Midterm

Glycine

Non-polar

Alanine

Non-polar

Valine

Non-polar
-shaped like a v

Leucine

Non-polar
-Longer than valine

Isoleucine

Non-polar
-ISOmer of LEUCINE
-sorta leucine

Proline

Non-polar
positive NH2+ because of looping
-PRO amino acid for pro chemists

Methionine

Non-polar
start codon
-3 nulceotides in a codon

Phenylalanine

Aromatic
-phenyl is a hydrocarbon ring

Tyrosine

Aromatic
pKa 10.1
-TYRe with an O following

Tryptophan

Aromatic
-you must TRY to remember the largest structure

Serine

Polar uncharged
pKa 13.6
-OH no

Threonine

Polar uncharged
pKa 13.6
-OH no

Cysteine

Polar uncharged
pKa 8.3
can create disulphide bonds
-Sistine chapel (two fingers "bonding)

Asparagine

Polar uncharged
-A before G

Glutamine

Polar uncharged
-A before G

Aspartate

Polar negative
pKa 3.9
-A before G

Glutamate

Polar negative
pKa 4.2
-A before G

Lysine

Polar positive
pKa 10.5 (HA)
-LY is a line

Arginine

Polar positive
pKa 12.5 (HA)

Histidine

Polar positive
(A-)

Main Biomolecules

Proteins
Lipids
Carbohydrates
Nucleic Acids

Biochemistry

principally concerned with the chemistry and molecular interactions of biological molecules associated with living systems

Enzymes

Proteins
catalyze biochemical reactions
-composed of amino acids

Metabolism

Catabolism -yield energy, degrade
Anabolism -take energy, assemble

Electronegativity

ability to attract electrons
H, P < C, S < N < O
-bond strength

Biochemical transfromation

1. Group transfer, add or remove
2. Oxidation-Reduction
3. Rearrangement, function changes
4. Cleavage, break, add water
5. Condensation, form, remove water

Saturated hydrocarbons

C-H, C-C
non-polar
non-reactive

Structure of liquid water

H-bonds are continually broken and reformed

Hydrogen bonding

electrostatic interaction between
O-H, N-H, F-H
explains why polar molecules can dissolve in water

strongest -linear
breaking -requires enthalpy

Electrostatic interactions

between oppositely charged ions
TdS >> dH

van der Waals interactions

short range, very weak interaction
induced dipole attraction

Hydrophobic Effect

non-polar hydrocarbon dissolves in water:
broken -van der Waals and H bonds
formed -H bonds in a cage
entropy is reduced

Amphipathic

polar and non-polar groups
-detergents, lipids, proteins
lowest free energy state is in hydrophobic clusters

Detergents

-sodium dodecyl sulfate
micelle -hydrophobic core

Ionization of water equations

pH = -log[H+]
pOH = -log[OH-]

Strong acid

complete dissociation
HA -> H+ + A-

Strong base

complete dissociation
BOH -> B+ + OH-

Weak acid

incomplete dissociation
proton donors

Weak base (Conjugate base)

incomplete dissociation
proton acceptor

Weak acid equations

Ka = [H+][A-]/[HA]
pKa = -log[Ka]

Buffer questions

1. M1/C1 = M2/C2
2. [A-] = x, [HA] = M2 - x
3. pH = pKa + log[A-]/[HA]
4. concentrations
5. A- & HA +/- change
6. pH

Henderson-Hassalbalch equation

pH = pKa + log[A-]/[HA

Non-polar AA

Gly, G
Ala, A
Val, V
Leu, L
Ile, I
Met, M
Pro, P
Phe, F
Trp, W

Polar Uncharged AA

Ser, S
Thr, T
Asn, A
Gln, Q
Tyr, Y
Cyc, C
His, H *

Polar + AA

anionic

Arg, R
Lys, K
His, H *

Polar - AA

Glu, E
Asp, D

pKa of AA

a - COOH 2.2
Aspartate 3.9
Glutamate 4.2
Histidine 6.0
Cysteine 8.3
a - NH3+ 9.5
Tyrosine 10.1
Lysine 10.5
Arginine 12.5
Serine 13.6
Threonine 13.6

Sterochemistry

conformation -rotation
configuration -breaking/forming

Isomers

same formula different arrangement
stereoisomer -same formula, different faces (up vs down)

