biochem topic 2

Lysine (Lys,K)

Arginine (Arg, R)

aspartate (Asp, D)

glutamate (Glu, E)

histadine (His, H)

cysteine (Cys, C)

glutamine (Gln, Q)

asparagine (asn, N)

tyrosine (tyr, Y)

threonine (thr, T)

serine (Ser, S)

proline (Pro, P)

methionine (Met, M)

tryptophan (Trp, W)

phenylalanine (Phe, F)

isoleucine (Ile, I)

leucine (Leu, L)

valine (val, V)

alanine, ala, A

glycine ( gly, G)

amphoteric

substance that can act as both an acid and base

zwitterion

A neutral molecule with localized positive and negative formal charges that cancel each other out

What is Biochemistry?

“A thorough understanding of each molecule’s physical structure and chemical reactivity helps to lead to an understanding of how molecules cooperate and combine to form larger functional units and, ultimately, the intact organism

4 classes of biomolecules

amino acids, carbs, nucleotides, lipids

biological polymers

nucleic acid, polysaccharides, polypeptide

central dogma of molecular biology

dna (transcription) rna (translation) protein

pka of arginine (Arg, R)

12.5

pka of lysine (lys, K)

10.5

pka of coo-

3.5

pka of n term

9

pka of histidine

6

• becomes basic

• under very low ph

pka of cysteine

8.4

• becomes acidic at very high ph > 8

pka of tyrosine (tyr, Y)

10.5

• becomes acidic at high pH

pka of aspartate (asp, D)

3.4

• acidic properties

• negative charge

pka of glutamate (glu, E)

4.1

• acidic properties

ligand

a compound that binds to a protein

• When the ligand binds to its target, it forms a complex, which often triggers a specific biological response or changes the protein's shape and function

• ex. hormones, neurotransmitters

zwitterion

molecule with side chains of negative and positve charges that cancel each other other

ex. amino acid in physiological conditions

achiral amino acid

glycine

aliphatic

lacking aromatic ring

imidazole ring

5-sided ring in histidine

ionization

process where neutral atom gains or loses electrons causing it to aquire net electric charge

when pH increases, acidic compounds _________ in ionization

increases

• more able to donate proton and gain - charge

when pH decreases, basic compounds _____ in ionization

increase

• can gain proton and charge

amphoteric

have both basic and acidic groups

amino acids have ____ acids and bases, so ionization ___ change based on pH

weak, CAN

in contrast, strong acids and bases ___ ionize

completely ionize even if pH changes, its irreversible

NH that’s in the peptide backbone is called

amide

lower pKa side chains are usually

deprotonated (higher pH acts basic so they donate)

higher pka side chains are usually

protonated (lower pH acts acidic)

imino acid

amino acid with nitrogen bonded to 2 carbons

• proline

amino vs amide

amino is bonded to single carbon , amide is bonded to a carbonyl