Final Exam Biochem

How many hydrogen bonds are in an adenosine-thymine/uracil bond

2 hydrogen bonds

How many hydrogen bonds are in a guanine-cytosine bond?

3 hydrogen bonds

In secondary structures, there is H-bonding every ______ amino acid residue

4th

Trypsin pairs well with positively charged amino acids because aspartate (negatively charged) is in the binding pocket. What amino acids would bind to trypsin?

Arginine and lysine

What do transferases do and what is a common transferase?

Catalyze group transfer reactions and usually require a coenzyme. Common transferase is a kinase which transfers a phosphate group from ATP.

What do hydrolases do?

Catalyze hydrolysis with water as the acceptor of the group transferred.

What do ligases do and what are they usually referred to?

Catalyze ligation (joining) of two substrates. Require energy like ATP. They are usually referred to as synthetases.

What do lyases do?

Catalyze lysis of a substrate generating a double bond in nonhydrolytic, nonoxidative, elimination reactions

What does an oxireductase do?

Catalyze oxidation-reduction reactions. Commonly known as dehydrogenases. Dehydrogenases will give you NADH.

What do isomerases do?

Catalyze structural change within a single molecule (isomeraztion)

What is the most common protein denaturants?

Chaotropic agents

Describe a secondary structure

Coils and folds held together by hydrogen bonding create alpha-helices and beta-pleated sheets

What nucleotides are pyrimidines?

Cysteine, thymine, and uracil

True or False: All proteins have quaternary structure

False

True or False: myoglobin delivers oxygen more efficiently to the tissues

False. hemoglobin does

True or False: the melting temperature of A-T bonds is higher than G-C bonds because of more H-bonds

False: G-C melting temperature is higher because of 3 H-bonds compared to 2 H-bonds in A-T

Elatase binds well to small amino acids. It's binding pocket is held together by valine and threonine. What amino acids would bind to elatase?

Glycine and alanine

What nucleotides are purines?

Guanine and Adenine. Purines are the bigger molecules with a imidazole and a pyrimidine

Amino acids in a neutral pH will look like what?

Have a positive charge on the amine group and a negative charge on the carboxyl

Kcat is a catalytic constant. What does it mean?

Kcat is a turnover number. How many substrate molecules can one enzyme molecule convert per second

Which of the following technique is NOT a protein purification technique? Single best answer. a) ion-exchange chromatography b) gel-filtration chromatography c) mass spectrometry d) affinity chromatography

Mass spectrometry

What are some mechanisms of enzyme reactions?

Mechanisms of enzyme catalyzed reactions include nucleophilic substitutions, cleavage reactions, and oxidation-reduction reactions.

What are the six classes of enzymes?

Oxidreductases, transferases, hydrolases, lyases, isomerases, and ligases.

___________ bonds remain intact when proteins are denatured.

Peptide. The primary structure for an amino acid that is denature will still be the same

Pure as Gold

Purine: adenine and guanine

What is a peptide bond?

The bond formed between a carboxly group of one amino acid and an alpha-amino group on another amino acid

Describe a quaternary structure

The overall protein structure from migrating two or more polypeptide chains.

Describe a tertiary structure

The overall shape of a polypeptide. Hydrogen bonds, ionic bonds, disulfide bonds, and hydrophobic interactions contribute to this structure

True of False: myoglobin has a higher affinity to oxygen

True

Chemotrypsin prefers bulky aromatic side chains. They fit into the hydrophobic pocket located near catalytic groups. The pocket is a serine residue. What amino acids would this be?

Tyrptohphan, tyrosine, and phenylalaine

You can determine the structure of a protein by _________ _____________

X-ray crystallography

What statements are true about SDS-PAGE, a method used to separate proteins? a) smaller proteins migrate faster through the polyacrylamide gel b) proteins are separated in a polyacrylamide gel matrix c) Protein-SDS complexes migrate towards the negative electrode d) a protein binds roughly 1.4 times its mass of SDS resulting in a large overall negative charge e) proteins are visualized using a a dye that binds to gel matrix, but not proteins f) Sodium dodecyl sulfate binds proteins, resulting in protein-SDS complexes that are similar in size.

a) smaller proteins migrate faster through the polyacrylamide gel b) proteins are separated in a polyacrylamide gel matrix d) a protein binds roughly 1.4 times its mass of SDS resulting in a large overall negative charge

Phi angles are based on the rotation of the _______ to ________ bond

alpa-carbon to carbon

Psi angles are based on the rotation of the ________ to __________ bond

alpha carbon to nitrogen

A peptide is positively charged at pH values __________ it's pI value (and can bind to a cation-exchange column)

below

Molecular ___________ help to fold proteins

chaperones

The binding pattern for oxygen to hemoglobin is __________

cooperative

NMR spectroscopy give interatomic ________ between specific protons in a protein of a known sequence

distance

Proteins containing more than 200 residues usually fold into globular clusters known as ________

domains

What forces stabilize protein structure?

electrostatic interactions (ion pair) and disulfide bonds

What is the major determinant of a native protein structure?

hydrophobic effect

The oxygen dissociation curve when binding to myoglobin is ____________

hyperbolic

greater the hydropathy, the more likely it is to be the ___________ of a protein

interior

Peptides can be separated using ion-exchange column based on their _________

isoelectric (pI) values

Hemoglobin the the T state has a __________ affinity for oxygen and a __________ affinity in the R state.

low; high

Which of the following is not a serine protease? a) trypsin b) chemotrypsin c) elatase d) lysosome

lysosome

SDS disrupts _________ bonds and stabilizes the 3D structures of proteins.

noncovalent

In a beta-sheet secondary structure, the chains run __________ or _____________

parallel or antiparallel

Serine proteases cleave the ________ bond of enzymes

peptide

In the primary structure, the bonds that hold it together are peptide bonds. These bonds are ___________ and can be described by psi and phi angles.

planar

After the protein is denatured with SDS and heat, it becomes negatively charged and migrates towards the _________ electrode

positive

Describe a primary structure of a protein

sequence of amino acids joined by peptide bonds

The oxygen dissociation curve when binding to hemoglobin is ___________

sigmoidal ("s"-shaped)

Proteins only separate (in SDS-PAGE) based on ___________

size

Km is the Michaelis constant and it ranges from 10^-2 to 10^-5. What does it represent?

substrate concentration when the rate of reaction if 1/2Vmax, an approximate measure of the stability of [ES].

What is Tm?

temperature at which 50% of DNA is annealed

Denaturation refers to the loss of _____________ structure.

tertiary

True or False: Side chains always face out

true

The inactive forms of the serine proteases are called.....

trypsinogen, chemotrypsinogen, and proelastase

What is the Michaelis-Menten equation?

vo = Vmax[S] /KM +[S]

Serine proteases are stored in inactive precursors called ___________.

zymogen