AP Biology Unit 1 - Chemistry of Life

Elements used to build biological macromolecules (carbohydrates, proteins, lipids and nucleic acids)

oxygen (o), carbon (c), hydrogen (h), and nitrogen (n)

Trace elements

elements required by an organisms only in very small quantities (iron (fe), iodine (i), copper (cu)

Isotopes

atoms that have the same number of protons but different in the number of neutrons in the nucleus

chemical compound

when two or more individual elements are combined in a fixed ratio

chemical bonds

hold atoms of a compound together (iconic, covalent, or hydrogen bonds)

ionic bond

formed between two atoms when one or more electrons are transferred from one atom to the other.

* one atom loses electrons and becomes positively charged
* the other atom gains electrons and becomes negatively charged

covalent bond

electrons are shared between atoms.

* if the electrons are equally shared between the atoms, the bond is called non polar.
* if the electrons are shared unequally, the bond is polar.

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In water molecules

the electrons are not shared equally in the bonds between hydrogen and oxygen.

* hydrogen atoms have a partial positive charge and the oxygen has a partial negative charge.

polar

molecules that have partially positive and partially negative charges.

hydrogen bonds

weak chemical bonds that form when a hydrogen atom that is covalently bonded one electronegative atom is also attracted to another electronegative atom

* hydrogen bonds are individually weka, but strong when present in large numbers

Properties of water

cohesion, adhesion, surface tension, high heat capacity, and expansion on freezing

cohesion

water molecules have a strong tendency to stick together

adhesion

water molecules also like to stick to other substances

capillary action

phenomenon that occurs in thin vessels, result of bth the adhesive and cohesive properties of water

surface tension

result of increased hydrogen bonding forces between water molecules at the surface

reactions can be

acidic, basic, or neutral

acidic

contains a lot of hydrogen ions h+

* if you dissolve an acid in water, it will release a lot of hydrogen ions

bases

when added to water, release a lot of hydroxide ions OH, they do not release h+

* solutions are said to be alkaline

pH scale

* 1-14
* the midpoint is 7 (neutral ph)
* if a solution contains a lot of hydrogen ions, then it will be acidic and have a low pH.
* an increase in H+ ions causes a decrease in the pH
* the pH scale is logarithmic
* stronger acids have lower pHs

organic compounds

chemical compounds in living organisms that contain a skeleton of carbon atoms surrounded by hydrogen atoms and often other elements

polymers

make up macromolecules, the building block chains, each individual building block is called monomer

dehydration synthesis

also known as condensation, a water molecule is lost and a larger compound is formed (joins things)

hydrolysis

polymers can be broken down into monomers, the water breaks the bond between the two monomers (separates things)

carbohydrates

organic compounds that contain carbon, hydrogen, and oxygen. CnH2nOn

* monosaccharides, disacharrides, polysaccharides

monosaccharides

simplest sugars, serve as an energy source for cells.

* glucose and fructose, others are galactose, ribose, and deoxyribose.

glucose and fructose

six carbon sugars (C6H12O6).

* glucose is the most abundant monosaccharide.
* organisms break down glucose in order to provide the cells with energy.
* glucose and fructose can be depicted as either straight or rings (carbon molecules with lots of OHs and Hs attached to them

disaccharides

they hydrogen -H from one sugar molecule combines with the hydroxyl group -OH of another sugar molecule

glycosidic linkage

when two monosaccharides are joined

* the resulting sugar is a disaccharide
* disaccharide formed from two glucose molecules is maltose
* sucrose (table sugar) and lactose (found in dairy products)
* if you want to break up the disaccharide and form two monosaccharides, just add water

polysaccharides

consist of branched or unbranched chains of monosaccharides

* starch, cellulose, glycogen
* glycogen (animals) and starch (plants) are sugar storage molecules
* cellulose, major part of the cell wall in plants, its function is to lend structural support

proteins

organic molecules that serve as the building blocks of proteins, they contain carbon, hydrogen, oxygen, and nitrogen atoms.

* 20 different commonly found amino acids in proteins.
* every amino acid has four important parts around the central carbon:
* an amino group: -NH2
* a carboxyl group: -COOH
* a hydrogen
* an R-group (side chain)
* they can vary in composition, polarity, charge, and chape depending on the de chain that they have
* side chain polarity affects whether an amino acid is more hydrophobic or hydrophilic

hydrophobic

non-polar and uncharged

hydrophilic

polar and uncharged

ionic

polar and charged

dipeptide

what is formed when two amino acids join

* the carboxyl group of one amino acid combines with the amino group of another amino acid

peptide bond

the bond between two amino acids

polypeptide

the resulting organic compound when a group of amino acids is joined together in a string

* once a polypeptide chain twists and folds on itself, it forms a 3d structure called protein
* the specific order of amino acids in a peptide can change the identity of the peptide and determine how the peptide affects the overall shape of a protein.

four levels of protein structure

* primary: linear sequence of the amino acids
* secondary: polypeptide begins to twist, forms a coil or zigzagging pattern
* formed by amino acids that interact with other amino acids close by in the primary structure
* tertiary: amino acids that were far away in the primary structure arrangement can now also interact with each other
* hydrophilic amino acids and regions of the peptide chain are often located on the exterior of the protein
* hydrophobic amino acids and regions are usually found on the interior of proteins
* tertiary structure often minimizes the free energy of the molecule and locks it into a stable 3D shape
* quaternary: several different polypeptide chains sometimes interact with each other to form a quaternary structure

chaperone proteins

also known as chaperonins, help the protein fold properly and make the process more efficient

lipids

consist of carbon, hydrogen, and oxygen atoms, but not in 1:2:1 ratio.

* triglycerides, phospholipids, and steroids
* non polar structure
* function as structural components fo cell membranes, sources of insulation, signaling molecules, and means of energy storage

triglycerides

adipocytes (cells in the adipose tissue that store fat) are filled with these types of lipids.

* made of a glycerol molecules with three fatty acid chains attached to it.

fatty acid chain

long chain of carbons in which each carbon is covered in hydrogen

saturated fatty acid

hydrogens along its long carbon chain or has a few gaps where double bonds exist instead of hydrogen.

* relatively linear molecules (solid at room temperature, easy for them to stack together)

unsaturated fatty acid

if there is a double bond in the chain.

* kinked, cannot pack as highly and tend to be liquid.

polyunsaturated fatty acid

many double bonds within the fatty acid.

* the extent of saturation in a lipid can affect its structure and function. the more double bonds that exist within a lipid, the more unsaturated it is

trans double bond

unsaturated fatty acid, exception where it is relatively linear (solid at room temperature)

phospholipid

two fatty acid tails and one negatively charged phosphate head

* two fatty acid tails are hydrophobic
* phosphate head is hydrophilic
* amphipathic molecule

cholesterol

type of lipid, four ringed molecule.

* increases membrane fluidity, except at very high temperatures where it helps hold things together instead

Nucleic acids

contain carbon, hydrogen, oxygen, nitrogen, and phosphorus

* made of nucleotides
* deoxyribonucleic acid (DNA)
* ribonucleic acid (RNA)