BIOL 200 Midterm Review Exam
Questions with Correct Answers
Tertiary structure of protein - ANSWER-long range folding
stabilized by hydrophobic interactions b/w non-polar side chains
H bonds b/w polar side chains
Disulfide bonds b/w cysteine residues (covalent bond)
Quaternary structure of protein - ANSWER-multi-meric structure
pores (4 proteins) = potassium ion channel protein
Supramolecule structure of protein - ANSWER-large-scale assembly
10-100 polypeptides chains
general transcription factors: RNA polymerase, mediator complex, promotor, pre-
initiation transcription complex
Motifs - ANSWER-combos of secondary structure proteins
Coil-Coil Motif - ANSWER-hydrophobic interactions
fibrous proteins
ex: collagen
Helix-loop-helix Motif - ANSWER-ionic bonds involving Ca2+
ex: Ca2+ binding proteins
Zinc-finger Motif - ANSWER-contains Zn2+
ex: RNA, DNA, binding proteins
Domains - ANSWER-need these for certain proteins to function
ex: pyruvate kinase needs 3 domains
Reshuffling of motifs and domains - ANSWER-new proteins made
Ingredients for transcription in bacteria - ANSWER-DNA template, ribonucleotides
(monomers for RNA polymerization), RNA polymerase (catalyze synthesis of RNA
Ist step of transcription - ANSWER-Initiation
- polymerase binds to promoter (upstream of gene) in duplex DNA
forms "closed complex"
- polymerase melts duplex DNA
forms "open complex"
- polymerase catalyzes phosphodiester linkage of two initial rNTPs
rNTP - ANSWER-ribonucleotide tri-phosphate, building blocks of RNA synthesis
,N = G, C, A, U
2nd step of transcription - ANSWER-Elongation
- polymerase goes from 3' to 5'
- continues to melt DNA
- adds rNTPS to growing RNA
- formation of phosphodiester bonds b/w 3' OH and alpha phosphate group of
incoming rNTP
3rd step of transcription - ANSWER-Termination
- at stop site, polymerase releases completed RNA and dissociates from DNA
Holoenzyme - ANSWER-subunit of RNA polymerase
consists of core enzyme + sigma factor
alpha: loading entire onto transcript
beta: helps with phosphodiester linkage
Sigma factor - ANSWER-subunit of RNA polymerase
scans DNA until encounters promoter to bind with and form "closed complex"/to start
transcription
How does sigma factor recognize promoter region? - ANSWER-RNA polymerase
subunit
binds to specific sequence motifs (-10, -35 regions = start, stop site)
Messenger RNA - ANSWER-mRNA
genetic info from DNA in form of codons
Transfer RNA - ANSWER-tRNA
key to decipher codons in mRNA
each tRNA has an associated a.a. and anticodon
Ribosomal RNA - ANSWER-rRNA
assiciates with proteins to from ribosomes
tRNA structure - ANSWER-folds with itself
acceptor stem, loop, anticodon, loop
specific tRNA to a.a.
Start and stop codon - ANSWER-Met = start
codon AUG
3 Stop codons
Wobble base pairs - ANSWER-Guanine-Uridine
Adenosine-Inosine
Cytidine-Inosine
Uridine-Inosine
Where does wobble base occur? - ANSWER-b/w the 3rd position of a codon and 1st
position of anticodon
, ex: anticodon GAC (3,2,1) can b.p. with codon GUC (3,2,1) or GUU (3,2,1)
1st step of protein synthesis - ANSWER-Initiation
- initiation factors associate w/ 30s subunit = pre-initiation complex (IF1 and IF3)
- IF1 and IF2-GTP loads 50s subunit and forms 70s initiation complex
IF1 and IF3 - ANSWER-Initiation factors in protein synthesis
loads mRNA and initiates aminoacyl-tRNA forming 30s initiation complex
30s initiation complex - ANSWER-In initiation step of protein synthesis
binds the transcript at initiation codon AUG
2nd step of protein synthesis - ANSWER-Elongation
- elongation factors (EFs) = required for addition of a.a. (ribozyme, 23s RNA)
- translocation occurs
Ribozyme, 23s RNA - ANSWER-Required for elongation of protein synthesis
carries out peptdyltransferase rxn = makes peptide bond
Translocation - ANSWER-tRNA movement
anticodon of tRNA moves to the next codon of mRNA
P site of tRNA displaced
3rd step of protein synthesis - ANSWER-Termination
mRNA-ribosome-tRNA-peptidyl complex reaches stop codon
release factors mediate termination
RF1 and RF2 = mimic tRNAs
RF3-GTP: catalyzes the cleavage of the peptidyl-tRNA, releases protein chain
ribosome recycled
Parental strand - ANSWER-template for the formation of a new daughter strand
Daughter strand - ANSWER-complementary to parental
Semi-conservative mechanism - ANSWER-DNA replication proceeds through this
system
dbl stranded DNA splits up, and each strand acts as parent strand
each parent strand makes a complementary strand = daughter strand
Nucleotide (DNA) polymerization - ANSWER-DNA polymerase: catalyzes the
polymerization
Substrate = 5' deoxynucleoside-triphosphates (dNTPS, N = A, C, T, G
Primer: can be DNA or RNA
proceeds in 5' to 3'
How are dNTPs added in DNA polymerization? - ANSWER-through the formation of
phosphodiester bonds on the 3' hydroxyl of terminal sugar
RNA polymerization does not require these - ANSWER-primers
