AP BIO UNIT 1

Nucleic acids

Biological macromolecules that store, transmit, and help express genetic information; the information is encoded in the sequence of bases; polymers of nucleotides; CHONP

DNA (deoxyribonucleic acid)

A nucleic acid used primarily for long-term information storage; typically double-stranded and forms a double helix.

RNA (ribonucleic acid)

A nucleic acid often involved in information transfer and functional roles; typically single-stranded and able to fold into complex shapes.

Nucleotide

The monomer of nucleic acids; composed of a phosphate group, a five-carbon sugar, and a nitrogenous base.

Nucleoside

A sugar + nitrogenous base (no phosphate group); differs from a nucleotide by lacking the phosphate.

Nitrogenous base

A ring-shaped, nitrogen-containing part of a nucleotide that carries genetic information; its order (sequence) encodes information.

Purines

Nitrogenous bases with two rings (larger); adenine (A) and guanine (G).

Pyrimidines

Nitrogenous bases with one ring (smaller); cytosine (C), thymine (T, in DNA), and uracil (U, in RNA).

Thymine (T) vs. Uracil (U)

Thymine is used in DNA and uracil is used in RNA; in RNA base pairing, adenine (A) pairs with uracil (U) instead of thymine (T).

Sugar-phosphate backbone

The repeating structural framework of a nucleic acid strand made of alternating sugars and phosphates; bases attach to the sugars and stick out from the backbone.

Phosphodiester bond

The covalent bond that links nucleotides in a strand by connecting the phosphate of one nucleotide to the $3'$ carbon (OH) of the next nucleotide’s sugar.

5′ and 3′ ends

The two chemically distinct ends of a nucleic acid strand: the $5'$ end has a free phosphate, and the $3'$ end has a free hydroxyl (-OH) on the sugar.

Directionality (polarity)

The property that nucleic acid strands have a 5′ end and a 3′ end; many enzymes add nucleotides only to the $3'$ end.

Dehydration synthesis (condensation reaction)

A polymer-forming reaction where a covalent bond forms and water is produced; nucleotides polymerize to build the sugar-phosphate backbone.

Complementary base pairing

Specific pairing between bases in double-stranded regions: A pairs with T in DNA (or with U in RNA), and G pairs with C; supports accurate copying.

Hydrogen bonds (in base pairing)

Weak bonds that hold complementary bases together across strands; A–T (or A–U) forms 2 hydrogen bonds, and G–C forms 3.

Antiparallel

Describes the orientation of two strands in double-stranded DNA (and many paired regions): one runs 5′→3′ while the other runs 3′→5′.

Deoxyribose vs. ribose

Deoxyribose (in DNA) has an H at the 2′ carbon, while ribose (in RNA) has an OH at the 2′ carbon; the 2′ OH makes RNA generally less chemically stable.

Double helix

The typical shape of DNA: two antiparallel strands twisted together, with sugar-phosphate backbones on the outside and stacked bases inside.

nucleotide

phosphate group. pentose sugar, nitrogenous base

polynucleotide

nucleotides joined together by a series of dehydation reactions

ATP

nucleotide composed of adenine, ribose, and 3 phosphates; high-energy molecule due to presence of last unstable phophate bonds (easily broken) —> hydrolysis of this bond yields the molcule ADP and energy to do cellular work

Biological macromolecules

Large, carbon-based molecules used by organisms to store energy, build cellular structures, transmit information, and carry out chemical reactions (carbohydrates, lipids, proteins, nucleic acids).

Structure determines function

Principle that a macromolecule’s specific arrangement of atoms (its structure) determines its chemical behavior and biological role.

Carbon backbone (of life)

Carbon’s ability to form four covalent bonds allows long chains, branches, and rings, creating diverse biological molecules with different shapes and properties.

Monomer

A small molecular subunit that can be linked to other subunits (e.g., an amino acid).

Polymer

A large molecule made of many repeating monomer units linked together (e.g., a polypeptide).

Dehydration synthesis (condensation reaction)

Builds polymers by forming a covalent bond between monomers while removing a molecule of water.

Hydrolysis

Breaks polymers into monomers by adding water to help break a covalent bond.

Functional group

A specific cluster of atoms that behaves in consistent ways and helps determine a molecule’s properties (polarity, acidity/basicity, reactivity).

