UGA BCMB 3100 Exam 1

Water

-major component of cells

-ability to dissolve a wide variety of molecules

-many biochemical reactions take place in watery environments

Shape of water

-angled shape

-polar bonds

-polar due to uneven distribution of electrons

-hydrogen has a partial positive charge and oxygen has a partial negative charge

Hydrogen bond in water

formed when a partially positive hydrogen atom attracts the partially negative oxygen atom of a second water molecule

Hemoglobin

-red blood cells carry oxygen from the lungs to tissues where oxygen is required

-four subunit protein with an oxygen binding pigment

Interactions in water

-solvation and desolvation

-micelle formation

-protein folding

Protein

-composed of 20 common amino acids

amino acid structure

-carboxylate group (-COO-)

-amino group (-NH2)

-side chain (R)

second law of thermodynamics

-total entropy of a system and its surroundings always increases in a spontaneous process

Entropy (S)

-degree of disorder in the system

-a measure of randomness

if 2 or more benzene molecules are added to water

-bond together to displace water molecules

-increases entropy of the system

-results from the hydrophobic effect

Hydrophobic effect

-nonpolar solute molecules are driven together in water not primarily because they have a high affinity for each other

-entropy driven association

-form spontaneously because the entropy increases

non covalent interactions

-essential for proper functioning of biomolecules

-much weaker than covalent bonds

-allow for constant forming and breaking of bonds

Types of non-covalent interactions

-electrostatic interactions

-hydrogen bonds

-van der Waals interactions

Electrostatic interactions

-between electrical charges

-ion-ion interaction

-between a full positive and a full negative charge

hydrogen bonds

-between an electronegative atom and hydrogen

-forms between H and O/N

Van der Waals interactions

-depend on transient asymmetry in electrical charge

-weak forces that occur between any 2 atoms that approach each other

primary structure

amino acid linear sequence

secondary structure

regions of regular repeating conformation of the peptide chain

tertiary structure

-describes the shape of the fully folded polypeptide chain

-held together by non covalent interactions

-hydrogen bonds and ion-ion interactions

quaternary structure

arrangement of 2 or more polypeptide chain into multi-subunit molecule

Henderson-Hasselbalch equation

-used to calculate pH of solutions created by mixing known amounts of acids and conjugate bases

-used to calculate relative amounts of protonated and deprotonated forms at a specific pH

enthalpy

the energy required to break bonds and gained by forming new bonds

exothermic

-energy released

-negative term

Lipid bilayers

structural basis for all biological membranes

hydrophilic

-water loving

-head

-interacts with H2O

-polar

hydrophobic

-water fearing

-tail

-nonpolar

cotransporter

secondary transporters

peptide bonds

-bonds between amino acids

-primary structure

-trans form is favored

-planer

-double bond character due to bond between C-N

polypeptide chain

series of amino acids joined by peptide bonds

alpha helix

-bond forms between i+4 residue

types of secondary structure

-alpha helix

-beta pleated sheets

-turns

beta sheet

-composed of 2 or more polypeptide chains called beta strands

turns and loops

-lie on the surface of protein and often participate in interactions between other proteins and the environment

soluble protein

hemoglobin

membrane protein

potassium ion channel

enzyme

carbonic anhydrase

delta g

-can be changed by changing the concentration of substrates or products

-enzymes can not change the delta g but they can change the rate of the reaction

Hyperventilation

-over-breathing

-underlying cause of respiratory alkalosis

respiratory alkalosis

-occurs when levels of CO2 and O2 in the blood are not balanced

Le Chatelier's Principle

if any change in imposed on a system that is in equilibrium then the system tends to adjust to a new equilibrium counteracting the change

Buffer

a solution that resists changes in pH when acid or alkali is added to it

properties of enzymes

-overall free energy of a reaction is unaffected by an enzyme

-enzymes decrease the amount of free energy that must be invested to reach the transition state

Keq = 1

delta g' = 0

Keq > 1

delta g' < 0 products are favored

Keq < 1

delta g' > 0 reactants are favored

osteoclast

-type of bone cell that breaks down bone tissue

-function is to maintain, repair, and remodel bone of the vertebral skeleton

kinetics

study of the rates of chemical reactions

enzyme kinetics

study of the rate of enzyme-catalyzed reactions

V

the velocity (rate) of the reaction

Vo

the initial rate of enzyme reaction when the reaction is just beginning

Vmax

-represents the fastest that the enzyme can turnover

-proportional to [E]

Km

-value describes the properties of an enzyme against a substrate

-lower the Km the tighter the substrate binding

-a measure of the affinity of E for S

-stability of ES

high Km

enzyme has low affinity for substrate

low Km

enzyme has high affinity for substrate

Kcat

-the rate constant of the rate-limiting step

-catalytic constant - first order rate constant for conversion of ES complex to E + P

-number of reactions per second

Michaelis-Menten plot

-initial velocity versus [S]

Lineweaver-Burk Plot

the double reciprocal graph of the Michaelis-Menten equation

1/Vo versus 1/[S]

Types of enzyme inhibition

reversible and irreversible

irreversible inhibitors

-covalently modify an enzyme and inhibition can therefore not be reversed

-decrease Vmax and no effect on Km

types of reversible inhibition

Competitive

Uncompetitive

Non-competitive

reversible inhibition

substrate binds to an enzyme's active site to form an enzyme-substate complex

competitive inhibition

-binds at the active site and thus prevents the substrate from binding

-competes with substrate for available active sites

uncompetitive inhibition

-binds only to the enzyme-substrate complex

-lowers catalytic rate

noncompetitive inhibitor

-does not prevent the substrate from binding

-lowers the catalytic rate