Proteins Flashcards
Non covalent interactions
Hydrogen bonding
Charge to charge/Electrostatic interactions e.g. in DNA, NaCl
Hydrophobic interactions e.g. hydrocarbons; oil + water
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
Electrostatic interactions features
Very pH dependant
Essentially, strong interactions between molecules with opposite charges
e.g. DNA and histones
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
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.
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
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
How does water attenuate charge-charge interactions? Use NaCl as an example
Dissolving NaCl >> individual molecules hydrated >> charge attenuated >> salt dissolves
The substrate-binding sites of enzymes are made of which non-covalent interactions?
All three of them
pH formula for strong acids and bases
pH = -log [H+];
pOH = -log [OH-];
pH + pOH = 14
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)
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.
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
Building blocks of proteins
Generally, at pH__, both the amino and carboxyl groups are ionized.
7
Because amino and carboxyl groups in AAs can dissociate, the net charge on an amino acid will depend on ___
pH
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
Bond between AAs that is found within proteins
Peptide bond
Peptide bond is formed between the __ of one amino acid and the __ of another amino acid
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
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)
Polar, uncharged AAs
Serine, Ser, S
Threonine, Thr, T
Asparagine, Asn, N
Glutamine, Gln, Q
Cysteine, Cys, C
(Stan Totalled A Great Car)
Aromatic AAs
hTTP
h-nothing
Tyrosine, Tyr, Y
Tryptophan, Trp, W
Phenylalanine, Phe, F
Basic/Positively charged AAs
Lysine, Lys, K
Arginine, Arg, R
Histidine, His, H
Acidic/Negatively charged AAs
Aspartate, Asp, D
Glutamate, Glu, E
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
Amino acids w/ hydroxyl groups
Serine
Threonine
Aromatic amino acids determine the __ absorption capacity of proteins
UV absorption
(Abs = higher w/ tryptophan compared to tyrosine)
___ has a pKa of 6 (near neutral) and will dissociate at neutral pH
___ and ___ are in high quantities in histones
Histidine
Lysine and Arginine
Amino acids w/ amide side chains
Asparagine and Glutamine
(basically, replace the COO groups on aspartate and glutamate and replace w/ an amide)
Sulfur-containing amino acids
Cysteine
Methionine
___ of ___ thiols forms disulfide bonds
Disulfide bonds can be broken using a ___ agent. A common one is ___.
Oxidation
Cysteine
Reducing; Betamercaptoethanol (BME)
Two types of disulfide bonds that can form in proteins
Interchain (between 2 polypeptide chains)
Intrachain (within a polypeptide)
What’s so special about proline?
Proline has a secondary amino group and thus forms a ring, which produces a “kink” in an alpha helix
What are the modified amino acids and their corresponding R groups?
Hydroxyproline: Proline w/ an OH group
y-Carboxyglutamate: Glutamate w/ 2 carboxyl R groups instead of 1
Phosphoserine: Serine w/ phosphate group instead of alcohol
Three letter and one letter codes for the 20 AAs
Protein structure and function is controlled by___
The amino acid sequence aka primary structure
True or False: Peptide bonds are highly flexible and will rotate around the N-C bond. Angles of rotation are not limited, thus multiple conformations are possible.
Thems is some lies!!
Levels of protein structure
Primary: AA sequence
Secondary: Alpha helices, Beta pleated sheets, Collagen Triple helix
Tertiary: Individual subunit
Quartenary structure: Multiple subunits
2ndary structure: Alpha helix characteristics
Stabilized by H bonds
Side groups of AAs stick out radially from helix axis
2ndary structure: Beta pleated sheet features
What is the difference between anti-parallel and parallel beta sheets? Which one is the most stable and thus the most abundant in proteins?
Exists as anti-parallel or parallel sheets
Hydrogen bonds between sheets
Anti-parallel: H bonds are straight, therefore stronger and most common
Parallel: Hydrogen bonds aren’t straight, thus they are not as strong
2ndary structure: Collagen triple helix features
3 helical strands of collagen wraped around each other
Extended structure with limited ability to stretch
Tertiary structure the folded ___ of a protein.
Where would you find hydrophobic side groups in a myoglobin subunit? What secondary structural motif comprises myoglobin?
Individual subunit
Where the alpha helices come in contact
Alpha helix
Quartenary structure is made up of ___. A classic example is hemoglobin, which is comprised of 4 ___ subunits.
Multiple subunits.
Myoglobin-like
Proteins domains are generally comprised of ___.
Single peptide chains
Polypeptides fold into __ structure, which is determined by their amino acid sequence.
Native
Where does the specificity of an Ig come from?
True/False: Ig domains have the different functions yet still the same structure.
Specificity is coded in the amino acid sequence.
True
What parts of an antibody determine its specificity?
What are the secondary, tertiary and quarternary structures of IgG?
The Variable domains on the heavy and light chains
2ndary = beta sheet
Tertiary: Individual heavy and light chain subunits
Quartenary: Combined subunits (linked at hinge region by disulfide bonds)
True/False: The Fc region of an antibody contains the antigen binding site.
Falsehood; The Fab region, made up of the Vh + Vl and Ch and Cl domains, contains the antigen binding site.
Hydrogen bond angles
Actually 0.17nm
0.27nm if you add 0.1nm from covalent bond