Hydroxyl group (-OH)

Functional group that often increases polarity and water solubility; common in sugars.

Carboxyl group (-COOH)

Functional group that can donate H+ (acidic); found in amino acids and fatty acids.

Amino group (-NH$_2$)

Functional group that can accept H+ (basic); found in amino acids.

Phosphate group (-PO$_4$)

Functional group that often contributes negative charge and is important in energy transfer and nucleic acids.

Hydrophilic

Describes polar or charged regions that interact well with water.

Hydrophobic

Describes nonpolar regions that do not interact well with water and tend to cluster away from it.

Isomer

A molecule with the same molecular formula as another molecule but a different structure, often leading to different biological function.

Covalent bond

A strong bond that holds the main backbone of polymers together (e.g., glycosidic, peptide, phosphodiester bonds).

Hydrogen bond

A weak interaction important for macromolecule shape, such as DNA base pairing and protein secondary structure (strong collectively, weak individually).

Glycosidic linkage

The covalent bond that links monosaccharides together in carbohydrates; formed by dehydration synthesis.

Triglyceride

A lipid made from glycerol and fatty acids; used for long-term energy storage and insulation due to many C-H bonds and low water attraction.

Saturated fatty acid

A fatty acid with no double bonds; straighter chains that pack tightly (often associated with more solid fats).

Unsaturated fatty acid

A fatty acid with one or more double bonds; kinked chains that pack less tightly, increasing membrane fluidity when present in phospholipids.

Peptide bond

The covalent bond linking amino acids in a polypeptide; formed by dehydration synthesis.

Nucleotide

The monomer of nucleic acids, consisting of a phosphate group, a five-carbon sugar (ribose or deoxyribose), and a nitrogenous base.

Phosphodiester bond

The covalent bond that links nucleotides, connecting the sugar of one nucleotide to the phosphate of the next to form the sugar-phosphate backbone.

carbohydrate

short-term energy storage + providing building material to cells and organisms; CHO; monosaccharides, polysaccharides

dissacharide

2 monosaccharides bonded together by dehydration synthesis; e.g. sucrose, lactose

glycosidic linkage

covalent bond formed between monosaccharides

polysaccharide

polymer of monosaccharides; storage and structural

starch

polysaccharide made up glucose monomers in alpha (helical) config.; used to store sugars; helical in shape, some branching

glycogen

polsyaccharide made of glucose monomers; used to store sugars in animals

cellulose

polysaccharide that makes up cell wall in plant cells; glucose monomers in beta (srtaight) config.; straight, no branching —> allows some hydroxyl groups on its glucose monomers to hydrogen bond with other cellulose molecules lying parallel to it, forming strong, cable-like microfibrils

chitin

used by insects and crustaceans to build their exoskeletons; building material for cells walls in fungi; nitrogen instead of just CHO in monomers

protein

defense, transport, cellular communication, movement, structural support; CHONS; amino acids, polypeptides

polypeptide

long chains of amino acids joined together; 2 ends: amino (N) terminus and carboxyl (C) terminus; new amino acids are added to carboxyl terminus

functional protein

2+ polypeptides; proteins can’t function properly unless folded into their proper conformation

primary level

linear sequence of amino acids

secondary level

patterns of hydrogen bonding between amino acids causes regions of polypeptdie to form alpha helices (coils) and beta pleated sheets (folds)

teriary levels

final folding and overall 3D shape of polypetide; interactions between R-groups: hydrophobic interactions, hydrogen bonding, van der waals interactions, ionic and covalent bonding, disulfide bridges

disulfide bridge

covalent bond between sulfur atoms of two different R groups

quaternary level

2+ folded polypeptides coming together to form a single, large functional protein; e.g. hemoglobin + collagen; only some proteins have this level

subunit

each individual polypeptide that makes up the final protein structure

denaturation

loss of a protein’s functional structure due to changes in environmental conditions; doesn’t affect primary structure; biologically inactive

enzymatic proteins

proteins that act as catalysts to accelerate chemical reations within cells

transport proteins

proteins embedded in cell membrane that control the movement of substances in and out of a cell

contractile and motor proteins

help cells move and move material inside cells. contracile are found in muscles and are responsible for muscle contraction

