AP Biology Unit 2: Carbon, Macromolecules, and Metabolism

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Organic chemistry

the chemistry of compounds containing carbon (originally defined as the chemistry of substances produced by living organisms but now extended to substances synthesized artificially)

Hydrocarbon

an organic compound containing only carbon and hydrogen

Isomer

compounds with the same simple formula but different three-dimensional structures resulting in different physical and chemical properties

Structural isomer

one of several compounds that have the same molecular formula but differ in the covalent arrangements of their atoms.

Cis-trans isomer

alkenes that have the same connections between atoms but differ in their three-dimensional structures because of the way that groups attach to different sides of the double bond

Enantiomer

either one of a pair of compounds (crystals or molecules) that are mirror images on each other but are not identical

Functional group

group of atoms within a molecule that interacts in predictable ways with other molecules

Hydroxyl group

a functional group consisting of a hydrogen atom joined to an oxygen atom by a polar covalent bond; molecules possessing this group are soluble in water and are called alcohols

Alcohol

an organic compound with a hydroxyl group attached to one of its carbon atoms

Ethanol

the intoxicating agent in fermented and distilled liquors

Carbonyl group

a carbon atom linked by a double bond to an oxygen atom

Ketone

an organic compound with a carbonyl group of which the carbon atom is bonded to two other carbons

Aldehyde

an organic molecule with a carbonyl group located at the end of the carbon skeleton

Acetone

the simplest ketone

Propanal

a colorless liquid aldehyde

Carboxyl group

a functional group present in organic acids and consisting of a single carbon atom double-bonded to an oxygen atom and also bonded to a hydroxyl group

Carboxylic acid

an organic acid characterized by one or more carboxyl groups

Acetic acid

a carboxylic acid known as vinegar

Amino group

a functional group that consists of a nitrogen atom bonded to two hydrogen atoms; can act as a base in solution, accepting a hydrogen ion and acquiring a charge of +1

Amine

an organic compound with one or more amino groups

Glycine

the simplest amino acid found in proteins and the principal amino acid in sugar cane

Sulfhydryl group

a functional group consisting of a sulfur atom bonded to a hydrogen atom

Thiol

organic compounds containing sulfhydryl groups

Cysteine

an amino acid containing sulfur that is found in most proteins

Phosphate group

a functional group consisting of a phosphorus atom covalently bonded to four oxygen atoms

Organic phosphate

phosphate bonded to any organic molecule

Glycerol phosphate

3 carbon alcohol molecule needed to form the backbone of triglyceride

Methyl group

a chemical group consisting of a carbon bonded to three hydrogen atoms; may be attached to a carbon or to a different atom

5-methyl cytidine

example of methyl group, component of DNA that has been modified by this group

Macromolecule

large organic molecule formed by joining smaller organic molecules together

Polymer

a naturally occurring or synthetic compound consisting of large molecules made up of a linked series of repeated simple monomers

Monomer

small unit that can join together with other small units to form polymers

Enzyme

any of several complex proteins that are produced by cells and act as catalysts in specific biochemical reactions

Dehydration reaction

a chemical reaction in which two molecules covalently bond to each other with the removal of a water molecule

Hydrolysis

process where water is added to break a larger molecule into smaller molecules

Carbohydrate

compound made up of carbon, hydrogen, and oxygen atoms; major source of energy for the human body

Monosaccharide

building block of a carbohydrate; simplest sugar

Disaccharide

a double sugar, consisting of two monosaccharides joined by dehydration synthesis

Glycosidic linkage

a covalent bond formed between two monosaccharides by a dehydration reaction

Polysaccharide

any of a class of carbohydrates whose molecules contain chains of monosaccharide molecules - 3 or more monosaccharides linked together

Starch

polysaccharide made up of a chain of glucose molecules; food storage molecule for plants

Glycogen

an extensively branched glucose storage polysaccharide found in the liver and muscle of animals; the animal equivalent of starch

Cellulose

chemical compound made out of glucose; forms tangled fibers in the cell walls of many plants and provides structure and support

Chitin

complex carbohydrate that makes up the cell walls of fungi; also found in the external skeletons of arthropods

