Exam 1 Flashcards
Lec 1-11
Max number of hydrogen bonds per water molecule
4 bonds
All of the amino acids are chiral except
a. Glycine
b. Alanine
c. Leucine
d. Tryptophan
a. Glycine
Which amino acids are negatively charged at neutral pH?
Glutamate and aspartate
Phosphoric acid has a pKa of 2.1. At what pH will 75% of phosphoric acid be in the conjugate base form? (HOW DO YOU FIND THIS?)
Math hints: log3=0.5 log.33=-0.5
The concentration of the conjugate base [A-] and weak acid [HA] in the Henderson-Hasselbach equation were flipped. When plugged into the equation, it would yield pH = 2.1 + log[.25/.75], => pH = 2.1 + log(.33) = 2.1 + (-.5) = 1.6 as the final pH answer
Which participates in acid-base chemistry and is located in the active site of the enzyme chymotrypsin?
Histidine
Why are oxyanion holes important?
They are commonly found in many enzyme structures. They are crucial for the stabilization of high energy oxyanion intermediates or transition states through hydrogen bonding. Typical functionalities found in enzyme oxyanion holes or chemically designed oxyanion-hole mimics are N-H and O-H groups.
What is feedback inhibition?
The process by which a product of an enzymatic pathway inhibits its own synthesis by negatively regulating an enzyme in the synthesis pathway
A series of enzymes perform a multi-step reaction pathway to produce the nucleotide cytidine triphosphate (CTP). CTP allosterically inhibits the first enzyme in the pathway. What is this an example of?
Feedback inhibition
How many ionizable groups are in the following peptide? Leucine-Valine-Aspartate-Tryptophan-Lysine
Any peptide must have at least two ionizable groups, Aspartate and leucine both contribute ionizable groups in their side chains. (3 ionizable groups)
What is the minimum amount of ionizable groups a peptide can have?
2
What are the two ends of a peptide?
Amino end (NH3+) and carboxyl end (COO-)
Why do valine and leucine not have an ionizable side chain?
Their side chains are non-polar.
What is special about the side chains of aspartate and lysine?
They both contribute ionizable grouos in their side chains.
Aspartate contains a side chain which can be negatively charged when the carboxyl group loses its protein.
Lysine contains a side chain which can be positively charged when the amine group is fully protonated.
Why is tryptophan unable to ionize?
Its side chain consists of only fused aromatic rings
At pH 7, glycine will have an overall charge of +1. Why is this false?
The amino group of glycine has a pKa of about 9 and the carboxyl group has a pKa of ~2. At pH 7, the amino group will be protonated and have a positive charge, but the carboxylic group will be deprotonated and have a negative charge. These cancel each other out and make a neutral charge. Glycine has no ionizable side chains, so you only need to be concerned with the two terminal end charges.
Energetically favorable reactions are exergonic and can be determined by (delta)G values that are….?
A. Positive
B. Negative
B. Negative
What is the central dogma of biology?
DNA->RNA->Protein
Between DNA, RNA, and protein, which one is a carrier of genetic information and can have catalytic properties?
RNA
How to find pH from [H+] concentrations:
pH=-log[H+]
H+ concentration is measured in mol/L
Which type of amino acids are most likely found buried in the interior of a protein?
Hydrophobic amino acids will most likely be in the interior (e.g. nonpolar amino acids like alanine,
leucine, etc. or aromatic amino acids like phenylalanine)
Which type of amino acids are most likely found on the exterior of a protein and exposed to the cytosol?
Hydrophilic amino acids will most likely
be on the exterior of proteins (e.g. polar amino acids – serine, threonine, or charged amino acids –
lysine, glutamate, etc.)
What is the predominant charge state of glycine dissolved in water at pH 9.8? pK1 (of COOH) =2.34 pK2 (NH3+) =9.60
Negative. It will be negative because the pH is above the pKa for both the carboxylic acid group and
the amino group. The carboxylic acid group will be essentially completely deprotonated, and the
majority of the amino groups (more than 50%) will be deprotonated
What value indicates ionizable side chains?
pKR value
What is the strongest angle of hydrogen bonds?
180 degrees
Which technique separates proteins by size?
gel filtration chromography
What is used for protein analysis, but not purification?
SDS-PAGE
Which amino acid absorbs UV light?
Tryptophan
Which technique is used to sequence a protein?
