Exam 3 Review
Supplemental Instruction
Iowa State University / Leader: / Jacob
Course: / BIOL/GEN 313
Instructor: / Dr. Rodermel
Date: / 10/25/16

This review is meant to be a study guide that covers the bulk of the material for the exam. The questions are not written as test questions.

Test will cover lectures 17-26 (Chapter 11.1-11.3; and Chapter 12.1+12.2) and all assigned problems (DO THESE)

  1. What are the 11 characteristics of the genetic code?
  1. Genetic code has _4_ letters
  2. Genetic code is a tripletcode: each amino acid is encoded by a sequence of 3 consecutive nucleotides in the mRNA called a _codon____.
  3. The codon table has ___64_____ codons
  4. The code is __degenerate____(64 codons, but only __20__ amino acids): an amino acid can be specified by more than one codon
  5. The code has 3 types of codons: (name them and how many of each)

61 sense codons

3 terminiation codons

1 initiation codon

  1. _____synonymous____ codons are codons that specify the same amino acid
  2. The code is ___nonoverlapping__: codons are read as successive groups of 3 nucleotides
  3. ____initiation codon______sets the reading frame, hence the first amino acid of a protein (at the _N_ terminus) is fMethionine. This codon is __AUG___
  4. What molecule serves as an adaptor molecule between mRNA and the ribosome?

tRNA

Base pairing between the anticodon of the molecule and the codon is _antiparallel__ and _complementary_

__tRNA__ have different sequences but all form a _cloverleaf_ structure with _5arms

Define the two important arms to know:

Acceptor arm-CCA sequence at 3’end, this is where amino acid binds

Anticodon arm-base pairs with codon on mRNA

There are ~40 different tRNAs, this means that different tRNAs can accept the same amino acid. These are called isoacceptingtRNAs

  1. What “solves” the problem that there are 20 amino acids and 61 sense codons but only `40 different tRNAs? Wobble Hypothesis

___ Wobble Hypothesis__ predicts that some tRNAs recognize more than one codon

What causes this? (be very specific!)

The third position of the codon does not properly base pair with anticodon resulting in a wobble

  1. The code is _~universal___. What does this mean?

Codons in codon table encode for same amino acid in every organism. VERY rare exceptions do occur

  1. Define translation.Process of protein synthesis by which a polypeptide is assembled from information on the mRNA
  2. What direction does the ribosome move on the mRNA? What direction is protein synthesized?Ribosome move 5’to 3’. Protein is synthesized N terminus to C terminus
  3. What subunits does the ribosome of prokaryotes have? Eukaryotes?

P: 50S and 30S combine to form 70S

E: 60S and 40S combine to form 80S

  1. Where is the ribosome assembled in eukaryotes?

Nucleolus

Translation: 4 stages

  1. Describe how tRNA charging works.

Aminoacyl-tRNAsynthetases is an enzyme with an active site that can recognize an amino acid and all its isoacceptingrRNAs. Enzyme uses energy from ATP hydrolysis to chemically link amino acid and tRNA

  1. Describe how prokaryotic initiation occurs (include mRNA, Shine-Dalgarno, 30S and 50S subunits, Initiation factors, fMet-tRNAfMet, GTP)figure 11.9 on pg 297 shows this process
  1. IF3 binds to small subunit(30S) This prevents binding of large subunit(50S)
  2. 30S binds to mRNA(16SrRNA binds to Shine Dalgarno sequence to position ribosome
  3. fMet-tRNAfMet forms complex with IF2 and GTP
  4. This complex then binds to initiation codon(AUG) (this binding occurs by hydrogen bonding between codon and anticodon)

IF1 join small subunit at this time as well

  1. All Ifs dissociate, GTP hydrolyzed to GDP
  2. Large subunit can now bind
  1. There were 3 major differences between prokaryotic and eukaryotic initiation. (hint: involve initiation codon, binding sequence, and ribosomal subunits)
  1. Initiation codon in Eukaryotes is Met-tRNAiMet
  2. They have different ribosomal subunits. Refer to #4
  3. Eukaryotes do not have Shine Dalgarno, their ribosome binds to 5’end of mRNA
  1. What is the closed loop configuration in Eukaryotes?

Proteins that bind to polyA tail interact with cap-binding proteins to form a closed loop structure. Ribosome joins on 5’end and moves down mRNA scanning for Kozak sequence to begin translating

  1. Where does the ribosome bind on prokaryotes? Eukaryotes?

P: Binds at Shine Dalgarnosequence(30S subunit)

E: binds at 5’end of mRNA

  1. Describe the process of elongation in prokaryotes. (Include ribosome and 3 tRNA binding sites: peptidyl, aminoacyl, and exit, 3 elongation factors: EF-Tu, EF-Ts, EF-G, GTP, ChargedtRNAs)figure 11.11 on pg 298/299 illustrates this
  1. Ef-Tu and GTP form complex with a charged tRNA
  2. That complex enters A site of the ribosome
  3. GTP cleaved to GDP which releases EF-Tu/GTP complex from tRNA
  4. EF-Ts regenerate the EF-Tu/GTP complex by converting GDP back into GTP
  5. Peptide bond forms between amino acids in the P and A sites
  6. When peptide bond forms, tRNA in P site lets go of its amino acid
  7. Ribosome translocates down to next codon which required EF-G and GTP(energy)
  8. tRNA in P site is now in E site and removed
  9. tRNA in A site, not in P site
  10. A site is ready for another tRNA to come in
  1. What catalyzes the peptide bond?