Lipid

an oily organic compound insoluble in water but soluble in organic solvents; macromolecule made mainly from carbon and hydrogen atoms, includes fats, oils, and waxes

Fat

organic compound consisting of a three-carbon backbone (glycerol) attached to three fatty acids; protects body organs, insulates body, and stores energy in the body

Fatty acid

a long carbon chain carboxylic acid, vary in length and in the number and location of double bonds; three of these linked to a glycerol molecule form fat

Triacylglycerol

three fatty acids linked to one glycerol molecule; also called a fat or a triglyceride

Saturated fatty acid

a fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that can attach to the carbon skeleton

Unsaturated fatty acid

a fatty acid possessing one or more double bonds between the carbons in the hydrocarbon tail; such bonding reduces the number of hydrogen atoms attached to the carbon skeleton

Trans fat

the fat that results when unsaturated fats are synthetically converted to saturated fats to prevent the separation of lipids (margarine and peanut butter are examples); this process produces saturated fats and unsaturated fats with trans double bonds

Phospholipid

a lipid made up of glycerol joined to two fatty acids and a phosphate group; the hydrocarbon chains of the fatty acids act as nonpolar, hydrophobic tails, while the rest of the molecule acts as a polar, hydrophilic head; form bilayers that function as biological membranes

Steroid

a type of lipid that consists of four carbon rings to which various functional groups are attached and that usually has a physiological action

Cholesterol

a steroid that forms an essential component of animal cell membranes and acts as a precursor molecule for the synthesis of other biologically important steroids

Catalyst

a substance that causes or hastens a chemical reaction; any agent that causes change

Polypeptide

a polymer (chain) of many amino acids linked together by peptide bonds

Protein

a molecule that is made up of amino acids and that is needed to build and repair body structures and to regulate processes in the body

Amino acid

monomer that makes up proteins; contains carboxyl and amino functional groups

Peptide bond

the covalent bond between two amino acid units, formed by a dehydration reaction

Primary structure

the first level of protein structure; the specific sequence of amino acids making up a polypeptide chain

Secondary structure

the localized, repetitive coiling or folding of the polypeptide backbone of a protein due to hydrogen bond formation between peptide linkages

Alpha helix

a spiral shape constituting one form of the secondary structure of proteins, arising from a specific pattern of hydrogen bonding

Beta pleated sheet

one form of the secondary structure of proteins in which the polypeptide chain folds back and forth, or where two regions of the chain lie parallel to each other and are held together by hydrogen bonds

Tertiary structure

the third level of protein structure; the overall, three-dimensional shape of a polypeptide due to interactions of the R groups of the amino acids making up the chain

Hydrophobic interaction

an interaction that contributes to tertiary structure; as a polypeptide folds into functional shape, amino acids with hydrophobic side chains usually end up in clusters at the core of the protein, away from water

Disulfide bridge

tertiary structure; strong covalent bond formed when one sulfur of one cysteine monomer bonds to the sulfur of another

Quarternary structure

the particular shape of a complex, aggregate protein defined by the characteristic 3D arrangement of its constituent subunits, each a polypeptide

Sickle-cell disease

a human genetic disease caused by a recessive allele that results in the substitution of a single amino acid in the hemoglobin protein; characterized by deformed red blood cells that can lead to numerous symptoms

Denaturation

for proteins, a process in which a protein unravels and loses its native conformation, thereby becoming biologically inactive;
occurs under extreme conditions of pH, salt concentration, and temperature

Chaperonin

a protein molecule that assists in the proper folding of other proteins; work by keeping the polypeptide "separated from bad influences"

X-ray crystallography

a technique that depends on the diffraction of an X-ray beam by the individual atoms of a crystallized molecule to study the three-dimensional structure of the molecule

Gene

sequence of DNA that codes for a protein and thus determines a trait

Nucleic acid

an organic compound, either RNA or DNA, whose molecules are made up of one or two chains of nucleotides and carry genetic information

Deoxyribonucleic acid

(DNA) molecule responsible for inheritance; nucleic acid that contains the sugar deoxyribose

Ribonucleic acid

(RNA) a type of nucleic acid consisting of nucleotide monomers with a ribose sugar and the nitrogenous bases adenine (A), cytosine (C), guanine (G), and uracil (U); usually single-stranded; functions in protein synthesis and as the genome of some viruses

