chapter 3 and 4: energy, catalysis, and biosynthesis/proteins

metabolism

the sum of all chemical rxns occuring in a cell or organism

catabolism

the breakdown of molecules that generally releases energy and produces smaller building blocks

anabolism

the synthesis of larger molecules from smaller molecules; generally requires energy

free energy

energy that can be harnessed to perform work or drive chemical rxns

deltaG

the change in free energy between products and reactants

-deltaG

the rxn is energetically favorable/spontaneous in that direction

+deltaG

the rxn is energetically unfavorable and requires energy input

deltaG = 0

the system is at equilibrium

activation energy

the energy barrier that must be overcome to initiate a chemical rxn

enzymes

catalyze rxns by lowering activation energy, increasing the rxn; do not change equilibrium and are not consumed and regenerated

enzymes effect on deltaG

lower AE but do not change the free-energy difference between reactants and products

heat

increases the rxn but nonspecifically unlike enzymes which are specific to rxns

substrate

a molecule that an enzyme binds and acts upon

enzyme-substrate complex

the temporary complex formed when an enzyme binds its substrate

enzyme binding specificity

complementary shape and chemical properties between the substrate and binding site

type of interactions between enzymes and substrates

hydrogen bonds, electrostatic attraction, van der Waals interactions, and hydrophobic interactions

binding/association constant (K)

larger K (equilibrium constant) means a stronger binding between molecules

oxidation

loss of electrons

reduction

gain of electrons

ATP

activated carrier that transfers chemical free energy to drive cellular processes

ATP hydrolysis

ATP + H2O --> ADP + Pi + energy; its hydrolysis can be coupled to energetically unfavorable rxns, helping drive them forward by creating a high-energy intermediate

coupled rxns (two)

link them so that the favorable free-energy change of one helps drive an unfavorable rxn; if deltaG < 0, it is an energetically favorable rxn

overall deltaG of coupled rxns

add the deltaG values of the individuals rxns

activated carriers

molecules that carry transferable chemical groups or energy used in biosynthetic rxns; ATP, NADPH, acetyl CoA, and biotin

acetyl-CoA

activated carrier that carries an acetyl group; this acetyl group is readily transferable because it is linked to the CoA through a high-energy thioester linkage

catabolism and activated carriers

catabolism provides energy that is used to generate ATP and other activated carriers, which then support anabolism

cellular respiration

extracts energy from organic molecules; organic molecules are oxidized using O2, producing CO2, H2O, and usable energy

photosyntheis

to capture light energy and store it in organic molecules; CO2 and H2O are used with light energy to produce organic molecules and O2

what determines a protein's 3-D structure?

amino acid sequence, through the interactions among its amino acid side chains and backbone

protein structure and function

a protein's specific 3D structure allows it to interact with particular molecules and perform its function

what holds amino acids together in a polypeptide?

covalent peptide bonds

protein backbone

repeating N-C-C structure of the polypeptide chain

unique chemical properties of a protein is determined by...

the sequence and chemical properties of its amino acid side chains

primary protein structure

amino acid sequence

secondary protein structure

local structures such as a-helices and b-sheets, stabilized mainly by hydrogen bonds between backbone atoms

tertiary protein structure

overall 3-D conformation of a single polypeptide chain

quaternary protein structure

arrangement of multiple polypeptide chains in a protein complex

protein domain

a segment of a protein that can fold independently into a stable structure; a single protein can contain multiple domains and are a part of a polypeptide; different domains can perform different functions or interact with different molecules

protein complex

contains multiple polypeptide chains

protein folding

protein fold into energetically favorable conformation based on interactions among their amino acids and with water

hydrophobic amino acid side chains in soluble protein are located…

in the interior, away from water

polar and charged amino acids location

on the protein surface where they interact with water

hydrophobic core

the interior region of a protein enriched in nonpolar side chains

hydrophobic effect on protein folding

nonpolar groups tend to minimize their exposure to water, causing them to cluster inside the proteins

interactions that stabilize protein structure

hydrophobic interactions, hydrogen bonds, electrostatic interactions, van der Waals interactions, and disulfide bonds

noncovalent bonds

hydrogen bonds, electrostatic interactions, van der Waals interactions, and hydrophobic interactions

disulfide bonds

stabilizes a protein's favored folded conformation, formed by AA cysteine, groups: two cysteine -SH groups, formed by oxidation of two cysteine -SH groups, producing an S-S bond, common in extracellular proteins, uncommon in cytosol due to -SH favored conditions

ligand

any molecule or ion that binds specifically to a protein due to the shape and chemical properties, binded by hydrogen bonds, electrostatic attractions, van der Waals interactions, and hydrophobic forces

ligand-binding site

located in a cavity or pocket on the protein surface; this pocket allows the protein to surround the ligand and form many complementary interactions

weak interactions produce highly specific protein-ligand binding

the ligand must simultaneously match the binding site in shape and chemistry for many interactions to form

molecular chaperones

help proteins fold properly and prevent inappropriate aggregation

type of amino acid side chains favored in a membrane-spanning region of a protein

hydrophobic/nonpolar side chains

membrane-spanning regions tendency to be hydrophobic

they interact with the hydrophobic fatty-acid tails of the lipid bilayer

scaffold protein

a protein containing binding sites that brings multiple interacting protein ; useful to increase the efficiency of a cellular process and localize it to a specific region of the cell