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.