biochem final
separation by solubility
(salting out) precipiation by ammonium sulphate: depends on polarity of protein surface, determines solubility in water
NOT a property of ATP synthase
(αγ)3 complex rotates relative to a fixed β-subunit
steps of PCR
1. separate DNA strands by heating 2. target the area to be copies by cooling 3. extend the target area by heating. allow enzyme Taq to attach 4. repeat. by repeating 30x, a DNA sequence can become over 1 billion.
How many nucleotide triphosphates are hydrolyzed per amino acid incorporated into a growing polypeptide chain during protein synthesis on the ribosome?
2 GTP
separation by multiple properties
2D gel electrophoresis, where protiens are separated in 1 direction by isoelectric focusing, performed ay 90 degree angle
Which of the following best describes the net energy equivalent products formed during the oxidation of one acetyl group to two molecules of carbon dioxide via the citric acid cycle?
3 NADH + 1 FADH2 + 1 GTP
true statements about enzymes
A substantial amount of their catalytic power results from binding of the substrate(s) through weak interactions. They increase the rate of reactions by decreasing the activation energy of the transition state. Enzyme active sites are most complimentary to transition state They do not alter the overall thermodynamics of a reaction.
In an N-linked glycoprotein, the carbohydrates are attached to which of the following amino acids?
Aspargine. in O linked, it is serine
All are stages in transcription EXCEPT: A binding of RNA polymerase holoenzyme at the promoter site B chain elongation C DNAse I activity on RNA polymerase/DNA complex D initiation of polymerization E chain termination
C
Sequence specific interactions between a DNA-binding protein and the major groove of DNA are likely to be mediated by
H-bonds between base edges and polar side chains
Citrate synthase is regulated by many different metabolites . Choose the condition where the indicated regulator activates citrate synthase.
Low [ATP/ADP] ratio since ADP is a positive allosteric regulator for citrate synthase.
what connects sugars together?
N glycosidic bond
A suspension of yeast cells is being grown under anaerobic conditions such that glucose is degraded to ethanol and carbon dioxide.Why would adding an inhibitor of alcohol dehydrogenase to the yeast cell suspension result in rapid cell death?
NADH generated during glycolysis cannot be recycled back to NAD+, thus anaerobic ATP production through glycolysis cannot be maintained
separation by size/shape
SEC, largest elutes first. PAGE allows for separation on the basis of mass to charge ratio. AGE is typically for DNA and run horizontally
properties of ATP synthase
The F1 subunit is attached to the integral membrane protein F0. It is a transmembrane channel for protons. Beta- subunits have the catalytic site for ATP synthesis. The ring of c subunits form a rotor with respect to the alpha subunits
Half the maximum reaction rate is reached
[S] = Km
doubling [S] will almost double the rate, less than 10% of the active sites are occupied by substrate
[S]<<Km
Doubling [S] will have little effect on reaction rate
[S]>>Km
Which of the following secondary structures would you expect to find on the surface of a globular protein?
a helix, B sheet, loops between two a helices
specific activity
amount of enzyme per milligram of total protein
In an alpha helix, the R groups on the AA resides
are all found on the outside of the helix spiral
Although the glycolytic degradation of glucose is a major source of energy, other dietary carbohydrates, such as galactose and fructose, are also important fuels. When being metabolized, fructose and galactose
are metabolized by conversion to intermediates in the glycolytic pathway
The long-chain fatty acids get transported through the inner mitochondrial membrane
as carnitine derivatives
Steroid hormones regulate gene expression by
binding to DNA binding receptor proteins, which then regulate gene expression
myoglobin
binds O2 with a Hill coefficient of 1
The conversion of Acetyl CoA to malonyl CoA requires
biotin
separation by density
centrifugal force
What is the key feature of DNA that allows it to be copied?
complementary base pairing
collagen
contains glycine and proline as the most abundant AA
base excision repair
corrects the most common mutation: the deamination of methyl cytosine to thymine
where are long chain FA first activated
cytosol
To increase the efficiency of an enzyme one can
decrease Km and increase kcat
separation by size/concentration difference
dialysis
the direction of proton movement relative to electron transfer and phosphorylation
electron transfer pumps protons out of the matrix. as protons reenter through the ATP synthase, ATP is produced in the matrix
In cells, NADH serves as a carrier of which of the following
electrons
In eukaryotes, DNA is present in a chromatin structure.Chromatin is made up of DNA that is
highly ordered by wrapping around histones
You need to run an experiment at pH 6.8 involving a reaction that releases hydronium (H3O+) ions. Which of the following buffers would you choose to use in your experiment?
histidine buffer (pKa = 6.4)
What makes the reaction catalyzed by citrate synthase in the citric acid cycle highly exergonic? Hint: Use the name of the enzyme to help you write out reaction that it catalyzes and consider what goes in and what comes out of the reaction
hydrolysis of thioester
What is the underlying biochemical principle for the ruptured biomembranes to reseal in an aqueous environment?
