biochem 1 Flashcards
What is a alpha-carbon stereocenter?
All human amino acids, except one, are chiral at the alpha carbon because the alpha carbon contains four different substituents, an –R group, a hydrogen, a carboxylic acid, and an amine.
What is absolute configuration?
all amino acids are designated as either L or D, depending on the side on which the amine group is located on the Fischer projection (native human amino acids are L)
__ groups determine the chemistry of an amino acid
R
What is the pKa of the COOH group of an amino acid?
~ 2
What is the pKa of Asp, Glu, Lys, and Arg?
asp - 3.7, glu- 4.5, lys- 10.7, Arg - 12
What is the pKa of His and the NH3+ group of an amino acid?
his - 6
NH3+ - 9
What are essential vs. nonessential amino acids?
essential - your body cannot synthesize aa. must be ingested
non-essential - body can synthesize
What is a zwitterion?
A dipolar version of an amino acid wherein positively and negatively charged functional groups cancel one another out, resulting in a neutral ion.
The amino acid acts as a buffer when the pH is ___
near the pKa of one of the acidic protons
What is the isoelectric point? What is the formula for PI?
the pH at which a molecule carries no net charge
(pKa 1 + pKa 2)/2
amino acids are __ acids
weak
What kind of reaction is peptide bond formation?
dehydration synthesis and acyl substitution
During peptide bond formation the amine group Nitrogen is the __, and the carbonyl carbon on the __ terminus of the growing peptide chain is the ___
nucleophile, C, electrophile
peptides are written, read, and synthesized from ___ terminus to __ terminus
N- C
In a peptide bond, both the C=O bond and the C-N bond have ___ character
double bond
peptide bonds are __ with limited __
rigid, rotation
trypsin and chymotrypsin cleave proteins on the ___ side of the specific amino acid residues
Carboxyl side
Trypsin cleaves at which amino acids?
arginine and lysine
Chymotrypsin cleaves at which amino acid?
phenylalanine, tryptophan, tyrosine
In alpha helices, there are hydrogen bonds between what atoms?
carbonyl oxygens and amide hydrogens that are 4 residues apart
R groups are directed exactly __ from the alpha helix cylinder.
away
In beta sheets, where is the hydrogen bonding between?
between ALL of the carbonyl oxygens and amide hydrogens in the adjacent row
In beta pleated sheets, R-groups are directed __ to the plane of the beta sheet on __ sides
perpendicular, both
proline is favored in __ but favored in ___ secondary protein structure
beta pleated sheets, alpha helices
What is an example of a protein with alpha helices?
keratin - found in hair and nails
What is an example of a protein containing beta sheets?
fibroin - makes up silk
What is the difference between tertiary and quaternary protein structure?
tertiary - geometric, 3D folding of secondary structures
quaternary - association of multiple folded proteins into multi-subunit complex
hemoglobin structure has __ protein chains, __ alpha subunits and __ beta subunits
4, 2, 2
What is positive cooperativity?
Ligand affinity increases with the binding of each subsequent ligand
What are the 3 states of protein folding?
globule (fully folded)
molten globule (partially folded)
molten (denatured)
The increase in __ is a major contributor to the overall conformational stability of the folded protein
entropy
What are some protein denaturing agents?
acid, heat, urea, mercaptoethanol
What steps are necessary to cause a simple denatured protein to re-fold? Will this process work, unaided, for all proteins?
When denaturing a protein that you want to re-fold, you want to denature slowly. Too quickly or too harshly and irreversible denaturing will occur, such as collapse of all hydrophobic amino acids into the center of the protein. To refold a denatured protein, you want to slowly remove the denaturant from solution. (heat denatured proteins cannot be refolded)
How does isoelectric focusing work?
A gel is created with stable pH gradient. A protein in a region of the gel with a pH lower than its isoelectric point will be positively charged (because it will be fully protonated) and so will move toward the negative cathode. A protein in a region with a pH higher than its isoelectric point will be negatively charged (because it will be fully unprotonated) and so will move toward the positive anode. As the protein moves through increasing pH in the gel, the protein’s charge will decrease until it reaches the pH of its pI, at which point it will become neutral. At this point the protein will cease to move through the gel, because it has no charge and so has no pull toward either electrode. This causes proteins to form very sharp bands at the pH equal to each protein’s pI.
What are some examples of binding proteins?
hemoglobin, calmodulin, troponin, tropomyosin, histones, transcription factors, cell adhesion molecules
What are some immune system proteins?
antigens and antibodies
What are some examples of structural proteins?
actin (thin filaments, microfilaments), tubulin (microtubules), keratin (hair and nails, intermediate filaments), elastin (connective tissue, extracellular matrix)
What are some examples of motor proteins?
myosin (power stroke, cellular transport), kinesins and dyneins (vesicles, cellular transport, cell division, cilia, flagella)
What are kinesins and how do they move?
Move along microtubules from (-) to (+) end [center of cell to periphery; nerve cell body → dendrite]
How do dyneins move along a microtubule?
Move along microtubules from (+) to (—) end [periphery to center of the cell; nerve cell dendrite → cell body]
What is the difference between a catalyst and an enzyme?
Both catalysts and enzymes increase the rate of a reaction by lowering the activation energy
Enzymes, however, are organic molecules, while catalysts can be inorganic molecules.
enzymes are more specific
How do enzymes affect each of the following? a) reaction rate, b) energy of activation, c) equilibrium, d) Keq, e) yield, and f) percent yield.
increase reaction rate, lower activation energy, and do NOT affect equilibrium, Keq, yield, or percent yield.