23S rRNA

  1. Where does the energy for movement of ribosome come from?

EF-G hydrolyzes GTP for energy

  1. What type of interaction holds together the tRNA and mRNA?

Hydrogen bonding between base pairs

  1. Describe the process of termination in prokaryotes (include termination codons, Release factors:RF1, RF2, RF3, GTP)figure 11.12 on page 300 shows this
  1. Ribosome hits stop codon and has no tRNA with a matching anti codon
  2. RF1 or RF 2 binds to A site depending on sequence

RF1-UAA or UAG

RF2-UAA or UGA

  1. RF3 forms complex with GTP and binds to 50S subunit
  2. Polypeptide is released from tRNA in P site
  3. GTP is hydrolyzed to GDP which releases ribosomal subunits and release factors from mRNA

Know 6 similarities/differences between translation in prokaryotes and eukaryotes. Page 301 of your book will help with this

  1. What are 3 common posttranslational modifications?

Chemical modification-methylation, phosphorylation, acetylation

Cleavage of amino acids

Protein folding

  1. What is an antibiotic?

Drug that kills bacteria

  1. Why is translation a good target for antibiotics?

Translation differs much more between prokaryotes and eukaryotes than transcription or replication. We only want to kill bacteria so good step to target

  1. What are the mechanisms of action of the following:?

Tetracycline-binds to A site of ribosome; blocks entry of charged tRNAs

Chloramphenicol-blocks peptide bond formation

Streptomyocin-binds to 16S rRNA and prevents binding on fMet-tRNAfMet

Erythromyocin-binds to 50S subunit and prevents translocation

  1. What are the 6 levels of gene regulation?

Alteration of DNA structure (chromatin remodeling), mRNA processing, transcription, translation, RNA stability, and posttranslational modification

  1. What is the purpose of gene regulation?

Produce the precise amount of a given protein

  1. Match the type of gene to its function:

Structural genesBA. expressed continuously; they code for essential functions that keep all cells alive

Regulatory genesCB. code for proteins that function in metabolism or cell structure

Constitutive genesAC. code for proteins that control expression of the structural genes at the transcriptional level

  1. Where is the operator on mRNA?

Located in the promoter region and sometimes extends into first gene

  1. Define the following:
  1. Operon-a single transcription unit that includes structural genes for a common process
  1. Operator-binding site of regulator protein
  1. Regulator gene-synthesizes a protein that controls transcription of the operon
  1. Regulatory protein-protein synthesized by regulator gene(activator or repressor)
  1. Negative control-regulator protein is a repressor. It binds to operator and inhibits transcription
  1. Positive control-regulator protein is an activator. It binds to operator and stimulates transcription
  1. Inducible operon-transcription is normally off, needs to be turned on(induced)
  1. Repressible operon-transcription is normally on, needs to be turned off(repressed)
  1. The lac operon is an example of what kind of operon?

Negative inducible

26. lac operon

a. what are the structural genes and what do they encode for?

lacA-transacetlyase (don’t know purpose)

lacZ-β-galastosidase (converts lactose to allolactose)

lacY-permease (permease allows cell to import lactose)

b. What does lacO do?

lacO encodes for the operator. A mutation here would cause a repressor being unable to bind to operator. This would result in constant transcription of the structural genes

c. What does lacI do?

lacI encodes for the repressor (regulatory protein). A mutation here could cause repressor to never be able to bind (lacI-) or a mutation could cause a super repressor than cannot bind the inducer (allolactose). The outcome of this would be constant repression and no transcription even in the presence of lactose

d. What would be the result of a (lacOC/LacO+) partial diploid? LacOCis a mutation in the operator that results in the operator being unable to bind a repressor. Is this mutation cis or trans?

*assume that both lacZ are actually functional and lacZ+. Not how they are shown in figure with one being mutant. Just looking at operator mutation for this question.

Result: this is a cis mutation because it only affects the strand of mRNA the mutation is on. The results in a partial diploid in an absence of lactose would be transcription of structural genes constitutively on one mRNA (lacOC). In the presence of lactose, both mRNAs would have transcription because the lacOC is constitutively expressed and the lacO+ has allolactose bound to repressor which makes it fall off and allow transcription

DO THE PRACTICE PROBLEMS THAT ARE ASSIGNED

Review vocab terms in lecture 25/26 that weren’t covered in here for sake of space. SI session on 10/27 at 5:10 will be doing jeopardy where the focus is on vocab