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117 terms

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