biochem unit one AMINO ACIDS WOOOOO

trace essential elements

need very few of these elements

• Mg, Cr, Mo, Co, Cu, Se, V, Mn, Fe, Ni, Zn, I

Bulk essential elements

H, K, C, O, S, Na, Ca, N, P, Cl

Water proeprties

high MP and BP

weaker and longer

H-bonds are________ and _______than covalent

linear

how do H-bonds like to be arranged

polar solvant

shields ionic interactions, non random orientation

• positive goes to negative

  • negative goes to positive

non-polar solvant

hydrophobic compounds mess with the structure of water, the water molecules cluster around the molecule in an orderly way that reduces entropy and favorbility

hydrophobic effect

hydrophobic molecules cluster together releasing some of the water molecules

• increases entropy and favorability

• displaces water

hydrolysis

consumes water and releases energy

• H2O —> H+ +OH-

  • break

condensation

releases water

• H+ + OH- —> H2O

  • form

peptide

small protein that doesn’t do chemical work

• signaling molecules and hormones

almost always an L stereoisomer

stereochem of amino acids

peptide bond

carboxylate and amino group become a carbonyl and amide group

• not ionizable

• formed through condensation

• the first one keeps the amino group

• the last group keeps the carboxyl group

first group

what group keeps the amino group?

last group

what group keeps the carboxyl group?

spontaneous clusters, hydrophobic carbon chain

aliphatic non polar group characteristics

aliphatic

glycine group

aliphatic

methionine group

aliphatic

leucine group

aliphatic

isoleucine group

aliphatic

alanine group

aliphatic

proline group

aliphatic

valine group

aromatic

phenylalanine group

aromatic

tryptophan group

aromatic

tyrosine group

positively charged

arginine group

positively charged

lysine group

positively charged

aspartate

negatively charged

glutamate group

negatively charged

aspartate group

polar uncharged

serine

polar uncharged

cysteine

polar uncharged

glutamine

polar uncharged

asparagine

polar uncharged

threonine

isoelectric point

PH where the net charge = 0

zwitterion

net zero charge

disulfide bonds, hydroxylation, metylation

common post translational modifications

purification

seperating proteins

uv light

purification for tryptohan

ion exchange chromatography

positive charge sticks to negative beads (at the top) negative charge goes to the bottom

• elution: changing salt conc

size exclusion chromatography

porous column (sieve) small molecules at top larger at bottom

affinity chromatography

ligand binding

• elution: high conc of ligand that binds to protein of interest

electrophoresis

electric current separates molecules (often in gel)

SDS PAGE

purification of more complex molecules—electrophoresis based on size

isoelectirc focusing

gel strip with PH purification based on PI

negative

basic compounds are more_____

• negative?

• positive

positive

acidic compounds are more_____

• negative?

• positive

planar

peptide bonds are____because of resonance with the double bond between C-O and C-N

alpha carbon

the central carbon atom to which both the amino and carboxyl groups are covalently linked

can’t

peptide bond ______rotate

can

psi and phi bonds____rotate

activity/total protein

specific activity

alpha helix

• right-handed

• 3.6 AA per turn (about 4)

• n-4 for bonding H-bonds

• C=O (n) and H-N (n+4)

• side chains protrude out

beta sheets

• NOT flat

• made up of strands of amino acids

• antiparallel and parallel

parallel beta sheets

• strands all go in the same direction

• les stable

• COO and NH are shifted—hydrogen bonds are shifted and not linear

• R-groups go in alt directions

• need a big loop to do this (can be unstructured or alpha helix)

antiparallel beta sheets

• strands go in alt directions

• more stable

• NH and COO line up—H-bonds are linear

  • R-groups go in alt directions

fibrous

tertiary structure that is highly extended sheets of helices and/or sheets

keratin

alpha helices with disulfide bonds

• hydrophobic AA residue

• high tensile strength

  • hair, skin, feathers, nails

collagen

triple helix of a polymer with; gly, pro, and hypro

• most abundant protein we have

• high tensile strength

• weird left-handed coil

  • three of these left-handed coils coil together in a right hand direction

• hypro: hydroxyproline—post-translational modification

stabilizing forces

hydrophobic effect

• more stable more energy needed to denature

stability

free energy between folded and unfolded proteins

quaternary structure

more stable than tertiary, route for regulating activity, multimer

myoglobin

oxygen storage

• higher binding affinity

• poor transporter of O2

• tertiary structure

• hyperbolic

heme

porphyrin ring

• O2 binds @ 120 degrees to Fe in the middle

hemoglobin

oxygen transporter

• quaternary structure

• lower binding affinity

  • alpha beta alpha beta

• sigmoidal

tensed and relaxed

two states of hemoglobin

relaxed state

higher O2 concentration state

tensed state

lower O2 concentration state

cooperativty

binding of one molecule causes the rest to bind tighter

• regulate affinity

carbamylation

mechanism that transports CO2

bohr effect

• low pH: T-state stabilizes lower binding affinity, O2 saturation decreases

• high pH: binding affinity increases, more O2 saturation

2,3 BPG

regulates binding affinity in hemoglobin as an allosteric regulator that makes the R state into T state

• more BPG lower BA

babies and BPG

lower BPG affinity and higher binding affinity (more storage O2)

High altitude

BPG increases at _____less oxygen is bound and less saturated

• less O2 in air less O2 bound in body

low O2 affinity

O2 given to tissues has _______

dissociation constant

Kd

half of binding sites are occupied

what does Kd or p50 mean?

enzyemes

biological molecule that catalyzes reactions

• increases rate of reaction (Ea)

substrate

any ligand the enzyme binds to

active site

where enzyme binds on substrate

T-state

not all reactants or products

T-state

enzymes complementary to ______

redox reactions

oxidoreductase

functional group transfer

transferase

hydrolysis

hydrolase

add groups to double bonds or make double bonds by removing groups

lysase

transfer groups to make isomeric forms

isomerase

join two molecules, often through hydrolysis

ligases

covalent catalysis

make covalent bond between enzyme and substrate

• will need to break this bond at some point—release enzyme

metal ion catalysis

the active site contains metal ions that help catalyze reaction

• good for stabilizing negative T-states

faster reaction

more substrate means _________

max speed

Vmax is the _____

K-2 ignored [ES] is constant (steady state)

Michaelis Menton assumptions

hyperbolic

Michaelis Menton is a _____ graph

Kcat/Km

catalytic efficiency equation

increases

as pH or temperature increases enzyme activity_______

RNA

ribosomes active site is _____

allosteric regulation

bind allosteric modulators non covalently