biochem lecture 1 notes

methyl

R-CH3

ethyl

R-CH2-CH3

phenyl

R-6 membered ring

carbonyl (aldehyde)

carbonyl (ketone)

carboxyl

R-COO-

hydroxyl

R-OH

enol

ether

R-O-R

ester

acetyl

anhydride

amino

R-NH3+

amido

imine

n-substituted imine

guanidinium

imidazole

sulfhydral

R-SH

disulfide

thioester

phosphoryl

phosphoanhydride

mixed anhydride

enantiomers

cis conformation

trans comformation

phototrophs

trap and use sunlight for energy

chemotrophs

derive their energy from oxidation of a

chemical fuel

autotrophs

Phototrophs and chemotrophs may be further divided into those that can synthesize all of their biomolecules directly from CO2 (______)

heterotrophs

those that require some preformed organic nutrients made by other organisms

chloroplast, glyoxysomes, cell wall, plasmodesa, vacuole

found in plant cells, but not animal cells

peroxisome, lysosomes

found in animal cells, but not plant cells

nucleoid, cell envelope, pili, flagella

parts of bacteria cells

catabolism

breaks down complex molecules into simpler ones, releasing the energy

anabolism

builds larger, complex molecules from smaller, simpler ones; requires energy

Exothermic (1), exergonic (2)

Exothermic and exergonic reactions both release energy, but ______ (1) deals with release of heat while _____(2) deals with the release of total free energy adn rxn spontaneity

deltaG = deltaH - TdeltaS

gibbs free energy equation

spontaneous

deltaG < 0 means rxn is

not spontaneous

deltaG > 0 means rxn is

at equilibrium

deltaG = 0 means rxn is

hypertonic

cell in a ______ solution means the solution has higher osmolarity than that of the cytosol; the cell

shrinks as water moves out.

hypotonic

cell in a ______ solution means the solution has lower osmolarity than that of the cytosol; the cell

expands as water moves in.

isotonic

cell in a ______ solution means there is no net movement of water

tugor

plant cells prefer ___ pressure

the cell wall in plant cells

neg

gram ___ contain both inner and outer membrane

pos

gram ___ contain only inner membrane and cell wall, no outer membrane. this type is also stained by gram’s stain

B-lactamase

_________ gene in plasmids of these bacteria break down penicilin

cell wall

___ ____ protects contents inside (prevents lysis)

transpeptidase

________ synthesis cell wall of bacteria

diffusion

movement of molecules down their gradient

peniclin

drug that kills bacteria by inhibiting transpeptidase

deltaG* = -RTln(Keq)

standard free energy change (deltaG*) and the equilibrium constant (Keq) are connected b

Kw = 1 × 10^-14

equilibrium constant for the of water at 25 ℃

[H3O+][OH-]

Kw equation

pKa = -log(Ka)

equation for pKa

Ka = [H3O+][A-] / [HA]

equation for Ka

pOH + pH = 14.0

relationship between pOH and pH

pH = -log[H+]

equation for pH

ATP

name this molecule

AMP

name this molecule

ADP

name this molecule

0.177 nm

hydrogen bond length

0.0965 nm

covalent bond length

the water-solute interactions are more energetically favorable than the solute-solute interactins

polar water molecules dissolve in water because ….

nonpolar (1), polar (2)

_______ (1) regions of the molecules cluster together to present the smallest hydrophobic area to the aqueous solvent, and the ____ (2) regions are arranged to maximize their interaction with the solvent

disordered

water is trying to move to a more _____ state (more energetically favorable)

LOWER

When substrates/ligands interact with

enzymes/receptors, the final interactions must have a

______ energy state than the initial “fully solvated”

state for each molecule

condensation rxn

this is an example of what kind of rxn

hydrolysis rxn

this is an example of what kind of rxn

acid-base

H+ in water “hop” fast — thus, ____-____ reactions in water are also fast

higher

The _____ the Ka, the stronger the acid

lower

the _____ pKa, the stronger the acid

pKa

_____ is the pH at which weak acid has an EQUAL concentration of conjugate acid & base

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

henderson-hasselbalch equation