Chirality

non-superimposable mirror images
-enantiomers D or L
AA are mostly L

Zwitterion

hybrid ion
-no net charge

Titration of glycine

pKa 1 = 2.4 (COOH)
pI = 6
pKa 2 = 9.6 (NH3+)

Isoelectric point

pI = pKa 1 + pKa/2

Calculating pH

1. determine form (A >6, B

Titration of AA

1. protein mols
2. NaOH or HCL mols (x)
3. determine form and direction (pH or pI)
4. pH = pKa + log (A-/HA)

Peptide bond

amide bond that joins two amino acids

residue

amino acid units in a protein

Amino acid sequence

N-C (NH3+ to COO-)
order of AA

Sanger protein sequencing

1. hydrolysis of polypeptide into small bits
2. separating bits
3. arranging bits to find the sequence

Fragmentation

Trypsin - Lys, Arg (+) KR
Chymotrypsin -Phe, Tyr, Trp (aromatic) FYW
CNBr - Met (start) M

Secondary structure

H-bonds between C=O & H=N
a-helix
-right handed spiral (1 turn is 3.6 residues)
b-sheet

a-Helix

peptide is planner (cis or tans)
H bond between every 4th aa

disruptions:
-electrostatic repulsion
-bulky R groups
-small R groups (favour b)
-proline

b-Conformation

peptide is planner (cis or trans)
H bond between adjacent strands
-antiparallel 7
-parallel 6.5
small R groups

Tertiary structure

globular form
-hydrophobic core (hydrophobic effect)

stablizing:
-disulfide
-electrostatic/ionic
-h bonds
-metal chelation

Disulfide bonds

crosslink protein with covalent bonds
Cys

Metal chelation

salt bridge to stabilize charges
N(+) |||| Me++ |||| O-

Quaternary structure

interaction of globular polypeptides
-same factors as 3

Protein folding

dependent on aa sequence

Protein denaturation

native protein converted to unfolded
1. heat
2, change in solvent
-few proteins can reverse spontaneously (need chaperons)

Prostheic groups

attached non-amino acids
cofactor
-organic (coenzymes)
-inorganic

Ion exchange chromatography

protein purification
1. beads with sulfonic acid (anionic)
2. AA in buffer at 2
3. AA washed with higher pH
4. pH is pI of AA it will wash away
-salt can remove AA (compete for binding sites)

Size-Exclusion (Gel Sieving) chromatography

1. bead with pores
2. mixture of proteins
Big proteins -quick, can't go through pores
Small proteins -slow, go through beads

Affinity Chromatography

1. beads with ligand
2. mixture of proteins
3. hexokinase binds, others washed
4. ATP added (takes binging site) to unbind hexokinase

SDS-PAGE

1. crosslinked polyacrylamide gel
2. detergent binds to proteins
3. electrical potential moves proteins
4. staine

Catalyst

speeds up the rate without being consumed
S + E -> E.S -> E.S# -> E.P -> E + P

Apoenzyme/Apoprotein

protein

Holoenzyme

protein + coenzyme

Enzyme substrate complex

E.S or E.P
non-covalent complex

Transition state theory

reaction rate = (constant)Te^-dG/RT
dG is out activation energy S#

Enzyme lowering the S#

formation of E.S is spontaneous
-binding energy used to fund
-weak but favorable interactions

E.S formation

decrease of entropy
desolvation -removing water cage
induced fit
alignment of reaction groups

Recognizing substrates

shape, consistency, or fit -lock and key
electrostatic consistency -correct bonds within site
thermodynamic consistency -flexing to fit

Binding energy is used for

entropy reduction -hold substrates
desolvation -cage must be removed to react
strain reduction -cushion that uncomfortably

Specificity

Chiral specificity -D vs L
Geometric specificity -trans vs cis

Chymotrypsin

Trp, Tyr, Phe
1. substrate enters active site
2. His N: -> H of S OH -> C of substrate C=O -> O of C=O
3. H to N+ -> C-HN of substrate to H -> - to bond
-tetrahedral intermediate
4. N of His -> H of water -> C=O -> O
5. O- -> bond O-C -> H -> N+
-tetrahedral intermediate