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Flashcards in Proteins Deck (50)
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1

Non covalent interactions

Hydrogen bonding

Charge to charge/Electrostatic interactions e.g. in DNA, NaCl

Hydrophobic interactions e.g. hydrocarbons; oil + water

 

2

Hydrogen bonding features

e.g. H2O

Bonding between H and only electronegative atoms, namely O and N

Occur in all proteins e.g. internal H-bonding stabilizes alpha-helix; many weak H-bonds provide stability as well

 

3

Electrostatic interactions features

 Very pH dependant

Essentially, strong interactions between molecules with opposite charges

e.g. DNA and histones

4

Hydrophobic interactions features

Will NOT form hydrogen bonds

Biggest thermodynamic driver of protein stability

Stabilizes proteins based on hydrophobic effect: polar/charged residues on exterior of protein vs non-polar/uncharged residues on interior of protein

e.g. oil and water

5

Explain the hydrophobic effect with regards to detergents/membranes in water.

Why do detergents decrease water's surface tension?

How is a micelle different from a bi-layer, and how is that different from a liposome?

Membranes: Phospholipids will spontaneously form membrane bi-layers in water b/c the phosphate group can interact w/ water but the lipid portion cannot.

Detergents have charged and uncharged portions. When the charged portions interact with water, water molecules will want to form bonds, thereby causing it to split and dirsupting the internal hydrogen bonds w/in the water molecules

Micelle: unit = wedge shaped; only one layer; cross section of head>>side chain

Bilayer: unit = cylindrical; cross section of head = side chain; 2 layers

Liposome: essentially a spherical bilayer with an aqueous cavity.

 

6

Explain the significance of the hydrophobic effect to protein structure

Polar/charged residues on exterior of protein vs non-polar/uncharged residues on interior of protein

e.g. myoglobin subunit

7

Properties of water

  • Tetrahedral structure (due to non-bonding electrons)
  • Lattice of hydrogen bonds contribute to high boiling point and heat of vaporization
  • Hydrogen bond = 1/20th strength of covalent bond
  • Density varies by state: solid = decreased density so ice floats; liquid = higher density
  • Attenuates charge-charge interactions e.g. dissolving NaCl >> individual molecules hydrated >> charge attenuated >> salt dissolves

8

How does water attenuate charge-charge interactions? Use NaCl as an example

Dissolving NaCl >> individual molecules hydrated >> charge attenuated >> salt dissolves

9

The substrate-binding sites of enzymes are made of which non-covalent interactions?

All three of them

10

pH formula for strong acids and bases

pH = -log [H+];

pOH = -log [OH-];

pH + pOH = 14

11

Weak acids and bases don't completely dissociate in water, so you'd need to use which equation to find the dissolved proportions of acid/base?

Which value serves as a measure of the dissociation ability of an acid?

Henderson-Hasselbalch equation: pH = pKa + log [conj base]/[acid]

Ka (dissociation constant) = [H+][A-]/[HA]

Ka or pKa are both measures of an acid's ability to dissociate, and thus an acid's strength.

High Ka = low pKa = stronger acid (the trend is similar for low Ka)

 

12

What proportion of the protonated form of an acid will exist in solution at a pH below the acid's pKa? what about above the pKa?

At pH below an acid's pKa, the protonated form will always be greater.

At pH above pKa, the acid will be predominantly de-protonated.

13

What's the buffering region for a simple amino acid?

If you add acid or base, what changes occur at pH near pKa? What about pH outside of the buffering range?

A total of 1 pH unit of the acid's pKa (so 0.5 at pKa1 and 0.5 at pKa2)

For something like acetic acid, at pH near pKa, adding acid/base won't change pH much. Outside of the buffering region, adding acid/base will change things quite a bit

14

Building blocks of proteins

15

Generally, at pH__, both the amino and carboxyl groups are ionized.

7

16

Because amino and carboxyl groups in AAs can dissociate, the net charge on an amino acid will depend on ___

pH

17

When an amino acid exists in a state in which both the amino and carboxyl group are charged, it is in its ___ form. This typically occurs at pH__pKa, aka the ___ point

Zwitterion 

pH = pKa

Isoelectric point

18

Bond between AAs that is found within proteins

Peptide bond

19

Peptide bond is formed between the __ of one amino acid and the __ of another amino acid

20

What are the types of amino acid isomers? Which one comprises proteins?

L and D stereoisomers (alpha carbon = asymmetric)

Proteins consist exclusively of L-amino acids

21

Non-polar, alipathic amino acids

Glycine, Gly, G

Alanine, Ala, A

Proline, Pro, P

Valine, Val, V

Leucine, Leu, L

Isoleucine, Ile, I

Methionine, Met, M

(GAP Va LIM)

 

22

Polar, uncharged AAs

Serine, Ser, S

Threonine, Thr, T

Asparagine, Asn, N

Glutamine, Gln, Q

Cysteine, Cys, C

(Stan Totalled A Great Car)

23

Aromatic AAs

hTTP

h-nothing

Tyrosine, Tyr, Y

Tryptophan, Trp, W

Phenylalanine, Phe, F

 

24

Basic/Positively charged AAs

Lysine, Lys, K

Arginine, Arg, R

Histidine, His, H

25

Acidic/Negatively charged AAs

Aspartate, Asp, D

Glutamate, Glu, E

26

pKas of:

Aspartate

Glutamate

Histidine

Cysteine

Lysine

Tyrosine

Arginine

Aspartate: 3.9

Glutamate: 4.1

(both close to 4ish)

Histidine: 6

Cysteine: 8.5ish

Lysine: 10.5

Tyrosine: 10.5

Arginine: 12.5

27

Amino acids w/ hydroxyl groups

Serine

Threonine

28

Aromatic amino acids determine the __ absorption capacity of proteins

UV absorption

(Abs = higher w/ tryptophan compared to tyrosine)

29

___ has a pKa of 6 (near neutral) and will dissociate at neutral pH

___ and ___ are in high quantities in histones

Histidine

Lysine and Arginine

30

Amino acids w/ amide side chains

Asparagine and Glutamine

(basically, replace the COO groups on aspartate and glutamate and replace w/ an amide)