Deoxyribose

five-carbon sugar that is a component of DNA nucleotides

Ribose

a pentose (five-carbon) sugar important as a component of ribonucleic acid

Double helix

two strands of nucleotides wound about each other; structure of DNA

Antiparallel

the pattern that describes the formation of DNA; the two sugar-phosphate backbones run in opposite 5' >> 3' directions from each other, somewhat like a divided highway

Nucleotide

monomer of nucleic acids made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base

Polynucleotide

a polymer consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities; the two types are DNA and RNA

Pyrimidine

one of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring; cytosine (C), thymine (T), and uracil (U)

Purine

a nitrogenous base that has a double-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; either adenine or guanine

Metabolism

set of chemical reactions through which an organism builds up or breaks down materials as it carries out its life processes

Metabolic pathway

a series of chemical reactions that either builds a complex molecule (anabolic pathway) or breaks down a complex molecule into simpler compounds (catabolic pathway)

Catabolic pathway

a metabolic pathway that releases energy by breaking down complex molecules to simpler compounds

Anabolic pathway

a metabolic pathway that consumes energy to synthesize a complex molecule from simpler compounds

Bioenergetics

the biology of energy transformations and exchanges within the body, and between it and the environment

Energy

the ability to do work or cause change

Kinetic energy

the mechanical energy that a body has by virtue of its motion

Heat (thermal) energy

kinetic energy associated with the random movement of atoms or molecules

Potential energy

the mechanical energy that a body has by virtue of its position

Chemical energy

potential energy stored in chemical bonds of molecules

Thermodynamics

the study of energy transformations that occur in a collection of matter

First law of thermodynamics

the principle of conservation of energy; energy can be transferred and transformed, but it cannot be created or destroyed

Entropy

a thermodynamic quantity representing the amount of energy in a system that is no longer available for doing mechanical work; a quantitative measure of disorder or randomness, symbolized by S

Second law of thermodynamics

when energy is changed from one form to another, some useful energy is always degraded into lower quality energy (usually heat); the entropy of a system always increases

Spontaneous process

physical/chemical change occurring without outside intervention

Free energy

the portion of a system's energy that can perform work when temperature and pressure are uniform throughout the system

Exergonic reaction

a spontaneous chemical reaction in which there is a net release of free energy

Endergonic reaction

a non-spontaneous chemical reaction in which free energy is absorbed from the surroundings

Energy coupling

in cellular metabolism, the use of energy released from an exergonic reaction to drive an endergonic reaction

Phosphorylated intermediate

the molecule which receives the high energy phosphate from ATP and becomes more reactive

Activation energy

the minimum amount of energy required to start a chemical reaction

Substrate

specific reactant acted on by an enzyme

Enzyme-substrate complex

a temporary complex formed when an enzyme binds to its substrate molecule(s)

Active site

the specific portion of an enzyme that attaches to the substrate by means of weak chemical bonds

Induced fit

induced by entry of the substrate, the change in shape of the active site of an enzyme so that it binds more snugly to the substrate

Cofactor

any nonprotein molecule or ion that is required for the proper functioning of an enzyme; can be permanently bound to the active site or may bind loosely with the substrate during catalysis

Coenzyme

an organic molecule serving as a cofactor; most vitamins function as coenzymes in important metabolic reactions

Competitive inhibitor

a substance that reduces the activity of an enzyme by entering the active site in place of the substrate whose structure it mimics

Noncompetitive inhibitor

a substance that reduces the activity of an enzyme by binding to a location remote from the active site, changing the enzyme's shape so that the active site no longer functions effectively

Allosteric reaction

a case in which a protein's function at one site is affected by the binding of a regulatory molecule to a separate site

Cooperativity

a kind of allosteric regulation whereby a shape change in one subunit of a protein caused by substrate binding is transmitted to all the others, facilitating binding of subsequent substrate molecules

Feedback inhibition

a method of metabolic control in which the end product of a metabolic pathway acts as an inhibitor of an enzyme within that pathway

ATP

(adenosine triphosphate) main energy source that cells use for most of their work

ADP

(adenosine diphosphate) molecule that ATP becomes when it gives up one of its three phosphate groups

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