How do each of the following affect reaction rate for an enzyme-catalyzed reaction? a) pH, b) temperature, c) substrate concentration, and d) enzyme concentration
- enzymes have an optimal pH
- mildly increasing temp will increase rate
- at low substrate concentrations, reaction rate will increase rapidly
- adding enzyme when enzyme concentration is low will increase rate
What class of enzymes deal with REDOX reactions?
Oxidoreductases
What class of enzymes transfer a functional group (eg kinases)?
transferases
What class of enzymes deal with hydrolysis?
hydrolases
What class of enzymes rearrange the structure of a molecule?
isomerases
What class of enzymes which catalyzes the breaking of a chemical bond through means not involving hydrolysis or oxidation, and forms a double bond or adds a group to a double bond?
lyases
What class of enzymes deal with addition or synthesis of LARGE molecules, usually ATP dependent?
ligases
Two theories of enzyme specificity are ___ and ___. Which has been largely dismissed by scientists?
induced fit and lock and key. lock and key
What is the difference between a coenzyme and a prosthetic group?
coenzyme is a non-protein species that are NOT permanently attached to the enzyme
prosthetic group - non protein species that is PERMANENTLY attached
What is an example of a coenzyme in a human?
NAD (transfers electrons from one molecule to another in REDOX reactions)
What is the difference between simple and conjugated proteins?
simple - protein that contains only amino acids and no non-protein cofactors or prosthetic groups (apoenzyme)
conjugated - protein associated w cofactors, either covalently or intermolecular attractions. (holoenzyme)
Which are the fat soluble vitamins?
A,D,E, K
What are the differences between vitamins and minerals?
Vitamins- small, organic molecules that are essential nutrients required in small amounts for proper metabolism
minerals - inorganic elements necessary for bone formation, ion gradients, oxygen transport, muscle contraction etc.
What is on the axis of a MM saturation curve?
[substrate] - x
reaction velocity - y
What is Km?
the michaelis constant (substrate concentration at half Vmax)
How to calculate the rate of the reaction at a given concentration of substrate
v =𝑉𝑚𝑎𝑥 [𝑆]/ 𝐾𝑚+[𝑆]
What is the MM equation?
V = Vmax[S]/(Km + [S])
The lower the Km, the __ the binding affinity
stronger
What is on the axis of a Lineweaver-Burk plot?
Y-Intercept = 1/Vmax
X-Intercept = -1/Km
What is reversible inhibition?
inhibitor is not permanently bound; enzyme is not completely disabled
What is competitive inhibition?
inhibitor binds at the active site; inhibitory effect can be overcome by increasing concentration of substrate
vmax- no change
Km - increases
What is uncompetitive inhibition?
inhibitor binds ONLY w enzyme-substrate complex
Vmax- decreases
Km - decreases
What is non-competitive inhibition?
inhibitor binds away from the active site and changes the shape of the enzyme. inhibitor has equal affinity for both ES complex and E.
Vmax- decreases
Km- no change
What is mixed inhibition?
inhibitor has unequal affinity for the ES and the E
Vmax - decreases
Km- decreases if binding affinity is greater for ES
Km - increases if binding affinity is greater for E
What is irreversible inhibition?
inhibitor binds covalently to enzyme or to active site, disabling the enzyme for either a prolonged period of time or permanently
What is positive feedback?
the product of a reaction acts as an agonist for the reaction
What is a zymogen?
An inactive enzyme precursor. Prothrombin is a zymogen
All human body sugars have what stereochemistry?
D-sugars
How can you tell the difference between L-glucose and D-glucose?
D- OH is on the right of the CH2OH
L- OH is on the left of the CH2OH
What is the difference between alpha-glucose and beta-glucose?
alpha - oh and ch2oh are opposite
beta - oh and ch2oh are same side
What is an epimer?
different molecules, similar to diastereomers
What is the difference between a reducing sugar and a non-reducing sugar?
reducing - free aldehyde group (aldose)
non-reducing - can’t participate in redox to reduce another molecule (ketose)
How do carbohydrates react to form a ring?
intramolecular nucleophilic substitution - OH group on chiral carbon acts as NUCLEOPHILE and carbonyl carbon is ELECTROPHILE, carbonyl oxygen is protonated to form OH
What is the difference between an alpha linkage and a beta linkage?
alpha - linked on oxygen on OPPOSITE side of CH2OH
beta - linked on oxygen on SAME side of CH2OH
What are the 3 glucose polysaccharides?
Glycogen: Branched, alpha-linked glucose polymer, used for energy storage in animals
Starch: Branched, alpha-linked glucose polymer, used for energy storage in plants
Cellulose: beta-linked glucose polymer, used for energy storage in plants, indigestible to animals without help from symbiotic bacteria.
Lipids are __ and ___
biomolecules and hydrophobic
What is the structure of triacylglycerols?
glycerol backbone, three fatty acids attached via ester linkages
Why are unsaturated fats better for human health?
cis- unsaturated fats generate fewer calories when metabolized
What is a phosphatid?
The most basic phospholipid, with two fatty acid moieties and ONLY a phosphate group—which is attached directly to the glycerol backbone. Most phospholipids in biological membranes have other functional groups attached to the phosphate head. You may also see this term as part of a named phospholipid, as in phosphatidylcholine.
What is saponification?
hydrolysis of an ester
steroids are a __ membered ring system
4
What are terpenes?
2 isoprene units (5 carbons)
What are prostaglandins?
lipid mediators that have autocrine and paracrine functions in the body
What lipids are amphipathic?
phospholipids, fatty acids, sphingolipids, glycolipids