Questions with Correct Answers
Tertiary structure of protein - ANSWER-long range folding
stabilized by hydrophobic interactions b/w non-polar side chains
H bonds b/w polar side chains
Disulfide bonds b/w cysteine residues (covalent bond)
Quaternary structure of protein - ANSWER-multi-meric structure
pores (4 proteins) = potassium ion channel protein
Supramolecule structure of protein - ANSWER-large-scale assembly
10-100 polypeptides chains
general transcription factors: RNA polymerase, mediator complex, promotor, pre-
initiation transcription complex
Motifs - ANSWER-combos of secondary structure proteins
Coil-Coil Motif - ANSWER-hydrophobic interactions
fibrous proteins
ex: collagen
Helix-loop-helix Motif - ANSWER-ionic bonds involving Ca2+
ex: Ca2+ binding proteins
Zinc-finger Motif - ANSWER-contains Zn2+
ex: RNA, DNA, binding proteins
Domains - ANSWER-need these for certain proteins to function
ex: pyruvate kinase needs 3 domains
Reshuffling of motifs and domains - ANSWER-new proteins made
Ingredients for transcription in bacteria - ANSWER-DNA template, ribonucleotides
(monomers for RNA polymerization), RNA polymerase (catalyze synthesis of RNA
Ist step of transcription - ANSWER-Initiation
- polymerase binds to promoter (upstream of gene) in duplex DNA
forms "closed complex"
- polymerase melts duplex DNA
forms "open complex"
- polymerase catalyzes phosphodiester linkage of two initial rNTPs
rNTP - ANSWER-ribonucleotide tri-phosphate, building blocks of RNA synthesis
,N = G, C, A, U
2nd step of transcription - ANSWER-Elongation
- polymerase goes from 3' to 5'
- continues to melt DNA
- adds rNTPS to growing RNA
- formation of phosphodiester bonds b/w 3' OH and alpha phosphate group of
incoming rNTP
3rd step of transcription - ANSWER-Termination
- at stop site, polymerase releases completed RNA and dissociates from DNA
Holoenzyme - ANSWER-subunit of RNA polymerase
consists of core enzyme + sigma factor
alpha: loading entire onto transcript
beta: helps with phosphodiester linkage
Sigma factor - ANSWER-subunit of RNA polymerase
scans DNA until encounters promoter to bind with and form "closed complex"/to start
transcription
How does sigma factor recognize promoter region? - ANSWER-RNA polymerase
subunit
binds to specific sequence motifs (-10, -35 regions = start, stop site)
Messenger RNA - ANSWER-mRNA
genetic info from DNA in form of codons
Transfer RNA - ANSWER-tRNA
key to decipher codons in mRNA
each tRNA has an associated a.a. and anticodon
Ribosomal RNA - ANSWER-rRNA
assiciates with proteins to from ribosomes
tRNA structure - ANSWER-folds with itself
acceptor stem, loop, anticodon, loop
specific tRNA to a.a.
Start and stop codon - ANSWER-Met = start
codon AUG
3 Stop codons
Wobble base pairs - ANSWER-Guanine-Uridine
Adenosine-Inosine
Cytidine-Inosine
Uridine-Inosine
Where does wobble base occur? - ANSWER-b/w the 3rd position of a codon and 1st
position of anticodon
, ex: anticodon GAC (3,2,1) can b.p. with codon GUC (3,2,1) or GUU (3,2,1)
1st step of protein synthesis - ANSWER-Initiation
- initiation factors associate w/ 30s subunit = pre-initiation complex (IF1 and IF3)
- IF1 and IF2-GTP loads 50s subunit and forms 70s initiation complex
IF1 and IF3 - ANSWER-Initiation factors in protein synthesis
loads mRNA and initiates aminoacyl-tRNA forming 30s initiation complex
30s initiation complex - ANSWER-In initiation step of protein synthesis
binds the transcript at initiation codon AUG
2nd step of protein synthesis - ANSWER-Elongation
- elongation factors (EFs) = required for addition of a.a. (ribozyme, 23s RNA)
- translocation occurs
Ribozyme, 23s RNA - ANSWER-Required for elongation of protein synthesis
carries out peptdyltransferase rxn = makes peptide bond
Translocation - ANSWER-tRNA movement
anticodon of tRNA moves to the next codon of mRNA
P site of tRNA displaced
3rd step of protein synthesis - ANSWER-Termination
mRNA-ribosome-tRNA-peptidyl complex reaches stop codon
release factors mediate termination
RF1 and RF2 = mimic tRNAs
RF3-GTP: catalyzes the cleavage of the peptidyl-tRNA, releases protein chain
ribosome recycled
Parental strand - ANSWER-template for the formation of a new daughter strand
Daughter strand - ANSWER-complementary to parental
Semi-conservative mechanism - ANSWER-DNA replication proceeds through this
system
dbl stranded DNA splits up, and each strand acts as parent strand
each parent strand makes a complementary strand = daughter strand
Nucleotide (DNA) polymerization - ANSWER-DNA polymerase: catalyzes the
polymerization
Substrate = 5' deoxynucleoside-triphosphates (dNTPS, N = A, C, T, G
Primer: can be DNA or RNA
proceeds in 5' to 3'
How are dNTPs added in DNA polymerization? - ANSWER-through the formation of
phosphodiester bonds on the 3' hydroxyl of terminal sugar
RNA polymerization does not require these - ANSWER-primers
