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Biochemistry Midterm #1
Terms in this set (74)
What does RTlnQ indicate?
how far the reaction is from standard state
What makes biological standard state conditions different from standard state conditions?
H+, OH-, and H2O are removed from the reaction quotient
When Delta G is negative, the reaction is...
When Delta G is positive, the reaction is...
When Delta G is at zero, the reaction is...
Which amino acids are basic?
Lysine and Arginine
Which amino acids are acidic?
Aspartic Acid and Glutamic Acid
Which amino acids are aromatic?
Phenylalanine, Tryptophan, and Tyrosine
Which amino acids have ionizable side chains?
Cysteine, Aspartic Acid, Glutamic Acid, Histidine, Arginine, Lysine, and Tyrosine
What makes proline unique?
Proline has a secondary amine
What makes glycine unique?
Glycine has a single hydrogen for its side chain and as a result is small and flexible
Under oxidizing conditions, how do cysteine residues react?
form disulfide bonds
What keeps disulfides reduced in the cytoplasm?
What is the van der Waals distance?
the distance of closet approach between non-bonded atoms
What are the characteristics of a peptide bond?
- partial double bond character
- planar geometry
- trans configuration
What makes an a-helix an ideal secondary structure?
- optimum intra-chain hydrogen bonding
- 3.6 residues per turn
- at most effective phi and psi angles in the Ramachandran plot
What structure does B-keratin assume?
a coiled-coil structure that has a heptad repeat that forms a hydrophobic strip
What structure does collagen assume?
a triple helix with a tripeptide repeat
What are some examples of collagen diseases?
Scurvy and Osteogenesis Imperfecta
Why don't proline and glycine bind in an a-helix?
Glycine is too flexible, while proline is too restricted
What makes up globular proteins?
a mixture of a-helices, B-sheets, and other secondary structures
What is a domain?
a unit of polypeptide
What force is most important for protein stability?
How was the idea that primary sequence dictates 3-D structure of the protein established?
Anfinsen's experiments with protein denaturation and renaturation
What is the role of PDI?
to isomerize disulfide bonds within the endoplasmic reticulum
How do Hsp70/ Hsp40 chaperones correctly fold newly synthesized polypeptides?
By binding hydrophobic stretches of residues and preventing protein aggregation
What are the two major pathways for protein degradation?
1. eukaryotic lysosome
2. Ubiquitin-Proteasome pathway
What causes cystic fibrosis in regards to protein instability and misfolding?
the mutant CFTR is degraded by ubiquitin before it reaches the plasma membrane of the lungs
What causes amyloid diseases such as Alzheimer's disease?
the formation of insoluble fibrous protein aggregates
What causes Cruetzfeldt-Jakob disease?
the aggregation of prion protein through the mutation of the PrP gene
Does myoglobin or hemoglobin bind oxygen more tightly?
What does a sigmoidal binding curve indicate?
The binding of oxygen initiates what kind of transition?
the transition of hemoglobin from the tense (T) state to the relaxed (R) state
How does pH modulate oxygen's binding to hemoglobin?
a decrease in pH stimulates the release of oxygen due to the uptake of H+ ions in the T-state (and vice versa)
How does CO2 modulate oxygen's binding to hemoglobin?
CO2 reduces hemoglobin binding to oxygen because the formation of carbamate results in free H+ ions (acidic conditions)
How does BPG modulate oxygen's binding to hemoglobin?
BPG binds in place of oxygen in the T-state of hemoglobin
How does fetal hemoglobin differ from adult hemoglobin?
fetal hemoglobin has a low affinity for BPG and a higher affinity for oxygen
What are allosteric interactions?
the binding of one ligand at one site affects the binding of another ligand at another site
What allows enzyme active sites to easily distinguish identical substituents attached to a prochiral carbon?
What are some examples of coenzymes?
NAD, NADP, FAD
What do catalysts do?
catalysts enhance the rate of the forward and the reverse reaction (i.e. they accelerate the approach to equilibrium)
What are some examples of cofactors?
What coenzymes do redox enzymes utilize?
either NAD or NADP
What does Delta G Double Dagger stand for?
the activation barrier for the reaction
What does Double Delta D Double Dagger stand for?
the reduction in the activation barrier by the catalyst
Can enzymes tell between the forward and reverse reactions?
What occurs in a covalent catalysis reaction?
the formation of transient enzyme-substrate intermediates
How do metal ions assist in the catalytic process?
- stabilizing the active site
- orientation of substrates
What sets the specificity for serine proteases?
the residues within the binding pocket
What does Km stand for?
the Michaelis-Menten constant (the affinity of substrate binding to an enzyme)
What does Kcat stand for?
the enzyme turnover number
What does Kcat/Km measure?
the catalytic efficiency of an enzyme
How do competitive inhibitors function?
competitive inhibitors bind to the substrate binding site
What are allosteric effectors?
molecules that bind at sites on the enzyme separate from the active site
How does chain length of a fatty acid affect its melting point?
increases the melting point
How does unsaturation of a fatty acid affect its melting point?
decreases the melting point
How does cholesterol affect the phase transition?
cholesterol eliminates the phases transition and increases the lateral mobility
How can lateral diffusion be monitored?
How is lipid bilayer asymmetry created?
due to the slow process of phospholipid flip-flopping
Why is the window size for an enzymatic protein 7-9 residues?
Because that is how many amino acids span the hydrophobic interior of the protein
Why is the window size for an integral membrane protein 18-20 residues?
Because that is the span of the membrane
Why cannot a porin be analyzed on a hydropathy plot?
Because every other residue is hydrophobic or polar-charged
What qualifies passive diffusion?
the movement of molecules down their concentration gradient
Is membrane transport unidirectional?
What is the driving force of passive-mediated transport?
What makes GLUT2 different from all the rest of the glucose transporters?
high Km value
What is the mechanism for GLUT4 for glucose uptake?
- endocytosis of transporters
- insulin binding to insulin receptor
What is a symport?
Movement of more than one molecule in the same direction
What is an antiport?
Movement of more than one molecule in opposite directions
What classifies active-mediated transport?
- movement of molecules against a gradient
- coupled transport with ATP hydrolysis
Metabolic pathways function in...
open, steady-state systems
All metabolic pathways are irreversible due to a...
large, negative Delta G
Why are there substrate cycles?
What does chiral mean?
a non-superimposable mirror image
Recommended textbook explanations
Fundamentals of Biochemistry
Charlotte W. Pratt, Donald Voet, Judith G. Voet
Biocalculus: Calculus for the Life Sciences
Lehninger Principles of Biochemistry
David L Nelson, Michael M. Cox
Miller and Levine Biology
Joseph S. Levine, Kenneth R. Miller
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