AP Bio Chemistry of Life Flashcards

Metabolism

the totality of an organism’s chemical reactions

Catabolic Pathways

break down large molecules into smaller molecules; release energy

Anabolic Pathways

form large molecules from smaller molecules; absorb energy

Bioenergetics

the study of how energy flows through living organisms

Energy

the capacity to cause change

Kinetic Energy

associated with the relative motion of objects

Thermal Energy

yay!

Heat

thermal energy in transfer of one object to another

Potential Energy

energy that matter possesses due to its location/structure

Thermodynamics

energy transformations that occur in a collection of matter

First Law of Thermodynamics

energy is not created or destroyed, only transferred

Second Law of Thermodynamics

every energy transfer increases the entropy of the universe

Exergonic Reaction

proceeds with a net release of free energy, -delta G, spontaneous

Endergonic Reaction

proceeds with a net absorption of free energy, +Delta G, nonspontaneous

Three kinds of work a cell does

Chemical work, transport work, mechanical work

Chemical work of a cell

pushing of endergonic reactions

Transport work of a cell

pumping of substances across membranes against the direction of spontaneous movement

Mechanical work of a cell

movement of cilia, muscles, chromosomes

energy coupling

the use of an exergonic process to drive an endergonic one

structure of ATP

ribose sugar, nitrogenous base adenine, three phosphate group

Phosphorylation

transfer of a phosphate group from ATP to another molecule, called the phosphorylated intermediate

Enzymes

macromolecules that act as catalysts: chemical agents that speed up reactions without being consumed by them

transition state

unstable state where bonds between reactant molecules can readily break

activation energy (Ea)

energy required to get to the transition state; energy required to start the reaction

substrate

the reactant an enzyme acts on

enzyme-substrate complex

enzyme binded to its substrate

active site

restricted site on enzyme that binds to the substrate

induced fit

active site changes after the substrate fits into the enzyme

lock-and-key fit

enzyme is perfectly made for the substrate

Mechanisms enzymes use to lower the activation energy

• active site provides a template where substrates can come together in proper orientation

• stretches bonds in the substrate

• provides a microenvironment suited to the reaction

• active site molecules participate with substrate in the reaction

Cofactors

inorganic molecules that aid enzymes in catalytic activity

Coenzymes

vitamins that aid enzymes in catalytic activity

Enzyme Inhibitors

inhibit the action of a specific enzyme

Cooperativity

binding of a molecule to one part of another molecule influences how molecules bind to other parts of that molecule

Feedback Inhibition

an end product acts as the inhibitor for its own production by binding to an enzyme used at the beginning of the reaction

Holoenzyme

enzyme with cofactor (functional/working)

Apoenzyme

enzyme without cofactor (non-functional/inactive)

Competitive Inhibition (Definition + Is it reversible?)

an inhibiting molecule sits on the active site, preventing the substrate from attaching to the active site. reversible

Noncompetitive/Allosteric Inhibition

an inhibiting molecule sits on the enzyme in a place other than the active site, changing the shape of the active site and the enzyme. quite often irreversible

Allosteric Activation

a molecule binds to an allosteric site on a molecule, which enhances the active site to make it optimal for the substrate

Isomers

compounds that have the same elements + same # of atoms but different arrangements of those atoms

structural isomers

differ in covalent arrangement of their atoms

cis-trans isomers

same atoms are covalently bonded to C, but spatial arrangement around the double bond differs

enantiomers

isomers that are mirror images of each other

Base formula of monosaccharides

CH2O (can be any number of C but must fit this formula)

Trademarks of a monosaccharide

a carbonyl (C=O) group at the end/on an interior carbon & multiple -OH groups

carbohydrate monomer

monosaccharide

disaccharide

two monosaccharides

bond that joins monosaccharides together

glycosidic covalent bond

starch

polymer of glucose that stores glucose in plants

glycogen

polymer of glucose that stores glucose in animals

two types of polysaccharides

storage and structure

cellulose

major component of plant cell walls

chitin

major component of insect exoskeletons + fungi cell walls

difference between cellulose and starch

both have 1-4 glycosidic linkages, but starch monomers are in the alpha configuration and cellulose monomers are in the beta configuration

biologically important lipids

fats, phospholipids, steroids

are triglyceride and fat referring to the same thing?

yes

glycerol

alcohol with 3 C, each bonded to an -OH

describe the chemical components of a fatty acid

one end contains a carboxyl group. the rest of is a nonpolar hydrocarbon chain

bond between lipid monomers

ester bond

in the formation of a fatty acid, which functional groups participate in dehydration synthesis?

the hydroxyl (-OH) on glycerol and carboxyl group on the fatty acid

saturated fatty acid

a fatty acid with no double bonds between carbons

unsaturated fatty acid

at least one double bonds between carbons in the fatty acid

main function of fats

energy storage

components of a triglyceride

glycerol, 3 fatty acids

describe the components of a phospholipid

one glycerol, two fatty acids. third -OH on the glycerol is bonded to a phosphate group, to which additional molecules can attach

state whether the head/tails are hydrophilic/hydrophobic

head is hydrophilic; tails are hydrophobic

describe the chemical components of steroids.

carbon skeleton of four fused rings

protein monomer

amino acid

bond that links amino acids together

covalent peptide bonds

components of an amino acid

central/alpha carbon, carboxyl group, amino group, hydrogen, R group

four groups of amino acids

• nonpolar side chains (hydrophobic)

• polar side chains (hydrophilic)

• acidic side chains (negative electrical charge)

• basic side chains (positive electrical charge)

functional groups that make a peptide bond

carboxyl of one amino acid & amino of the other amino acid

polypeptide

more than one amino acid linked together

ends of a polypeptide (names + what they consist of)

N-terminus (amino group) & C-terminus (carboxyl group)

primary structure

linear chain of amino acids

secondary structure

coils & folds within the backbone molecules of a polypeptide

tertiary structure

overall shape of a protein; results from interactions between side chains of a polypeptide

quaternary structure

association of two or more polypeptides

denaturation

a protein loses its shape, and thus loses its function

bonds in primary structure

peptide bonds

bonds in secondary structure

hydrogen bonds

two types of secondary structure formations

alpha helices & beta sheets

functional groups that participate in hydrogen bonding in the secondary structure

amino group + carboxyl group

bonds in tertiary structure

hydrogen bonds, ionic bonds, vanderwaal forces/hydrophobic attractions, disulfide bridges

bonds in quaternary structure

hydrogen bonds, ionic bonds, vanderwaal forces/hydrophobic attractions, disulfide bridges

functions of proteins

act as enzymes; protection against disease; storage of amino acids; transport of substances; produce hormones; act as receptors; facilitate movement; provide structural support

monomer of nucleic acids

nucleotides

components of nucleotides

• nitrogenous base (contains N)

• five-carbon sugar

• one to three phosphate groups

pyrimidines

cytosine, uracil, thymine

purines

adenine, guanine

structure of pyrimidines

six-membered ring of carbon + nitrogen atoms

structure of purines

six-membered ring fused to a five-membered ring

potential sugars present in a nucleotide

deoxyribose, ribose

difference between deoxyribose and ribose

deoxyribose has one less oxygen on the second carbon

which carbon are the phosphate groups added to?

5th carbon

bond between two nucleotides

phosphodiester linkage

molecules involved in a phosphodiester linkage

phosphate group links two sugars

what do the two ends of a polynucleotide contain?

a phosphate attached to a 5’ carbon; -OH attached to a 3’ carbon

antiparallel

DNA double helix runs in opposite directions