week 1- Biochem

Glycine

(Gly, G) —- not chiral

Alanine

(Ala, A)

Isoleucine

(lle, l)

Valine

(Val, V) hydrophobic and aliphatic

Leucine

(Leu, L)

Phenylalanine

(Phe, F) Aromatic, hydrophobic

Proline

(Pro, P)

Serine

(Ser, S)

Threonine

(Thr, T)

Tyrosine

(Tyr, Y) hydrophilic (polar) and aromatic

Glutamine

(Gln, Q)

Asparagine

(Asn, N)

Methionine

(Met, M)

Cysteine

(Cys, C)

Tryptophan

(Trp, W) aromatic and hydrophobic

Glutamic Acid

(Glu, E) — acidic (- charge)

Histidine

(His, H) aromatic and basic (because of nitrogen that has extra lone pairs—- + charged)—- pka = 6-6.5

Arginine

(Arg, R)— aliphatic and basic because of nitrogen so has a + charge (pka - 12.5)

Aspartic Acid

(Asp, D) — acidic (- charge)

Lysine

(Lys, K) - aliphatic and basic because of nitrogen so has a + charge (pka = 10.5)

Principle elements

CHNOPS

What is glycolysis

breaking down carbohydrates

Basic solvent of biology

Water

What can form hydrogen bonds

FON

What is a hydrogen bond?

A weak attraction between molecules where one molecule give a hydrogen and the other accepts it.

Hydrogen bond donor

has a hydrogen attached to a FON and gives the hydrogen (ex: OH,NH)

Hydrogen bond acceptor

Receives the hydrogen and is either a FON with enough lone pairs to grab they hydrogen (ex: C=O, OH)

Amino Acid R groups

acids, anime, amides, thiol

alcohol

hydroxyl group, polar (so water soluble) and forms hydrogen bonds

aldehyde

carbonyl, polar and found in some sugars

ketone

carbonyl, polar and found in some sugars

acids

carbonyl, weak acid (bears a negative charge when it donates a proton

Amine

Amino, weak base that bears a positive charge when it accepts a proton

Amide

Amido, polar but doesn’t bear a charge

Thiol

easily oxidized and can form disulfide bonds readily.

Ester

found in certain lipid molecules

Alkene

Important structural component in many biomolecules.

What determines amino acid properties

r chains

What kind of amino acids do all proteins contain

L- animo acids

Non covalent interactions Ranked

1. ionic interactions

2. hydrogen bonds

3. hydrophobic interaction

4. van der Waals

n-terminus

nh3 or nh2 not attached to amino acid sequence (start of chain)

c-terminus

COOH bond

pH < pka

amino acid will protonate so makes acid positive

pH > pka

amino acid will deprotonate so negative

1. NH3—- ph<pka = +1

2. Arg—- ph<pka = +1

3. Asp—- ph>pka = -0.5 (because pka and ph are similar)

4. Lys—- ph<pka = +1

5. Glu—- ph<pka = +0.5

6. COOH —-ph>pka = -1

Total: 2

delta G < 0

forward rnx spontaneous

delta G > 0

reverse rxn spontaneous or forward rxn non spontaneous

Catalyst (enzymes)

DO NOT change delta G values, they only change the activation energy by lowering it so the reaction can happen more readily in the forward and reverse. It doesn’t change the ratio of products and reactants.

6 types of enzymes

1. Oxidoreductases

2. transferase

3. hydrolases

4. lyases

5. isomerases

6. ligases

IMF

Intramolecular (in the same molecule)

1. ionic bonds (crystal)

2. single, double, triple covalent bonds

Intermolecular bonds (between molecules)

1. ionic interactions

2. hydrogen bond

3. dipole dipole interactions

4. London dispersion forces

A good substrate

doesn’t need to bind tightly to the enzyme but binds tightly when activated to the transition state

Enzyme complementary to substrate

“lock and key” and more energy is needed to bind

• larger activation energy

Enzyme complementary to transition state

promotes the traditions state (lowers it) by causing hydrogen bonding between substrate and enzyme so the substrate can bind and break.

• conformation change

• shorter activation energy