Midterm study guide Flashcards
How do prions cause CJD?
prions infect the body, then replicate, causing misfolded proteins to accumulate, ultamately infecting all the body’s proteins so they too misfold
What is the post-translational modification that happens to proline residues in collagen?
Hydroxylation occurs to proline and lysine to form hydorxyproline and hydroxylysine.
What is the role of Vitamin C in the structure and function of collagen
Hydroxylation of proline is protected from oxidation to iron by vitamin C. Hydroxylation reactions require iron and vitamin c, because otherwise hydroylase enzymes can’t function
What is the relationship between collagen and osteogenesis imperfecta
Mutations in the gene coding for collagen, so there are abnormally shaped a-helices that are bound together less tightly, making bones structurally less sound
What are the hallmark signs of scurvy and what causes it?
- Swollen and bleeding gums, loose teeth, bruise discolyration, easy bruising
- Vitamin C deficiency leads to inability to synthesize proline and lysine properly, so collagen fibers don’t cross link well (weak fibers in blood vessils)
Glutamic acid IMFs
polar, negatively charged molecule, with hydrophillic side chain. Forms hydrogen bonds, charge-induced dipole interactions, charge-dipole interactions, charge-charge interactions
Valine IMFs
Valine is a nonpolar, hydrophobic molecule. (usually inside molecule since hydrophobic)
- Hydrophobic interactions and LDFs
What causes sickle cell anemia considering valine
protein aggregation is caused by the hydrophobic interactions caused by valine on psoition 6, leading to aggreation of mutated sequences, chaing blood’s shape.
Elaborate on Folic acid’s role in the body’s ability to transfer oxygen from lungs to tissues
Folic acid helps produce healthy cells, including red blood cells. When there is a folic acid deficiency, the body doesn’t have enough cells to bring o2 to tissues.
How does alcoholism cause anemia
alcoholism decreases the amount of folic acid metabolism in the body, which inhibits RBC production.
3 causes of folate deficiency
Alcoholism, not enough ditary intake through veggies, taking medications that impair absorbtion
What does chemotrypsin cleave
bulkey, non-polar side chains (hydrophobic)
What does trypsin cleave
lysine and arginine (Lys, arg)
What type of protease are trypsin and chemotrypsin
Serine (it’s at their active site to help cut peptide bond)
What kind of bond is between O and H in water
Covalent
Is making a bond exo or endo thermic
Making is exothermic
Is breaking a bond endo or exothermic
Endothermic
What are the most stable elements on the periodic table
Noble gasses (Electronegativity- no desire to have more electrons)
What is the most reactive element on the periodic table
Flourine- really reactive, really wants to gain one electron
Where do you find LDF’s/Vanderwalls
In hydrophobic interactions in proteins, very very weak (until in water, and then strong, like in vinagarette)
Describe where you find covalent bonds vs IMFs in DNA
Covalent bonds=backbone, IMFs=Shape (H bonds between base pairs)
What does a low pka indicate
The product is a stronger acid, more readily donates a protein
In an acidic environment, which side of the reaction holds the proton
The acid holds it when the environment is more acidic
In a basic environment, which side of the reaction holds the proton
the base holds it when the environment is more basic (the products
Are amines basic or acidic
Basic
What is an amino acid that is an acid and base at the same time
zwitterion ( negative and positive charge)
What intermolecular interactions occur between charged amino acids
acids and bases do charge-charge interactions
Where is the N terminus
the amino terminus (NH3)
Where is the C terminus
Carboxy terminus, with the Carboxyl (COOH group)
What types of bonds rotate
single bonds- double cannot or triple
What occurs at alpha carbons
free rotation- single bonds
What is the primary structure of protein?
sequence of amino acids that are linked by covalent bonds
Describe the secondary structure
3-D form of LOCAL segments of proteins (Hydrogen bonds between backbone atoms)
How close do atoms need to be for a hydrogen bond
less than 3.5 A
What rules should the secondary structure follow in protein bonding
- Bond lengths not distorted more than necessary
- Steric clashes minimized
- Only alpha bond adjuncts can rotate
- maximize H-bonds
Where are the hydrogen bonds in alpha helices
Between backbone carbonyl oxygen and amide H from 3.6 aa away
Where are hydrogen bonds in B sheets
Between neighboring backbone segments
Describe the tertiary structure of the protein
single polypeptide chain (backbone) with secondary structures stabilized by side chain interactions
What are some of the side-chain interactions in tertiary structure
H-bonds, hydrophobic interactions, salt bridges, disulfide bonds
What is the group that myoglobin and hemoglobin have in common
the heme group
Why does myoglobin bind to oxygen really well
It is in a puckerd shape without oxygen because of the bond angles, but when oxygen is added, it is much more comfortable
How do muscles know when to release O2?
When O2 is low, they shift theiir reaction to the right to get O2 off of myoglibin and into the free O2
What kind of binding does Myoglibin do
Hyperbolic binding- non-cooperative
What type of binding does hemoglobin do
cooperativec binding (allosteric binding)- binds tightly to O2 in lungs to carry it to O2, but then has to release into blood)
In hemoglobin, describe T state vs R state
T state- when oxygen is not binded, uncomfortable, puckered state.
R state- when oxygen is binded, comfortable, non-puckered shape.
T state is “Tense,” R state is “Relaxed”
When is hemoglobin in R state
When it is oxygenated ( (R)eady to donate O2)
What stabilizes the T state
Salt bridges
2,3-BPG
What is the change between the lungs and tissue that protonates the histone in hemoglobin to make the salt bridge
Difference in pH between lungs and tissue (7.6 in lungs, 7.2 in tissues)
What stabilizes the R state
Oxygen binding (inherently stable)
Which amino acid is responsible for salt bridges in T state
Histidine (sensitive to changes at physiological pH)
Describe the substrate-active site- enzyme interaction
An enzyme has an active site on it, and the substrate binds to the active site.
Do enzymes change equilibrium?
no! only activation energy
What does Km tell us
the concetration of substrate at which the enzyme is at half its maximum velocity
What is Vmax
When enzyme is fully saturated, the number of substrate molecules converted into product
