Chapter 2: Chemical Principles

atomic mass

total number of protons and neutrons in an atom

isotopes

atoms with the same number of protons but different numbers of neutrons; they share almost the same chemical properties, but differ in mass and therefore in physical properties

atomic number

number of protons in the nucleus

the elements of life

hydrogen (H), carbon (C), nitrogen (N), & oxygen (O)

atoms form molecules

through chemical bonds; by combining to fill their outermost shells

valence

the number of missing or extra electrons in the outermost shell

molecules hold together

because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei

compound

molecule that contains two or more kinds of atoms

cations

atoms that lose electrons & become positively charged ions

anions

atoms that gain electrons & become negatively charged ions

ionic bonds

attractions between ions of opposite charge; one atom loses electrons & another gains electrons (aka transfer of electrons)

in neutral atoms

the number of protons equals the number of electrons

ions

charged atoms that have gained or lost electrons

covalent bonds

form when 2 atoms share one or more pairs of electrons; stronger & more common in organisms

molecular mass

the sum of the atomic masses in a molecule

one mole of a substance equals

its molecular mass in grams

dalton (da)

unit of molecular mass

water

inorganic, polar molecule, solvent, hydrogen bonding (absorbs heat)

hydrogen bonds

form when a hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O atom in another molecule

chemical reactions

involve the making or breaking of bonds between atoms

a change in chemical energy

occurs during a chemical reaction

endergonic

reactions absorb energy

exergonic

reactions release energy

synthesis reactions

occur when atoms, ions, or molecules combine to form new, larger molecules (ex: A + B → AB)

anabolism

the building up (or synthesis) of molecules in a cell; endergonic

decomposition reactions

occur when a molecule is split into smaller molecules, ions, or atoms (ex: AB → A + B)

catabolism

the breakdown (or decomposition) of molecules in a cell; exergonic

pH

expresses the concentration of H⁺ in a solution

acidity correlates with

the H⁺ concentration; lower pH

alkalinity (basicity) correlates with

the OH^- concentration; higher pH

range most organisms grow best

pH of 6.5-8.5

acids

substances that dissociate into one or more hydrogen ions & one or more negative ions (ex: HCl → H⁺ + Cl^-); has proton (H⁺) by itself

bases

substances that dissociate into one or more hydroxide ions & one or more positive ions (ex: NaOH → Na⁺ + OH^-); has hydroxyl (OH^-) group by itself

salts

substances that dissociate into cations and anions, neither of which is H⁺ or OH^- (ex: NaCl → Na⁺ + Cl^-)

inorganic compounds

typically lack carbon; usually small & structurally simple

organic compounds

commonly contain hydrogen, oxygen, and/or nitrogen in addition to carbon

carbon skeleton

the chain of carbon atoms in an organic molecule

functional groups

bond to carbon skeletons & are responsible for most of the chemical properties of a particular organic compound

hydrocarbons are an example of

organic compounds

Hydrogen atomic number & atomic mass

1 & 1

Carbon atomic number & atomic mass

6 & 12

Nitrogen atomic number & atomic mass

7 & 14

Oxygen atomic number & atomic mass

8 & 16

small organic molecules

can combine into large macromolecules

macromolecules

polymers consisting of many repeating molecules call monomers

monomers join by

dehydration synthesis or condensation reactions

carbohydrates

serve as cell structures and cellular energy sources; include sugars and starches, consist of C, H, and O with the formula (CH₂O)_n; many carbohydrates are isomers

isomers

molecules with the same chemical formula, but different structures

monosaccarhides

simple sugars with 3 to 7 carbon atoms

examples of common monosaccharides

glucose & deoxyribose

disaccharides

formed when 2 monosaccharides are joined in a dehydration synthesis

dehydration synthesis

the creation of larger molecules from smaller monomers where a water molecule is released

hydrolysis

breaks the bonds of polymers by the addition of water

disaccharides can be broken down by

the chemical process of hydrolysis

polysaccharides

consists of tens or hundreds of monosaccharides joined through dehydration synthesis

polymers of glucose that differ in their bonding & function

starch, glycogen, dextran, & cellulose

lipids

fats or triglycerides; contain glycerol & fatty acids; formed by dehydration synthesis

saturated fat

no double bonds in the fatty acids

unsaturated fat

one or more double bonds in the fatty acids

cis

H atoms on the same side of the double bond

trans

H atoms on the opposite sides of the double bond

complex lipids

contain C,H and O + P, N and/or S

cell membranes are made up of

complex lipids, called phospholipids

phospholipids contain

glycerol, two fatty acids, and a phosphate group; also has polar & nonpolar regions

steriods

type of lipid; part of membranes that keeps them fluid; has 4 carbon rings with an —OH group attached to one ring

proteins

made of C, H, O, N & sometimes S; essential in cell structure and function; examples include enzymes, transporter proteins, compose flagella & pili, and some bacterial toxins and cell structures

enzymes

speed up chemical reactions

transporter proteins

move chemicals across membranes

flagella & pili

aid in movement

amino acids

proteins consist of these; contain an alpha-carbon that has an attached: carboxyl group (—COOH), amino group (NH₂), & side group; exist in either of 2 stereoisomers D or L

L-form stereoisomers are

most often found in nature

peptide bonds

are between amino acids and formed by dehydration synthesis

primary structure of a protein

a polypeptide chain

secondary structure of a protein

occurs when the amino acid chain folds and coil in a helix or pleated sheet

tertiary structure of a protein

occurs when the helix or sheet folds irregularly, forming disulfide bridges, hydrogen bonds, & ionic bonds between amino acids; folds into 3D shape

quaternary structure of a protein

the arrangement of multiple polypeptide chains (subunits) within a protein complex, where these subunits are held together by non-covalent interactions like hydrogen bonds, ionic bonds, and hydrophobic interactions, forming the final functional structure of the protein

conjugated proteins consist of

amino acids and other organic molecules

proteins can undergo

denaturation

denaturation occurs

when proteins encounter hostile environments such as temperature & pH, and therefore lose their shapes and functions

nucleic acids

consist of nucleotides

nucleotides

consist of a 5-carbon (pentose) sugar, phosphate group, & nitrogen-containing base

purines

A & G

pyrimidines

T, C, & U

nucleosides

consist of pentose & nitrogen-containing base

DNA

deoxyribonucleic acid; contains deoxyribose, exists as a double helix, Adenine hydrogen bonds with Thymine, Guanine hydrogen bonds with Cytosine

the order of the nitrogen-containing bases

forms the genetic instructions fo the organism (organized into codons)

RNA

ribonucleic acid; contains ribose, is single-stranded, Adenine hydrogen bonds to Uracil, Guanine hydrogen bonds to Cytosine

the types of RNA that play a specific role in protein synthesis

rRNA, mRNA, tRNA

adenosine triphosphate (ATP)

made of ribose, adenine, and 3 phosphate groups; is formed from ATPase complex

functions of ATP

stores chemical energy released by some chemical reactions, releases phosphate groups by hydrolysis to liberate useful energy for the cell

components of central dogma

ATP, DNA, amino acids, codons, & ribosomes