Ch. 2-3 Biochemistry

Polar covalent bonds

chemical bond where electrons are shared unequally between 2 atoms, creating one positively and one negatively charged

Polar molecule

the water overall charge is unevenly distributed

Cohesion

the hydrogen bonds hold the substance together

Adhesion

the clinging of one substance to another

Surface tension

a measure of how difficult it is to stretch or break the surface of a liquid

Thermal energy

the kinetic energy associated with the random movement of atoms or molecules

Temperature

a measure of energy that represents average kinetic energy of molecules in a body of matter

Heat

thermal energy in transfer from one body of matter to another

Specific heat

the amount of heat that must be absorbed or lost for 1 g of that substance to change its temperature by 1 degree Celsius

Heat of vaporization

the quantity of heat a liquid must absorb for 1 g of it to be converted from the liquid to the gaseous state

Evaporative cooling

as a liquid evaporates the surface of the liquid that remains behind cools down

Solution

a liquid that is a completely homogeneous mixture of two or more substances

Solvent

the dissolving agent of a solution

Solute

the substance that is dissolved

Aqueous solution

the solute is dissolved in water; water is the solvant

Hydration shell

the sphere of water molecules around each dissolved ion

Hydrophilic

(water loving) any substance that is attracted to water

Hydrophobic

(water fearing) any substance that repels to water

Hydrogen ion

(H+) a single proton with a charge of 1+

Hydroxide ion

(OH-) has a charge of 1-

Hydronium ion

(H₃O+)

Acid

a substance that increases the hydrogen ion concentration of a solution

Base

a substance that reduces the hydrogen ion concentration of a solution

pH scale

measures how acidic or base a substance is (0-14)

pH

pH= -log (H+)

Buffer

a substance that minimizes changes in the concentrations of H+ and OH- in a solution

Carbohydrates

-serve as a cell's fuel and building material

-composed of C, H, and O

-hydrophilic

-has two types : monosaccharides and polysaccharides

-have molecular formulas that are multiples of CH2O (e.g. C60H100O50)

hydrolysis reaction

A chemical reaction that breaks apart a larger molecule by adding a molecule of water

enzymes

Proteins that speed up chemical reactions

Glycogen

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

Cellulose

A substance (made of sugars) that is common in the cell walls of many organisms;

polysaccharide consisting of glucose monomers that reinforces plant-cell walls

Starch

A storage polysaccharide in plants consisting entirely of glucose.

Monosaccharides

glucose, fructose, galactose

Polysaccharides

large macromolecules formed from monosaccharides; Carbohydrates that are made up of more than two monosaccharides

monomers

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

dehydration reaction

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

Polymer

A long molecule consisting of many similar or identical monomers linked together.

Methyl

-CH2, Non-polar, Hydrophobic, found in R groups and lipids

Carbon

C 6

polar molecule

a molecule in which one side of the molecule is slightly negative and the opposite side is slightly positive

ionic bond

Formed when one or more electrons are transferred from one atom to another; A chemical bond resulting from the attraction between oppositely charged ions.

Covalent bond vs Ionic bond

Covalent bonds involve the sharing of electrons; while ionic bonds involve the transfer of electrons, creating positive and negative ions that are attracted to each other

Hydrocarbons

organic molecules consisting of only carbon and hydrogen

Isomers

Same atoms but different arrangement.

saturated fatty acid

A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, saturated with hydrogen, forms straight lines, stacks up on top of other fatty acids, solid at room temp

unsaturated fatty acid

a fatty acid whose hydrocarbon chain contains one or more double bonds, creating kinky tails that can’t pack together, liquid at room temp

Chitin

A structural polysaccharide, consisting of amino sugar monomers, found in many fungal cell walls and in the exoskeletons of all arthropods.

monosaturated fatty acid

A fatty acid with one double bond between carbon atoms

polysaturated fatty acids

Has many double bonds. Not packed tightly at all. Liquid at room temp. Double bond susceptible to oxidation. Ex: Vegetable Oil.

Lipids

Energy-rich organic compounds, such as fats, oils, and waxes, that are made of carbon, hydrogen, and oxygen.

gylcerol

an alcohol composed of a 3-carbon chain, which can serve as the backbone for a triglyceride

fat

A lipid consisting of three fatty acids linked to one glycerol molecule; also called a triglyceride.

trans fats

An unsaturated fat, formed artificially during hydrogenation of oils, containing one or more trans double bonds.

Protein

An organic compound that is made of one or more chains of amino acids and that is a principal component of all cells

carboxyl group

(-COOH), Polar, hydrophillic, found in all proteins

carbonyl group

C and O double bond

hydroxyl group

(-OH), Polar, Hydrophillic, found in some R groups and fatty acids

amino group

(-NH2), Polar, Hydrophillic, found in all proteins

peptide bond

covalent bond formed between amino acids;

R groups

groups give different amino acids different properties

Polypeptide

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

primary structure

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

secondary structure

Either an alpha helix or beta pleated sheet.

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.

quaternary structure

The fourth level of protein structure; the shape resulting from the association of two or more polypeptide subunits.

DNA

deoxyribonucleic acid, a self-replicating material present in nearly all living organisms as the main constituent of chromosomes. It is the carrier of genetic information.

RNA

A single-stranded nucleic acid that passes along genetic messages; its job is in assembling the polypeptides according to the instructions of DNA.

nucleotides

monomers of nucleic acids

N (element)

Nitrogen

Sulfhydrl

-SH, Polar, Hydrophillic, found in cysteine (protein)

Phosphate

-PO4, Polar, Hydrophillic, found in phosphorylated proteins and phospholipids

Protein elements

CHON, sometimes SP

Nucleic acid elements

CHNOP

Carbohydrate elements

CHO

Lipid elements

CHO, sometimes NPS

Polar R groups in amino acids

Presence of O and N

Non-polar R groups in amino acids

Presence of hydrocarbons (H and C)

Glucose

Monosaccharide, C6H12O6

Phospholipids

hydrophillic (negatively charged) phosphate head, two fatty acid tails (uncharged), make up cell membranes

Cholesterol

maintains fluidity of the membrane

Hydrophobic interaction

Amino acids with hydrophobic (non-polar) side chains end up in clusters at the core of the protein, out of contact with water

Disulfide bridges

covalent bonds that form when 2 cysteine monomers (which have -SH groups) on side chains are brought close together by folding of protein

Nucleic acids

made of nucleotides: nitrogenous base, pentose 5 carbon sugar, and 1-3 phosphate groups

Pyramidines

6 membered ring of carbon and nitrogen atoms (C,U,T)

Purines

6 membered ring fused to 5 membered ring (A, G)

Polar molecules

Hydrophillic because uneven charge dist. creates partial positive and negative poles that attract opposite charges in polar solvents like water

Non polar molecules

Hydrophobic because they lack electrical charge, so they cannot interact with polar water molecules