hydrophobic effect between membrane lipids
successful purification scheme
increases fold purification with each step with minimum compromise of the % yield
separation by charge
ion exchange chromatography. if pH<pI, proteins will be positive if pH>pI, proteins will be negative
ribonuclease
is a monomer stabilized by disulfide bonds
In the synthesis of triacylglycerols, the fatty acid attached to C‑3 of the glycerol backbone
is added to diacylglycerol after removal of the phosphate group from phosphatidate
Fatty acids are activated by attachment to coenzyme A at the outer mitochondrial membrane. However, the resulting fatty acyl‑CoA is not degraded until it reaches the mitochondrial matrix.The fatty acyl‑CoA
is transferred to another molecule that is involved in the transport of the FA into the mitochondrial matrix
shine dalgamo sequence
it is a polypurine sequence involved in the initiation of translation
Why is the TCA cycle the central pathway of metabolism of the cell?
its intermediates are commonly used by other metabolic reactions
contains a hydrophobic residue every 4th AA enabling a coiled coil quaternary structural arrangement
keratin
What product of contracting muscle tissue is used by the liver as the starting material for gluconeogenesis?
lactate
The presence of uncoupling proteins allows
less energy from the mitochondrial electron transport chain to be used for ATP synthesis and more for the production of heat.
The process of glycolysis occurs in the cytoplasm. The electrons from the NADH generated during glycolysis
may enter the ETC either at the level of NADH or FADH2, depending on the shuttle system used to transport them into the mitochondria
The process of glycolysis occurs in the cytoplasm. The electrons from the NADH generated during glycolysis
may enter the electron transport chain either at the level of NADH or FADH2, depending on the shuttle system used to transport them into the mitochondria.
list post translational modifications
proteolysis, phosphorylation, glycosylation, ubiquination, methylation, N-acteylation, gamma carboxylation, lipidation
how can double stand DNA breaks be repaired?
recombination
Proton flow through the ATP synthase enzyme
results in the release of ATP from its tightly bound state in the active site.
During transcription, separation of the DNA strands is necessary. This separation involves
separation in only a small segment of DNA at a time
fold purification
specific activity after/specific activity before
Given a cell in glycolysis with a ΔG′ of -2.5 kJ/mol for the phosphoglucose isomerase reaction (Step 2), you can conclude with certainty that this reaction is:
spontaneous under the given cellular conditions
Referring to the glycolytic pathway shown in the figure Identify the oxidation-reduction reaction(s) of glycolysis. Enter the step number(s) in the blank space separated by commas when needed.
step 6. it is the 1,3-bisphosphoglycerate step
Termination of protein synthesis occurs when a stop or termination codon is in the A site. Termination occurs because
stop codons are recognized by specific proteins that release the newly synthesized protein chain from the ribosome
Of the electron transfer complexes associated with the inner mitochondrial membrane, which one does NOT directly produce a portion of the proton gradient?
succinate-Q reductase (complex II)
DNA replication involves multiple steps that require different enzymes. Which process does primase catalyze in DNA replication?
synthesis of a short RNA sequence that initiates DNA synthesis
The anticodon for tRNAPhe is shown below. Click on the 'wobble' position in this tRNA
the codon closest to the 5' end
Based on the given table for standard energies of hydrolysis, the hydrolysis of phosphate from which of the following molecules is most thermodynamically favorable?
the compound with the most negative kcal mol-1 value
Why can't cells use the breakdown of glucose to pyruvate to generate energy without further conversion of pyruvate via aerobic or anaerobic respiration?
the electron acceptor reduced during glycolysis must be regenerated
which of the following is true under the following conditions: the enzyme concentration is 5nM, the substrate concentration is 5nM, and the KM is 5 uM
the enzyme is saturated with substrate
the driving force for a water-soluble protein to fold is
the hydrophobic effect
the strong conclusion from Anifinsen's work on RNaseA was that
the native conformation of a protein is adopted spontaneously based on the primary structure of the protein
% yield
total enzyme activity divided by the initial specific activity
Active transport across membranes are uniquely characterized by:
transport of molecules with the tight coupling of an input of energy to drive a thermodynamically unfavorable movement
Electron flow down the electron transport chain leads to the:
transport of protons across the inner mitochondrial membrane from inside the matrix to the intermembrane space
The interactions that are the basis of molecular recognition in biological systems have the following common characteristics
weak, non-covalent, reversible, and specific
nucleotide excision repair
when damaged DNA is recognized by response to helix distortion rather than a specific sequence
what is a reducing sugar?
when there are H+ ions attached to the anomeric carbon along with the o
During the catabolism of glycogen, the glycogen phosphorylase enzyme breaks the:
α‑1,4 linkages but not the α‑1,6 linkages.