Midterm study guide

Question 1

How do prions cause CJD?

Answer 1

prions infect the body, then replicate, causing misfolded proteins to accumulate, ultamately infecting all the body’s proteins so they too misfold

Question 2

What is the post-translational modification that happens to proline residues in collagen?

Answer 2

Hydroxylation occurs to proline and lysine to form hydorxyproline and hydroxylysine.

Question 3

What is the role of Vitamin C in the structure and function of collagen

Answer 3

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

Question 4

What is the relationship between collagen and osteogenesis imperfecta

Answer 4

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

Question 5

What are the hallmark signs of scurvy and what causes it?

Answer 5

1. Swollen and bleeding gums, loose teeth, bruise discolyration, easy bruising
2. 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)

Question 6

Glutamic acid IMFs

Answer 6

polar, negatively charged molecule, with hydrophillic side chain. Forms hydrogen bonds, charge-induced dipole interactions, charge-dipole interactions, charge-charge interactions

Question 7

Valine IMFs

Answer 7

Valine is a nonpolar, hydrophobic molecule. (usually inside molecule since hydrophobic)
- Hydrophobic interactions and LDFs

Question 8

What causes sickle cell anemia considering valine

Answer 8

protein aggregation is caused by the hydrophobic interactions caused by valine on psoition 6, leading to aggreation of mutated sequences, chaing blood’s shape.

Question 9

Elaborate on Folic acid’s role in the body’s ability to transfer oxygen from lungs to tissues

Answer 9

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.

Question 10

How does alcoholism cause anemia

Answer 10

alcoholism decreases the amount of folic acid metabolism in the body, which inhibits RBC production.

Question 11

3 causes of folate deficiency

Answer 11

Alcoholism, not enough ditary intake through veggies, taking medications that impair absorbtion

Question 12

What does chemotrypsin cleave

Answer 12

bulkey, non-polar side chains (hydrophobic)

Question 13

What does trypsin cleave

Answer 13

lysine and arginine (Lys, arg)

Question 14

What type of protease are trypsin and chemotrypsin

Answer 14

Serine (it’s at their active site to help cut peptide bond)

Question 15

What kind of bond is between O and H in water

Answer 15

Covalent

Question 16

Is making a bond exo or endo thermic

Answer 16

Making is exothermic

Question 17

Is breaking a bond endo or exothermic

Answer 17

Endothermic

Question 18

What are the most stable elements on the periodic table

Answer 18

Noble gasses (Electronegativity- no desire to have more electrons)

Question 19

What is the most reactive element on the periodic table

Answer 19

Flourine- really reactive, really wants to gain one electron

Question 20

Where do you find LDF’s/Vanderwalls

Answer 20

In hydrophobic interactions in proteins, very very weak (until in water, and then strong, like in vinagarette)

Question 21

Describe where you find covalent bonds vs IMFs in DNA

Answer 21

Covalent bonds=backbone, IMFs=Shape (H bonds between base pairs)

Question 22

What does a low pka indicate

Answer 22

The product is a stronger acid, more readily donates a protein

Question 23

In an acidic environment, which side of the reaction holds the proton

Answer 23

The acid holds it when the environment is more acidic

Question 24

In a basic environment, which side of the reaction holds the proton

Answer 24

the base holds it when the environment is more basic (the products

Question 25

Are amines basic or acidic

Answer 25

Basic

Question 26

What is an amino acid that is an acid and base at the same time

Answer 26

zwitterion ( negative and positive charge)

Question 27

What intermolecular interactions occur between charged amino acids

Answer 27

acids and bases do charge-charge interactions

Question 28

Where is the N terminus

Answer 28

the amino terminus (NH3)

Question 29

Where is the C terminus

Answer 29

Carboxy terminus, with the Carboxyl (COOH group)

Question 30

What types of bonds rotate

Answer 30

single bonds- double cannot or triple

Question 31

What occurs at alpha carbons

Answer 31

free rotation- single bonds

Question 32

What is the primary structure of protein?

Answer 32

sequence of amino acids that are linked by covalent bonds

Question 33

Describe the secondary structure

Answer 33

3-D form of LOCAL segments of proteins (Hydrogen bonds between backbone atoms)

Question 34

How close do atoms need to be for a hydrogen bond

Answer 34

less than 3.5 A

Question 35

What rules should the secondary structure follow in protein bonding

Answer 35

1. Bond lengths not distorted more than necessary
2. Steric clashes minimized
3. Only alpha bond adjuncts can rotate
4. maximize H-bonds

Question 36

Where are the hydrogen bonds in alpha helices

Answer 36

Between backbone carbonyl oxygen and amide H from 3.6 aa away

Question 37

Where are hydrogen bonds in B sheets

Answer 37

Between neighboring backbone segments

Question 38

Describe the tertiary structure of the protein

Answer 38

single polypeptide chain (backbone) with secondary structures stabilized by side chain interactions

Question 39

What are some of the side-chain interactions in tertiary structure

Answer 39

H-bonds, hydrophobic interactions, salt bridges, disulfide bonds

Question 40

What is the group that myoglobin and hemoglobin have in common

Answer 40

the heme group

Question 41

Why does myoglobin bind to oxygen really well

Answer 41

It is in a puckerd shape without oxygen because of the bond angles, but when oxygen is added, it is much more comfortable

Question 42

How do muscles know when to release O2?

Answer 42

When O2 is low, they shift theiir reaction to the right to get O2 off of myoglibin and into the free O2

Question 43

What kind of binding does Myoglibin do

Answer 43

Hyperbolic binding- non-cooperative

Question 44

What type of binding does hemoglobin do

Answer 44

cooperativec binding (allosteric binding)- binds tightly to O2 in lungs to carry it to O2, but then has to release into blood)

Question 45

In hemoglobin, describe T state vs R state

Answer 45

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”

Question 46

When is hemoglobin in R state

Answer 46

When it is oxygenated ( (R)eady to donate O2)

Question 47

What stabilizes the T state

Answer 47

Salt bridges
2,3-BPG

Question 48

What is the change between the lungs and tissue that protonates the histone in hemoglobin to make the salt bridge

Answer 48

Difference in pH between lungs and tissue (7.6 in lungs, 7.2 in tissues)

Question 49

What stabilizes the R state

Answer 49

Oxygen binding (inherently stable)

Question 50

Which amino acid is responsible for salt bridges in T state

Answer 50

Histidine (sensitive to changes at physiological pH)

Question 51

Describe the substrate-active site- enzyme interaction

Answer 51

An enzyme has an active site on it, and the substrate binds to the active site.

Question 52

Do enzymes change equilibrium?

Answer 52

no! only activation energy

Question 53

What does Km tell us

Answer 53

the concetration of substrate at which the enzyme is at half its maximum velocity

Question 54

What is Vmax

Answer 54

When enzyme is fully saturated, the number of substrate molecules converted into product