal sequences.
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1) proteins destined for the nucleus
2) proteins destince for mitoch. |
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describe nuclear proteins
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Require nuclear localization signal for processing. ~7-19 AAs in size. Allows them to pass through the highly selective nuclear pores into the nucleus. Signal is embedded in the molecule
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How do mito. proteins function?
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Synth. as cytosolic proteins on free ribosomes and targeted to the mito. by mito. entry sequences located on the N-terminus of the protein.
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Why do proteins need to constantly be degraded and re-synthesized?
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1) allow for removal of damaged/misfolded proteins
2) degradation of transient regulatory proteins 3) allows organism to adapt to changing conditions |
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What degrades extracellular proteins (proteins that have entered the cell)?
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lysosomal proteases
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What degrades intracellular proteins?
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Large protein complexes called proteosomes by ATP-dependent proteases.
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Describe the role of ubiquitin in protein degradation.
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Small protein that modifies intracellular proteins destined for degradation by proteosomes.
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What genes perform a "housekeeping" function?
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constitutive. these genes are "on" all the time since the cell needs the proteins they provide to survive.
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Describe an inductible gene.
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one that is turned off/on in response to a metbolic need or environmental change
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Glucose metabolizing genes and genes for structural proteins are examples of _________ genes
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constitutive
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What does controlling gene expression allows a cell to do?
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1) respond to change in the environment
--response to hormones --cellular energy levels --metabolic activity 2) be specialized into a specific cell type --muscle cells -vs- skin cells |
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Hormone responses genes are example of ___________ genes
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inductible
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What is another term for an inductible gene?
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repressible gene
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Regulation is gene expression is mostly controlled by inhibiting which step?
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The initiation step of transcription; involves promoters
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What are the major mech. for controlling transcription initiation?
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1) RNA polymerase
--diff. affinities for diff. promoters -- 3 diff RNA poly. in eukary 2) Gene Regulatory proteins 3) changes in DNA structure |
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_____ affects ability of ____ to be transcribed
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protein binding, DNA
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T/F
Activators activate RNA poly. activity |
True
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T/F
Enhancers bind to activators and silencer bind to repressors. |
False
Activator bind to enhancer; silencer bind to repressors. |
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Activators/repressors bind on the DNA _____ from the promoter whichaffects activity at the promoter region.
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upstream
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What is the role of structural motifs in gene regulation?
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facilitate the binding to DNA
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What types of motifs are involved in gene regulation?
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Zinc fingers, leucine zippers and helix turns
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How does structural changes in DNA affect gene expression regulation?
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affects the binding ability of RNA poly. Examples are degree of coiling of DNA, nucleosome structure and DNA methylation.
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T/F
Steroid hormone response elements assist in controlling translation. |
False;
Transcription |
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Steroid hormone response regulation is in response to changes in _____.
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cell environment
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T/F
Metallothionein (MT) is a protein in prokary. that detoxifies ingested metals |
False
Eukary |
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MT present in ____ concentration under normal conditions, but ______ when metal ion concentrations in the body ______.
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low, increases, increases
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What are the components of an MT gene promoter?
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1) 4 metal response elements (MREs)
2) one glucocoricoid response element 3) TATA box |
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______ promotes the transcription of the MT gene.
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RNA poly II
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T/F
TFs must always be bound to metal in order to bind to the promoter MRE regions |
True
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What metals bind to TFs?
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Cadmium, zinc, copper, lead, mercury
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T/F
The rate of transcription of mRNA depends on it's abundance. |
False
translation, not transcription |
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What are the two methods of controlled mRNA concentration in the cytoplasm?
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1) control mRNA export
2) mRNA stability |
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mRNA is exported through the ______
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nuclear pores
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T/F
mRNA export is an energy driven, random process that requires 5' 7-MetG cap and 3' Poly-A tail. |
False;
highly controlled process |
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mRNA lifetime ranges from ____ to ____.
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~20 min, ~24 hours
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What is an RNAse ?
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enz the cleaves RNA
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What are some determining factors of mRNA stability?
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1) if if contains stabilizing/destabilizing sequences
2) binding of certain proteins can protect the mRNA from degradation 3) length of the poly-A tail and the presence of 5' 7MetG cap 4) presence of siRNA (ribozymes) that bind to complementary mRNAs and cleave them |
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What are some other mechanisms of gene expression regulation outside of transcription and translation?
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1) Gene amplification
2) gene rearrangements 3) RNA processing |
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Describe gene amplification.
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Some genes are amplified at certain stages of dev.
eg, methotrexate can cause multiple copies of DHFR gene in tumor cells |
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Give an exmaple of gene rearrangement.
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production of antibodies; alternate splicing of genes. Rearrangment of the gene itself, NOT the RNA
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______ is an example of RNA processing in which ____ diff. gene products are formed.
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alternate splicing, 2
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_____ help regulate gene expression in prokary.
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operons
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Describe an operon
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groups of functionally related structural and regulatory genese that are clustered together on the DNA
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The ___ operon controls ____ metabolism
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lac, lactose
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What are differences btw prokary and eukary translation?
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1) Eukary is more complex; requires more IFs, EFs and TFs
2) Translation coupled to transcription in prokary; no need to trasport mRNA out of a nucleus in prokary. 3) Diff. mech. for detecting start codon in prokary - Shine Delgarno sequences do this in prokary. 4) Ribosome size is diff 5) fMet if first AA in prokary; Met in eukary |
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What antibiotic(s) inhibit translocation?
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1) cycloheximide - eukary
2) erythromycin - prokary |
