Week 1 Day 2 Flashcards
What protein solves the problem of DNA shortening that causes senescence?
Telomerase
Telomerase permits cells to continue dividing beyond their____
Hayflick limit
What are some ways that DNA synthesis is used as a therapeutic target?
- Nucleoside analogues (chain terminators)
- Reverse-transcriptase inhibitors
- Promutagenic nucleoside analogs
Name an endogenous and exogenous process that use reverse transcriptase.
Endogenous-telomerase
Exogenous-retroviral integration
A rxn driven by either change in entropy to a more disordered state or by liberation of heat (enthalpy) would have a _____ change in free energy.
negative (and proceed spontaneously in forward direction)
If change in free energy (ΔG) is positive, the rxn will proceed spontaneously in the ___ direction.
Reverse
If order increases, ΔS is:
less than zero. (negative)
How can you overcome an unfavorable ΔG to drive a rxn forward? (not ΔG°)
ΔG=ΔG°+RTln(product/substrate)
By removing product, you can make ln of a fraction negative, decreasing ΔG.
OR couple it with a favorable rxn
T/F: Enzymes lower ΔG of a rxn.
False, they increase rxn rate and lower activation energy but CAN’T lower ΔG (ΔG only depends on concentrations of product/substrate)
List 4 ways enzymes lower EA
- Provide proximity and orientation of reactants
- Ensure specificity of substrates and products
- Stabilize transition complex
- Link energetically unfavorable rxns (+ΔG) with favorable rxns (-ΔG). Remember multiple rxn’s ΔG’s add together
Explain the function of hexokinase:
Links ATP hydrolysis to phosphorylation of glucose to create an energetically favorable rxn.
Hexokinase is located in ____
all tissues
Glucokinase is a form of _____ found ______
hexokinase; in the liver and beta cells in the pancreas
Define Km
Substrate concentration at which V=1/2Vmax
The maximum reaction rate at an infinite substrate concentration where all enzyme is bound to a substrate is:
Vmax
Km of Enzyme A = 0.1 mM
Km of Enzyme B= 3 mM
At a substrate concentration of 2 mM which enzyme is creating products faster?
Enzyme A (2mM»Km of 0.1, so it is functioning at close to Vmax)
Allosteric activators shift a Michaelis-Menten plot:
to the left and more hyperbolic. (Decrease Km and may increase Vmax)
Allosteric inhibitors ____ the Michaelis-Menten plot of rxn velocity.
flatten
A Lineweaver-Burk plot is the reciprocal of a _____ plot
Michaelis-Menten
The y-intercept of a Lineweaver-Burk plot is:
1/Vmax
The x-intercept of a Lineweaver-Burk plot is:
–1/Km
The slope of a Lineweaver-Burk plot is:
Km/Vmax
On a Lineweaver-Burk plot, if the x-intercept moves to the left, Km ____
decreases.
x-intercept is –1/Km so if it moves left = gets more negative = 1/Km gets larger = Km decreases
Name 3 possible inhibitor drug mechanisms
- Competitive
- Noncompetitive
- Allosteric
If a drug increases Km but Vmax stays constant, the drug’s mechanism is:
competitive inhibition
Substrate analogs and transition-state analogs are:
competitive inhibitors
Competitive inhibitors ____ Km and ____ Vmax
increase; do not change
On a Lineweaver-Burk plot if the x-intercept moves to the right but the y-intercept doesn’t change, the mechanism of inhibition is:
Competitive (increases Km, doesn’t change Vmax)
Why doesn’t a competitive inhibitor change the Vmax?
Because the competitor can be overcome by excessive amounts of substrate. So it can still reach Vmax, it just takes a much higher [substrate] to get there (increasing Km)
Suicide inhibitors are a form of _______
Noncompetitive inhibitor (permanently inactivate the enzyme)
What type of inhibitor cannot be overcome by excess substrate specifically because it makes a conformational bond change at the site of catalytic cleft?
Noncompetitive
What effect would a noncompetitive inhibitor have on the x- and y-intercepts of a Lineweaver-Burke plot?
X-intercept would not change (Km)
Y–intercept would be higher
(Vmax decreases, 1/Vmax gets bigger)
Allosteric inhibitors ___ Km and ___Vmax
increase;decrease
may change both, flatten the curve
X –(enzyme A)–> Y
Y –(enzyme B)–> Z
If you increase the rxn rate of enzyme B, what effect will it have on the ΔG of enzyme A?
ΔG of rxn A will decrease.
Increasing enzyme B removes Y faster, removing product of rxn A, which decreases ΔG of rxn A.
X –(enzyme A)–> Y
Y –(enzyme B)–> Z
If you increase the rxn rate of enzyme B, what effect will it have on the Vmax of enzyme A?
NO CHANGE. Vmax depends on amount of SUBSTRATE, not product, so removing product doesn’t affect Vmax.
In RNA, uracil binds ____
Adenine
The ability to fold into complex 3D shapes permits some RNA molecules to have both ___ & ___ function.
Structural & Catalytic
Describe the RNA formed from the DNA template:
5’-ATCG-3’
5’-CGAU-3’
Which DNA strand has the opposite sequence from an RNA product?
The template strand
T/F: Transcription and translation can occur simultaneously in eukaryotes.