receptor proteins

proteins that bind to chemical signals and initate a cell response

hormonal/signaling proteins

proteins released into the blood and bind to receptors on cells throughout the body to regulate the activity of an organism

defense proteins

antibodies; assist the immune system in destroying viruses and bacteria and protecting organisms from infection

structural proteins

many long, fibrous proteins play structural roles in organisms; e.g. keratin proteins form hair, nails, horns. collagen proteins form connective tissue that holds organs together. cytoskeleton proteins provide supportive framework inside cells

lipid

CHOP; no true monomer

fats

large unpolar molecules called triglycerides; energy storage, insulate body heat in mammals

triglycerides

formed from bonding together of four monomers, forming 3 covalent bonds called ester linkages

phospholipid

one glycerol molecule linked to 2 fatty acids and a modified phosphate group; fatty acids (tails) are nonpolar and hydrophobic, modified phosphate group (head) is polar and hydrophilic; structural function, main component of all cell membranes; aggregate to form a lipid bilayer in water

lipid bilayer

polar phosphate heads are oriented toward outsides of bilayer, interacting with each other and the water inside and outside a cell; nonpolar fatty acid tails are oriented toward inside of bilayer away fromwwater

steroid

carbon skeleton of four fused carbon rings; nonpolar; e.g. cholesterol is a component in animal membranes. testosterone and estrogen regulate and control the body.

Polar molecule

A molecule with an uneven distribution of electrical charge (partial positive and partial negative regions) but no net charge overall; water is polar.

Covalent bond

A strong chemical bond formed when atoms share electron pairs; doesn’t dissociate in water; aka molecules

Electronegativity

An atom’s ability to attract shared electrons in a covalent bond; oxygen is more electronegative than hydrogen.

Hydrogen bond

A weak attraction between a δ+ hydrogen (bonded to an electronegative atom like O or N) and a nearby electronegative atom with a partial negative charge.

Cohesion

Attraction between molecules of the same substance; in water, cohesion results from hydrogen bonding between water molecules.

Adhesion

Attraction between molecules of different substances; water adheres to other polar surfaces (e.g., cellulose in plant cell walls).

Capillary action

The movement of water up narrow spaces (like tubes) due to the combined effects of cohesion and adhesion.

Surface tension

A “skin-like” effect at water’s surface caused by cohesive hydrogen bonding among surface molecules, making the surface resistant to breaking.

Specific heat

The amount of energy required to raise a substance’s temperature; water’s high specific heat helps buffer temperature changes because heat is used to disrupt hydrogen bonds first.

Heat of vaporization

The energy required to convert a liquid to a gas; water’s relatively high value is due to the energy needed to break hydrogen bonds.

Evaporative cooling

Cooling that occurs when high-energy molecules evaporate from a liquid surface, lowering the average kinetic energy (temperature) of the remaining liquid (e.g., sweating).

Density anomaly of ice

Water’s unusual property that solid ice is less dense than liquid water because hydrogen bonds form an ordered lattice that spaces molecules farther apart, causing ice to float.

Solution

A homogeneous mixture in which one substance is dissolved in another (e.g., saltwater).

Solvent

The dissolving agent in a solution; in biology, water is the most common solvent.

Solute

The substance dissolved in a solution (e.g., NaCl in saltwater).

Hydration shell

A layer of water molecules surrounding an ion in solution; water’s partial charges orient to stabilize separated cations and anions.

Hydrophobic interaction

The clustering of nonpolar molecules in water because it allows water to maintain hydrogen bonding with itself; important in membrane formation and protein folding.

Element

A pure substance made of only one kind of atom; cannot be broken down by chemical methods into simpler substances

Atom

The smallest unit of an element that retains that element’s properties; composed of protons and neutrons in the nucleus with electrons around it.

Isotope

Atoms of the same element with different numbers of neutrons; isotopes can be stable or radioactive and are used as tracers in biology/medicine.

Valence electrons

Electrons in the outermost energy level of an atom; they largely determine bonding behavior and reactivity.

Ionic bond

An electrostatic attraction between oppositely charged ions formed after electron transfer; in water, many ionic compounds dissociate into ions; salts

trace elements

required by organisms in minute quantites