Edman Degradation
How many hydrogen bonds will be found in an alpha helix that is 18 amino acids long?
14
Are beta sheets flat?
No, they are pleated
Which contributes the most to protein stability?
Hydrophobic effect
Does myoglobin have a quaternary structure?
No, but it does have a tertiary structure
What is stabilized by oxygen binding?
R-State
Is the T-state or R-state more stable?
The R-state is more stable at a lower pH. The T-state has a lower affinity for oxygen than the R-state.
What amino acid(s) in hemoglobin is(are) carbamylated at low pH?
The first amino acid of each subunit
What describes KM?
concentration of substrate needed to get to 1/2 Vmax
Do enzymes raise activation energy?
No
What is Le Chatelier’s Principle?
If a dynamic equilibrium is disturbed by changing the conditions, the position of the equilibrium will shift in order to counteract the change and reestablish equilibrium.
How do you find the specific activity of an enzyme?
Activity ÷ total protein (mg) = specific activity
You think you have purified a protein in the laboratory. What would be a good way to check to see if the protein is indeed pure and not a mixture of proteins?
Stain an SDS-PAGE gel. This will be the cheapest and most common method. If you have to check for
the presence of a small amount of impurities, you may want to perform mass spectrometry. Isoelectric
focusing could also show purity.
How does the presence of a sodium dodecyl sulfate (SDS) allow all proteins to migrate towards the
positive electrode during SDS-PAGE? Explain.
Sodium Dodecyl Sulfate (SDS) contains a charged sulfate with a hydrophobic (12- carbon) tail. The
hydrophobic tail helps denature protein and make proteins rod-shaped (instead of globular). This will
allow proteins to be coated with SDS. The negative charged sulfate on each SDS molecule will make
each protein negatively charged and thus migrate towards the positive electrode and be separated by
size
The proteins FosB, Hemoglobin, and Myosin are added to an SDS-PAGE gel and run for 1 hour at 200 volts. The gel is stained with the dye, Coomassie blue, to visualize the proteins. Draw the order in which the proteins would travel through the gel (negative electrode at the top, positive electrode at the bottom). How many bands would be seen on the gel for hemoglobin?
Myosin (200 kDa): Top of gel
FosB (45 kDa)
Hemoglobin (16 kDa): Bottom of gel; 1 band for Hb as all monomers are same size
What does SDS-PAGE require?
SDS-PAGE requires that proteins are denatured and broken into their individual
subunits
What does protein purification require?
During a purification, you usually want your proteins to maintain their native conformation and not
unfold.
What kind of post-translational modification is found in keratin, the alpha-helical protein found
in hair, skin, and nails?
Disulfide bonds
What is the major force that stabilizes protein folding?
Hydrophobic effect. Think of
the dispersion of lipids as a primary structure of non-polar amino acids and clustering of lipids as the secondary structure of non-polar amino acids
folding into an alpha helix.
Does the release of ordered water molecules result in a decrease or increase in the entropy of water?
Entropy increases as a result of fewer ordered water molecules around the protein.
What do parallel and antiparallel mean?
Parallel and antiparallel indicate the direction that the strands are orientated in relation to one another. In a parallel beta sheet the strands are in the same direction; in an antiparallel beta sheet the strands run in the opposite direction of one another.
What type of bonds are formed between the beta sheet strands?
Hydrogen bonds
What is the equation for binding a ligand to a protein and what do the variables stand for?
(Theta) = [L] / [L] + Kd
Theta = the fraction of protein bound to ligand
Kd = dissociation constant (inverse of the association constant, a measure of how tightly the protein binds to the ligand)
What is the hydrophobic effect due to?
The hydrophobic effect is due to a favorable increase in the entropy of water when it is
released from non-polar molecules.
What is a ligand?
a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein.
How many CO2 molecules can hemoglobin bind to in its T-state?
4 CO2
What is carbamylation?
Binding of CO2 (Stabilizes the T-state)
How is the binding of H+ and CO2 by Hb related to the binding of oxygen?
the binding of H+ and CO2 by hemoglobin (Hb) is inversely related to the binding of oxygen by Hb.
Explain how the protein changes from R to T states in the presence of oxygen and carbon
dioxide. (Hemoglobin)
More R state is found when oxygen is bound while more T state is found when hemoglobin is
carbamylated (CO2 is bound)