AP Biology Unit 1 Chemistry of Life

chemistry of life

chemistry of life

elements

substances that cannot be broken down into simpler substances by chemical means

oxygen

essential element of life; found in all macromolecules

carbon

most essential element of life; found in all macromolecules

hydrogen

essential element of life; found in all macromolecules

nitrogen

essential element of life; found in proteins and nucleic acids

trace elements

required in very small quantities

atom

smallest unit of an element that retains its characteristic properties

protons

subatomic particle with a positive charge

neutrons

subatomic particle with no charge

electrons

smallest subatomic particle with negative charge

nucleus

the core of the atom where protons and neutrons are packed together

isotopes

same number of protons but differ in the number of neutrons in the nucleus

radiometric dating

examining the rate of decay of carbon-14 and other isotopes in an artifact can date it because some isotopes are radioactive and decay predictably over time

compound

two or more individual elements are combined in a fixed ratio

chemical reaction

the process by which one or more substances change to produce one or more different substances

• hydrogen atoms get together with oxygen atoms to form water

chemical bond

what atoms of a compound are held together by

ionic bond

formed between two atoms when one or more electrons are transferred from one atom to the other which causes one atom to lose electrons and become positively charged and the other to gain electrons and become negatively charged

covalent bond

formed when electrons are shared between atoms

hydrogen bond

type of chemical bond which is usually weak and happens with water molecules (4 hydrogen bonds per molecule) but they contribute to water's special properties

ions

charged forms of the atoms

nonpolar covalent

If electrons are shared equally between atoms

polar covalent

if electrons are shared unequally between atoms

polar molecule

molecules that have partially positive and partially negative charges

cohesion

water molecules have a strong tendency to stick together

adhesion

water molecules like to stick to other substances

surface tension

cohesion of water molecules creates tension on the surface of water which allows light things like leaves and water striders to sit atop the surface without sinking

heat capacity

water has a high heat capacity which means it's harder to increase the temperature which helps keep ocean temperatures stable and helps us keep a stable body temperature

expansion on freezing

water expands when freezing because liquid water is denser and solid water because the lattice structure of four water molecules together causes it to expand upon freezing which helps aquatic life survive because bodies of water freeze from top to bottom

capillary action

cohesion and adhesion help water rise up roots, trunks, and branches of trees

acidic

contains a lot of hydrogen ions (H+) and has a pH less than 7 like lemons which have citric acid in them

basic

contains a lot of hydroxide ions (OH-) and is said to be "alkaline" and has a slippery consistency like soap which is composed largely of bases

neutral

midpoint (7) on the pH scale

alkaline

fancy name for basic solutions

pH scale

measures acidity or alkalinity of a solution

organic compounds

chemical compounds that contain a skeleton of carbon atoms surrounded by hydrogen atoms and often other elements (CH4)

inorganic compounds

molecules that do not contain carbon atoms (NaCl)

polymer

chains of building blocks that make macromolecules

monomer

individual building blocks of a polymer (subunits)

carbohydrates

organic compounds that contain carbon, hydrogen, and oxygen

monosaccharides

simplest sugars like glucose, fructose, galactose, ribose, and deoxyribose that serve as an energy source for cells and a subunit for polysaccharides

disaccharides

two monosaccharides formed by removing hydrogen and hydroxide from each sugar molecule to form water (dehydration synthesis)

polysaccharides

many repeated units of monosaccharides that consist of branched or unbranched chains of monosaccharides such as starch, cellulose, and glycogen

glucose

most common monosaccharide, main source of energy for cells

fructose

second most common monosaccharide

dehydration synthesis (condensation)

hydrogen is removed from one molecule and hydroxide from the other to form a new joined molecule and water

glycosydic linkage

the bond formed between two monosaccharides

hydrolysis

breaking two substances by adding water and restoring the hydroxyl and hydrogen removed from dehydration synthesis

starch

sugar storage molecule in plants

cellulose

made of β-glucose and is a major part of the cell walls in plants

chitin

a polymer of β-glucose molecules that serves as a structural molecule in the walls of fungus and in the exoskeletons of arthropods

glycogen

sugar storage molecule in animals

amino acids

organic molecules that serve as the building blocks of proteins

amino groups

-NH2 part of the amino acid

carboxyl group

-COOH part of the amino acid

R-group

what differentiates amino acids

side chain

another name for R-group which differentiates amino acids

how do side chains differ?

• composition of elements (C, H, O, N, and S)

• polarity (polar, nonpolar) which affects whether an amino acid if more hydrophobic or more hydrophilic

• charge (neutral, positive, negative)

• shape (long-chain, short-chain, ring-shape)

dipeptide

two amino acids joined

peptide bond

the bond between two amino acids

polypeptide

group of amino acids joined together in a "string"

protein

three-dimensional structure after polypeptide chain twists and folds on itself

primary structure

linear sequence of amino acids (polypeptide chain)

secondary structure

polypeptide begins to twist, forming either a coil (alpha helix) of a zigzagging pattern (beta-pleated sheets)

tertiary structure

after secondary structure is formed the amino acids can interact with each other moving the hydrophilic amino acids outside and the hydrophobic amino acids inside minimizing the free energy of the molecule and locks it into a stable 3D shape

quaternary structure

several different polypeptide chains interacting with each other making the individual polypeptide chains called subunits of the final whole protein

chaperone proteins (chaperonins)

help the protein fold properly and make the process more efficient

lipids

consist of carbon, hydrogen, and oxygen atoms but not in the 1:2:1 ration typical of carbohydrates and example being triglycerides, phospholipids, and steroids that serve as insulation, signaling molecules, and a means of energy storage

triglycerides

bodies store fat in tissue called adipose which is made of cells called adipocytes which are filled with triglycerides made of a glycerol molecule (glycerol backbone) with three fatty acid chains attached to it (a long chain of carbons in which each carbon is covered in hydrogen and one end of the chain has a carboxyl group formed by dehydration synthesis

phospholipids

contain two fatty acid "tails" (hydrophobic) and one negatively charged "phosphate" head (hydrophilic) meaning it's an amphipathic molecule which contributes to the shape and structure of the cell membrane

steroids

four-ringed hydrophobic molecules that are used for the structure of the cell membrane and signaling hormones/molecules the most common being cholesterol and is the precursor to vitamin D, testosterone, estrogen, progesterone, aldosterone, cortisol, and bile salts.

glycerol

backbone of triglycerides

ester linkage

the linkage formed between the glycerol molecule and the fatty acids by dehydration synthesis

saturated

hydrogens along its long carbon chain

unsaturated

double bond in chain

polyunsaturated

many double bonds in the chain

hydrophobic

water hating and insoluble in water

hydrophilic

water loving and soluble in water

amphipathic molecule

has both a hydrophilic region and a hydrophobic region

cholesterol

four-ringed molecule found in membranes that increases membrane fluidity except at very high temperatures when it helps to hold things together instead and is important for making certain types of hormones and for making Vitamin D

nucleic acids

made of simple units called nucleotides that contain carbon, hydrogen, oxygen, and nitrogen, like proteins, but also contain phosphorus examples being deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)

nucleotides

subunits of nucleic acids

deoxyribonucleic acid (DNA)

nucleic acid that contains the sugar deoxyribose and is a double-stranded, helical nucleic acid molecule capable of replicating and determining the inherited structure of a cell's proteins

ribonucleic acid (RNA)

a single-stranded nucleic acid that contains the sugar ribose that is present in all living cells and that plays a role in protein synthesis