Week 1 Flashcards
Describe how a reaction will proceed if delta G is negative.
spontaneously in the forward direction
Describe how a reaction will proceed if delta G is positive.
spontaneously in the reverse direction
When entropy is less than 0, order____________.
increases
ΔGo’
change in free energy under standard conditions of 25 degrees Celsius and pH of 7.0 with equimolar substrates and products
Keq=
[product] / [substrate]
What will happen to ΔG if the [product] decreases?
the reaction becomes more energetically favorable
Describe three ways enzymes decrease activation energy and increase reaction rates.
- provide proximity and orientation of reactants
- ensure specificity of substrates and products
- stabilize the transition complex
True or False: Enzymes change the ΔG of a reaction.
False
Vmax [S]
v= —————————————–
Km + [S]
identify and explain the elements of this equation
v= rate or velocity of the reaction (amount of product / unit of time)
Vmax= maximum reaction rate at an infinite substrate concentration where all enzyme is bound to substrate
[S]= concentration of substrate
Km= Michaelis constant, the [S] at which v= 1/2Vmax
True or False: enzymes increase reaction rates (v)
true
Name four isoforms of pyruvate kinase and where they are found in the body.
PK-M1: most tissues
PK-M2: embryonic tissue, cancer
PK-L: liver
PK-R: Red blood cells
Describe the affect of an allosteric activator and an inhibitor on the reaction rate curve in the Michaelis-Menten graph.
Activator: shifts curve to the left and changes curve from sigmoid to hyperbola, increasing the rate of reaction.
Inhibitor: shifts curve to the right, decreasing the reaction rate.
What type of enzyme inhibitor increases Km but does not change Vmax?
Competitive Inhibitor
Describe the characteristics of a competitive enzyme inhibitor.
Molecules that bind at the substrate binding site(s) and prevent substrate binding. Substrate analogs and some transition state analogs are competitive inhibitors. Competitive inhibitors increase Km, but do not change Vmax.
Describe the characteristics of a noncompetitive enzyme inhibitor.
Molecules which bind an enzyme and inhibit its activity without inhibiting substrate binding. Suicide inhibitors and some transition state analogs are in this class. Noncomptetive inhibitors decrease Vmax, but do not change Km
create covalent bonds—permanent for the life of the enzyme
Describe the characteristics of a allosteric enzyme inhibitor.
Molecules which bind an enzyme distant from the substrate binding site and cause a conformational change which alters the substrate binding site and prevents substrate binding. Allosteric inhibitors function primarily on oligomeric enzymes, and can not be described by Michaelis-Menten kinetics.
Both Km and Vmax may be changed.
For the reaction A–>B the ∆G is negative. This reaction:
- will proceed spontaneously in the forward direction, A–> B.
- will proceed spontaneously in the reverse direction, B –>A.
- is at equilibrium.
1.will proceed spontaneously in the forward direction, A–> B.
For the reaction: 1 mol H2 + ½ mol O2 –> 1 mol H2O:
- order increases (ΔS > 0)
- order increases (ΔS < 0)
- order decreases (ΔS > 0)
- order decreases (ΔS < 0)
2.order increases (ΔS < 0)
The ΔG0’ for formation of water from oxygen and hydrogen is -238 kJ/mol. The ΔG0’ for dissolving table salt in water is -9 kJ/mol. Which reaction(s) will proceed spontaneously?
Both
There are different isoforms of hexokinase expressed in different tissues. Erythrocyte (red blood cells) hexokinase has a Km of 0.05 mM glucose. Hepatic (liver) glucokinase has a Km of 5.0 mM glucose.A 36 year old male fasted for four days, and his serum glucose concentration was 4.5 mM. What tissue is phosphorylating glucose most rapidly?
Red Blood cells (lower Km)
Penicillin is an antibiotic that targets glycoprotein transpeptidase, an enzyme essential for cross linking the bacterial cell wall. Penicillin’s structure is similar to transpeptidase’s natural substrate when it is in its highest energy state during the reaction. Penicillin also becomes covalently bound to to the enzyme’s active site, permanently disabling the enzyme. How would you describe penicillin?
- non-competitive inhibitor
- competitive inhibitor
- transition state analog
- heavy metal
- suicide inhibitor
1.non-competitive inhibitor (?)
Cancer cells generally proliferate faster than normal cells, and thus have a greater requirement for nucleotides than normal cells. Drugs that block pathways for nucleotide synthesis are generally more lethal to cancer cells than normal cells.Methotrexate is a cancer drug that resembles folate, the natural substrate for dihydrofolate reductase and a precursor of dTTP. Methotrexate increases the Km of dihydrofolate reductase without changing its Vmax.What kind of drug is methotrexate?
- non-competitive inhibitor
- competitive inhibitor
- transition state analog
- heavy metal
- suicide inhibitor
2.competitive inhibitor (?)