False, they can occur simultaneously in prokaryotes.
Prokaryotic mRNA has multiple start sites, so 1 mRNA can make multiple proteins, and is _____
polycistron.
In what direction are codons and anticodons read?
codons : 5’-3’
anticodons: 3’-5’ –> third position in codon matches first position in anticodon
What are the 2 specific regions on tRNA that are needed for protein synthesis?
anticodon and short single stranded region on 3’ end
What explains why there 20 amino acids, but 61 codons and only 48 kinds of tRNAs?
wobble base-pairing: some tRNA only require accurate base pairing of first two positions
Where does energy come from to add amino acids to the growing polypeptide chain?
from the energy released from breaking of the high-energy amino acid – tRNA bond
What enzyme couples amino acids to their appropriate tRNA?
aminoacyl-tRNA synthetases
What end are amino acids added to on a growing polypeptide chain?
added to the C-terminal end
T/F: In order to elongate an RNA strand, RNA pol. requires a primer.
False, can start without a primer, just needs to recognize transcription factors bound to cis sequences of a promoter.
What controls the frequency of transcription?
Cis regulatory sequences in a promoter, enhancers
Differences in transcription initiation between prokaryotes and eukaryotes.
Prok. RNA pol. + sigma factor can initiate without help of other proteins.
Euk. RNA pol.’s require over 100 protein subunits (general transcription factors and specific transactivator proteins) to assemble for initiation.
What does a ribosome recognize/bind to on eukaryotic and prokaryotic mRNA?
euk: 5’ cap
pro: Shine-Delgarno sequence
What do the small and large subunits of the ribosome match do during protein synthesis?
small: matches tRNAs to codon
large: catalyzes formation of the peptide bonds
What are RNA molecules that possess catalytic activity?
ribozymes
What are the subunits of the eukaryotic and prokaryotic ribosomes?
pro: subunits are 50S and 30S, making up 70S ribosome
euk: 60S and 40S make up 80S ribosome
What do eukaryotes use to initiate translation?
initiation factors (eIFs) which load tRNA into the small ribosomal subunit
What proteins are used in the elongation step of both prokaryotic and eukaryotic translation?
elongation factors which drive translation forward; can be a target for antibiotics using prokaryotic specific EFs
What terminates translation?
binding of a release factor to an A-site that is occupied by a stop codon
What is a polyribosome?
series of ribosomes that can simultaneously translate the same eukaryotic mRNA molecule
Describe the functions of the 3 eukaryotic RNA polymerases that recognize different promoter types.
Pol I: rRNA
Pol II: mRNA
Pol III: tRNA, small subunit rRNA
Name the consensus sequence that binds trans-acting factors to attract RNA pol.
TATA box (form of a cis sequence)
Besides the cytoplasm, where else can translation occur?
rough ER
Tetracycline function
blocks binding of aminoacyl-tRNA to A-site of ribosome
Streptomycin function
prevents the transition from translation initiation to chain elongation and also causes miscoding
Chloramphenicol
blocks the peptidyl transferase rxn on ribosomes
Erythromycin function
binds in the exit channel of the ribosome and thereby inhibits elongation of the peptide chain
Rifamycin function
blocks initiation of RNA chains by binding to RNA polymerase (prevents RNA synthesis)
Define cistron
A region of DNA that encodes for a single polypeptide chain.
Describe the transcription cycle of bacterial RNA polymerase:
- sigma factor binds TATA box and RNA polymerase
- RNA pol. unwinds DNA with helicase
- Elongation starts, after 10 nucleotides sigma factor falls off
- RNA pol. reaches termination signal, which forms an RNA structure (like a loop), destabilizing pol., and it falls off
RNA processing is carried out in which cell organelle?
Nucleus (RNA can’t leave until it’s capped/tailed/spliced)
Differences in transcription initiation between prokaryotes and eukaryotes.
Prok. RNA pol. + sigma factor can initiate without help of other proteins.
Euk. RNA pol.’s require over 100 protein subunits (general transcription factors) to assemble for initiation.
Describe eukaryotic transcription elongation
Euk. RNA pol. moves jerkily, pausing until elongation factors associate with it and help move it, and topoisomerases relieve tension ahead of it.
What is the significance of the mRNA 5’GTP cap?
- Protects primary transcript from degradation
2. Recognized by small ribosomal subunit to begin translation
What structure carries out splicing?
Spliceosome (containing snRNPs)
What are the invariant consensus nucleotide sequences in RNA that signal beginning/end of introns?
5’GU–AG3’
Describe the RNA splicing rxn
3’ invariant A does nucleophilic attack on 5’ splice site and links to it, forming lariat. Released free 3’OH then Nu. attacks the next exon, joining exons together and releasing intron.
Name 2 types of splicing errors.
- Exon skipping
2. Cryptic splice-site selection (splices at sequences other than the invariant splice sites)
Abnormal processing of beta-globin primary RNA transcript causes the disease beta-thalassemia. This disease is caused by:
abnormal splicing
Besides having the right processing done, mRNA needs help from ____ to get through nuclear pores
chaperone proteins
Describe the properties of lincRNAs
long-intergenic non-coding RNAs: similar to mRNAs in length and processing, but function in gene silencing
