biochem: lec 1

roles of water

• 70% of human body mass

• allows moc to take shape

• req for metabolic activties

  • ex: chemical rxn needs solvent

water structure

• bond length: 1A

• angle: 104.5

  • polarity —> life

  • linear —> no life

how many h-bond can a water moc do?

4

H donor group

• O—H, N—H, S—H (can do h-bond in protein struc)

• weakly acidic

H acceptor group

O, N, S,

• weakly basic

h bond w/ func groups

H: monovalent

O: bivalent/ di

N: trivalent

C: tetravalent

add extra bond: +

take away: -

what is bond strength

how much energy to break bond

• KJ - mol^-1

3 types of dipole dipole

• permanent dipoles

• dipole-induced dipole

• London dispersion force

permanent dipole

• both polar moc

• strong charge

dipole- induced dipole

• polar & np

ldf

• very weak

• btw np

solubility

• ability of solvent to interact w solute > strongly than solute particles intx w/ e/o

• water: good solvent for ionic & polar

ex: solvation of NaCl

• strong ionic bond

• water tries to break bond via compensation

  • uses partial charges to replace

gibbs free energy equation (combo for always spontaneity)

• delat G: <0

• delta H: <0

• delta S: >0

delta H: enthalpy change

• heat

• break bond: need energy, >0

• form bond: energy rel, <0

delta S, entropy change of system

• randomness

• >0, more randomness, more spon

• 
  

hydrophobic effect

• tendency of water min contact w/ hp moc

• aggregation of np moc in water

• water drives np mic tgt→ water more favorable, less ordered state

what drives oil tgt-?

• entropy of the system (Delta S)

• water increases in entropy → more random, less contact w/ oil

• 
  

amphiphlies

• moc w/ polar & np grps

  • ex: micelle & bilayer

  • hydrocarbon tails come tgt- inside 2/ polar heads interact w/ water outside

3 key things why protein structure is important

• life

• disease

• pharmaceuticals

disease

• ex: sickle cell disease

• SCD → mutation in one aa of hemoglobin

• changes shape → np aggregate tgt → block blood vessels

what’s a protein

• a polymer of amino acids

how can proteins become active

• must twist & fold into their final, native conformation

an a amino acid

• all aa derived from proteins (except glycine) are chiral

• all chiral aa → L-stereochemistry

pH

measure of acidity/ basicity of aq solution

pka= - logka

Ka: measure of acid strength

• lower pka = stronger acid

pH < pKa

• protonation

• low pH, more H, protonate moc

pH > pKa

• un-protonate

• high pH, less H, deprotonate moc

pH = pKa

50:50 (de/protonated)

ionized vs un-ionized

• ionized: has charge, likes water

• unionized: lipophilic (likes fat)

difference in 1 unit of pKa & pH

ex: pka 9 & pH 8

• pronation, 90% protonated species

• if more than 1 unit, >90%

zwitterions

• aa are dipolar ions

• at 7.4, amino is protonated & COOH 9s unprotonated

• pK1(alpha) COOH: 2.2

• pk2 amino: 9.4

isoelectric point (pI)

• pH where moc has no charge

cysteine residues bond

• disulfide bon forms

  • two thiol groups get oxidized

  • ½ O2 gets reduced to H20

Asp side-chain

• side chain: –CH₂–COO⁻

• α-carbon → β-carbon (CH₂) → β-COOH

Glu side chain

• side chain: –CH₂–CH₂–COO⁻

• α-carbon → β-carbon (CH₂) → γ-carbon (CH₂) → γ-COOH

lysine side chain

• α → β → γ → δ → ε

peptide bond

• condensation of 2 aa

• CO—NH form, water is romved → dipeptide

• peptide bond forms

what structure is polypeptide

• linear, not branched like polymers

what are aa in a polypeptide called?

• residues

how does glutathione (GSH) act as a cellular antioxidant?

• cysteine -SH group can donate electrons to reactive moc → less harmful

• two GSH form disulfide bond (S–S) → GSSG (glutathione disulfide) → gets oxidzied

glutathione redox rxn

2GSH + X(oxidized) —> GSSG + X (reduced)

• lose water

what is GFP (Green Fluorescent Protein)

• protein in jellyfish → green glow

Chromophore

• part of moc that absorbs light & give color

• it forms inside GFP protein

how does GFP (green fluorescent protein) produce fluorescence?

• chromophore forms inside GFP

  • made of Ser–Tyr–Gly residues.

  • undergo rearrangement + oxidation → emits green light