What type of bond links nucleotide subunits in DNA and RNA?
phosphodiester
List two differences between prokaryotic and eukaryotic mRNA.
Eukaryotic mRNA has 5’ cap and poly-A tail
The main enzyme in transcription.
RNA polymerase
Name one similarity and one difference between RNA polymerase and DNA polymerase.
Both move in the 3’-5’ direction on DNA creating a chain that is 5’-3’ in orientation.
RNA polymerase can start a growing chain without a primer
How many types of RNA polymerase are in prokaryotes and eukaryotes, respectively?
Prokaryotes: one
Eukaryotes: three
What type of RNA polymerase produces rRNA in eukaryotes?
Pol I
What type of RNA polymerase produces mRNA, miRNA, and lincRNA in eukaryotes?
Pol II
What type of RNA polymerase produces small RNAs such as tRNAs and 5S rRNAs?
Pol III
cis DNA sequences recognized by RNA polymerase that determine the start point and frequency of transcription are called__________.
promoters
Describe the processing of eukaryotic mRNA that occurs before the mature mRNA is transported out of the nucleus for translation in the cytosol.
processing involves the addition of a 5’ cap in the leader sequence, splicing out of non-coding introns and the addition of a poly-A tail in the 3’ trailer sequence, thus the mature mRNA has a 5’ capped leader untranslated region, an exon coding translated region (usually corresponding to the amino acid sequence of a polypeptide) and a 3’ untranslated region containing a poly-A tail
The promoter DNA sequence identified by transcription factor TFIID located 25 nucleotides away from the site at which transcription is initiated by RNA Pol II is called______.
TATA box
What relieves the superhelical tension created by DNA unwinding during transcription in eukaryotes?
topoisomerases
What relieves the superhelical tension created by DNA unwinding during transcription in prokaryotes?
gyrase
Describe two functions of the 5’ cap on eukaryotic mRNA.
- protection from degradation
2. recognition site for protein synthesis in the ribosome.
Which nucleotides mark the beginning and end of intron splicing in mRNA?
GU (5’ start of intron) and AG (3’ end of intron)
Splicing is done largely by small nuclear RNAs (snRNAs) which combine to form the core of the _________.
spliceosome
Which codon in mRNA acts as both the stop codon and specifies methionine?
AUG
What are the two most critical regions of tRNA with regards to protein synthesis?
The 3’ single stranded end which is bonded to the specific amino acid indicated by the matching mRNA codon and three nucleotide anticodon that pairs with that codon.
Describe wobble base pairing
differences in the third nucleotide of the codon that do not change the identity of the amino acid it pairs with, this is why the genetic code is redundant
aminoacyl-tRNA synthetases
recognize and attach correct amino acid to a tRNA (3’ single strand end) via ATP hydrolysis to produce a high energy covalent bond; in humans there is a different synthetase for all 20 amino acids
Where does the energy come from to link amino acids covalently to grow the polypeptide chain?
from the high energy bond between the 3’ single strand end of the tRNA and the amino acid
List two mechanisms that ensure synthetases link to the correct amino acid (overall process is called activation)
- selection-correct amino acid has highest affinity for for the active site pocket of its corresponding synthetase
- editing-removes incorrectly bonded amino acids (acids of similar size and shape that are not easily discriminated)
Where are incoming amino acids added to the polypeptide chain, carboxyl (C) terminal or amino (N) terminal?
carboxyl
N-C(polypeptide chain)-N-C- <—-N-C (incoming amino acid)
What are the main roles of the large and small ribosomal subunits and what order do they occur in?
First: small subunit recognizes the mRNA cap
Later: large subunit is responsible for catalyzing the formation of the peptide bonds linking amino acids
An RNA molecule that posses catalytic activity is known as a __________.
ribozyme
Translation begins with codon ______.
AUG
eIFs
eukaryotic initiation factors: proteins that load initiator tRNA into the small ribosomal subunits
initiator tRNA
special tRNA adds initial Met at AUG on mRNA
substitute for 5’ cap in prokaryotes (5’-AGGAGGU-3’) that positions AUG codon in the ribosome
Shine-Delgarno sequence
What are the stop codons for protein synthesis?
UAA UAG UGA
Antibiotic which blocks the binding of aminoacyl-tRNA to A site of ribosome
Tetracycline
Antibiotic which prevents the transition from translation initiation to chain elongation and also causes miscoding
Streptomycin
Antibiotic which blocks the peptidyl transferase reaction on ribosomes
Chloramphenicol
Antibiotic which binds in the exit channel of the ribosome and thereby inhibits elongation of the peptide chain
Erythromycin
Antibiotic which blocks initiation of RNA chains by binding to RNA polymerase, preventing RNA synthesis
Rifamycin
