biochemistry unit 1

prefix for pico

10^-12

prefix for nano

10^-9

prefix for micro

10^-6

prefix for milli

10^-3

prefix for centi

10^-2

prefix for deci

10^-1

prefix for kilo

10^3

what are the 3 domains of organisms

bacteria, archaea, eukarya

what do bacteria inhabit?

soils, surface waters, tissues of living or decaying organisms

what do archaea inhabit?

extreme environments

what is the main difference between prokaryotic and eukaryotic cells?

eukaryotic cells have nucleus and membrane bound organelles

where do prokaryotes store their genome?

in a nucleoid

where do eukaryotes store their genome?

in membrane-enclosed nucleus

what are the 4 main classes of biological compounds?

nucleic acids, proteins, carbohydrates, lipids

what are the monomer units of nucleic acids?

nucleotides

what are the monomer units of proteins?

amino acids

what are the monomer units of carbohydrates?

monosaccharides

what are the monomer units of lipids?

glycerol and fatty acids

what are the 2 types of geometric isomers?

cis/trans isomerism

what are stereoisomers?

molecules with same chemical bond and formula but different shape

what are the reactants in photosynthesis?

carbon dioxide and water

what are the products in photosynthesis?

glucose and oxygen

what are the reactants that nonphotosynthetic cells use to obtain energy?

glucose and oxygen

what are the products when nonphotosynthetic cells obtain energy?

carbon dioxide, water, energy

what are the 3 intermolecular forces?

van der waals, hydrogen bonding, ionic interactions

what is water doing during the hydrophobic effect?

surrounding the solute

what types of gases are poorly soluble in water?

nonpolar

electrostatic interactions are responsible for dissolving what?

salts and charged organics

solvation is governed by changes in what?

entropy and enthalpy

what type of molecules are soluble in water?

charged or polar

what do amphipathic molecules form when in water?

micelles or lipid bilayer

what is the formula for pKa?

pKa= -logKa

what is the formula for Ka?

Ka= \[H\]\[A\]/\[HA\]

what is the relationship between acid and pKa?

stronger acid=lower pKa

what can buffer solutions against changes in pH?

conjugate acid-base pairs

how do buffer solutions work?

buffer solutions are weak acids and their conjugate base which exchange H and OH ions to form water

what is an important buffer in blood?

bicarbonate

lungs affect the blood pH level by changing the amount of what?

carbon dioxide

kidneys affect the blood pH level by regulating the level of what?

bicarbonate

what type of molecules can diffuse through the bilayer?

small nonpolar

what type of molecules can’t cross the cell membrane without a transporter or channel?

small polar

are amino acids weak or strong acids/bases?

weak

what determines the buffering range of a weak acid?

amount of dissociation of the acid at a given pH

what makes up an amino acid?

chiral alpha carbon, amine, carboxyl, functional R group

what are the 4 levels of protein structure?

primary, secondary, tertiary, quaternary

what is an important element in protein structure and oligomerization?

disulfide bonds

what is the primary structure of of a protein?

the sequence of amino acids-polypeptide

why are peptide bonds planar?

double bonded C

what are secondary structures made of?

polypeptides connected together by hydrogen bonding

what are common secondary structures?

alpha helix, beta sheet, beta turn

in what secondary structure do all peptide bonds participate?

alpha helix

how are beta sheets stabilized?

through hydrogen binding between adjacent strands

how are beta turns stabilized?

through hydrogen bonding between the first and fourth residue of the turn

what is a motif?

recognizable patter formed from tertiary structure

what is a quaternary structure?

protein composed of 2 or more polypeptide chains

what is a structural protein with quaternary structure?

collagen

how is an alpha helix formed?

hydrogen bonding between carbonyl oxygen and n+4 amino hydrogen

the primary structure of a protein determines what?

secondary, tertiary, and quaternary structure

what is Kd?

ligand concentration where hlaf the active sites are occupied

what is the relationship between Kd and affinity of ligand for protein?

inverse

what is allostery?

where binding of a ligand to one site affects binding of ligands at other sites

what do ligands and oxygen bind to in myoglobin and hemoglobin?

heme group

ligand binding is sensitive to what at the binding site?

steric effects

when does allostery occur in hemoglobin?

t state to r state

describe the concerted model

all subunits undergo conversion simultaneously between low and high affinity forms

describe the sequential model

each subunit can be in either low or high affinity form

what state is monomeric myoglobin always in?

high-affinity state

what is a bpg?

a bridge between subunits

what is the rationale drug design?

process of using known tertiary structure of an active site to design an inhibitor that blocks ligand binding

what does an inhibitor do to a substrate?

decrease product

what is an antigen?

ligand that an antibody binds

what is IgG?

mature Ab form that is very common in the blood

what forces participate in forming tertiary and quaternary structures in proteins?

weak forces

how do ligands bind to active sites?

complimentary and stabilization of interactions between ligand and protein

what is the definition of life?

metabolism, growth, reproduction

why are enzymes essential?

accelerate reactions in meaningful way critical for life

what do enzymes do?

increase reaction rates without being used up

why are biocatalysis beter than inorganic catalysts?

has greater reaction specificity, milder reaction conditions, higher reaction rates, capacity for regulation

what is the ground state?

starting point for either forward or reverse reaction

what is the transition state?

the point at which decay to substrate or product are equally likely

how do enzymes speed up reactions?

by lowering activation energy

what are simple enzymes composed of?

protein

what are complex proteins composed of?

protein and cofactor

what is a covalently bound cofactor?

prosthetic group

what is a non-covalently bound cofactor?

coenzyme

what are the 7 enzyme classes?

oxidoreductases, transferases, hydrolases, lyases, isomerases, ligases, translocases

what is the clinical significance of enzymes?

treat diseases

what is an active site?

specific region on an enzyme where the substrates are bound

when do interactions between substrate and enzymes formed?

when the substrate reaches the transition state

what are the 3 catalytic mechanisms?

acid-base, covalent, metal ion

what happens during acid-base catalysis?

protons are transferred between enzyme and substrate or intermediate

what is covalent catalysis?

transient covalent bond forms between enzyme and substrate

when does covalent catalysis result?

when the new pathway has a lower activation energy than the uncatalyzed pathway

what do metals do in metal ion catalysis?

orient substrate, stabilize charged reaction transition states, mediate redox reactions

what is a protease?

enzyme that catalyzes hydrolytic cleavage of peptide bonds

where does chymotrypsin cleave the peptide bond?

the bond adjacent to aromatic amino acids

what determines substrate specificity?

structure of the substrate binding site

what are serine proteases?

proteases with ser residue that act as nucleophile

what is the catalytic triad in chymotrypsin?

ser195, his57, asp102

what is a catalytic triad?

hydrogen bonding network