Midterm biochem review study guide Flashcards
Which amino acids are positively charged (basic) and negatively charged (acidic)?
Positively charged: Histidine, Lysine, Arginine
Negatively charged: Aspartic Acid (D) , Glutamic Acid(E)
Which amino acids are hydrophobic?
GLAM VIP FW
Which amino acids can be phosphorylated?
Serine, Threonine, Tyrosine (OH group on side chain)
Which amino acids have aromatic side chains
Phenalanine, Tyrosine, Tryptophan
Which amino acids have S on them
Cystine, methionine
Which molecules have a nitrogen ring
Proline, Histidine
Which amino acid can form a covalent link with another of the same amino acid
Cysteine (S-S bond disulfide). Tertiary structure form
Which amino acid has the smallest side chain
Glycine (Just a H)
What is unique about histidine’s side chain compared with the other 4 charged amino acids?
Histidine has a charge of 6.04 which is uncharged at 7.4 (physiological ph)
Lysine and Arginine are positively charged at 7.4 because their pKa is above 7.4
Aspartic and glutamic acid are negatively charged at 7.4 bc their pKa is below it
Why are vanderwall interactions stronger in water and not in air
In water, hydrophobic interactions are strong because water is polar
in air, there is not a polar medium for the molecules to be pressured on.
3 types of secondary structures
A helix, B sheet, turns and loops
What types of interactions are in tertiary structures
H bonds, hydrophobic interactions, salt bridges, disulfide bonds
What is a leucine zipper
a coiled coil (2 alpha helices that interact because leucine repeats ever 7 residues, they pack to the center since they are nonpolar) Leucines are all on the inside of the zipper bc nonpolar and hydrophobic
Type of a tertiary structure
Describe the cytoplasm environment
polar environment, globular proteins are hydrophillic on the outside and hydrophobic on the inside
Membrane is made of lipids- nonpolar (Hydrophobic outside, hydrophibllic inside)
Which amino acids are found in the transmembrane domain?
Nonpolar amino acids- GLAM VIP FW
What are some charachteristics of alpha keratin
Leucine zipper- coiled coil, cytoskeleton, muscle proteins, heptad repeats, strong and flexible
What are some distinguisihing characteristics of collagen
short repeating heptatd sequences, triple coil
What do myoglobin and hemoglobin have in common
Myoglobin and hemoglobin both have iron that holds onto oxygen for transport
What are hemoglobin and myoglibin’s structures
Myoglobin is a monomer, hemoglobin is a tetramer
How do the quaternary structures influence the ability for oxygen to bind in myoglobin and hemoglobin
Myoglobin is a monomer and binds to oxygen non cooperatively (releases oxygen when levels are low)
Hemoglobin is a tetromer and binds to oxygen cooperatively, and it has a T/R state with high or low oxygen binding (sigmoidal binding)
What is a hyperbolic binder
Myoglobin (Binds to oxygen until concentration is 0, then releases)
How many oxygens bind to myoglobin vs hemoglobin
myoglobin- 1
hemoglobin- 4
Which salt bridge is sensitive to the pH change between the lungs and tissues
the histidine and aspartic acid salt bridg. histidine is sensitive to pH changes, and when deprotonated, won’t form salt bridges
Which amino acid residue enables salt bridge formation when pH drops
histidine protonation
Why is the pH lower at the surface of tissues compared w the lungs
the lungs generate CO2 which is an acid, donating H into blood
What stabilizes the T state of hemoglobin
2,3, BPG
salt bridges between histidine and aspartic acid
Is sickle cell hemoglobin more or less soluble
less- protein aggregation makes proteins less soluble
What do enzymes change
ONLY the kinetics of a reaction- make more product over time by lowering activation energy
What is the Km
The amount of substrate needed for catalysis
What is V max for a reaction
the rate of product formation (number of substrate converted into product when fully saturated)
Equation for slope
Km/Vmax
Equation for X intersept
-1/km
equation for Y intersept
1/V max
What type of reaction do proteases use
nucleophillic substitutions
What does a protease have on its active site
a nucleophile
What amino acid does chymotrypsin recognize
large, nonpolar, bulkey side chains
Alanine, Leucine, Methionine, Valine (GLAM VIP FW)
What amino acids does trypsin recognize
Lysine and arganine
Why are trypsin and chemotrypsin serine proteases
they use serine at their active site to cleave
Competitive inhibition
Uncompetitive inhibition
noncompetitive inhibition
Why is competitive inhibition the only inhibition that can be reversed by increasing substrate concentration
the substrate can increase to the point that it out competes the competitor because of its concentration
What is the charge on the amide group of an amino acid at physiological pH?
Positive (protonated)
What is the charge on the carboxyl group of an amino acid at physiological pH?
negative (deprotonated)
Are you protonated or deprotonated in an acidic environment
protonated
are you protonated or deprotonated in a basic environment
deprotonated
