College Bio Midterm Review

electronegativity

the tendency for atoms to draw electrons toward themselves

electronegativity and covalent bonds

some atoms will "grab" the electron more in a covalent bond, some share it equally

polar molecule

have an uneven charge distribution while being electrically neutral, formed when atoms show strong electronegativity differences

non polar molecules

have even charge distributions, formed when atoms have similar electronegativity

ion

a charged atom or molecule

nucleus in an atom

contains protons and neutrons

atomic number

number of protons in an atom

atomic weight

protons plus neutrons

chemical bonding

process by which atoms becomes physically attached through electron exchange or sharing (involves valence electrons)

ionic bonding

transfer of electrons

covalent bonding

sharing of electrons

hydrogen bonding

a weak charge attraction between positive and negative charges

solute

a substance that is dissolved in a solute

solvent

the substance in which the solute is dissolved

reference solvent for polar molecules

water (H20)

reference solvent for non polar molecules

liquid fats (oils)

hydrophilic

loves water (polar)

hydrophobic

hates water (non polar)

acid

any molecule that releases a proton (H+) in water solution

base

any molecule that absorbs a proton in water solution

pH

a measure of the acidity or alkalinity of a water solution

pH 7

neutral

pH < 7

acidic

pH > 7

basic

buffer

any molecule that can act as an acid or base, minimizes pH shifts in solutions

definition of organic chemistry

the chemistry of carbon, hydrogen, and any atom that can replace a hydrogen around a carbon

number of bonds in a carbon containing molecule

four

hydrocarbons

nonpolar, consist entirely of C and H, building blocks of all other organic molecules

hydrocarbons functional group

methane

alcohols

polar, modified water molecules

alcohols functional group

special case of alcohols

waxes are large multicarbon alcohols that do not dissolve in water because they have large hydrocarbon tails

amines

polar, modified ammonia molecules, can be powerful bases

amines functional group

C-NH2

aldehydes and ketones

polar

aldehydes and ketones functional group

carbonyl

carboxylic acids

polar, weak acids

carboxylic acids functional group

esters

non polar, combination of an alcohol and a carboxylic acid, fats are special cases, formed by dehydration, responsible for scents and flavors

esters functional group

carbohydrates definition

polyhyrdoxy aldehyde or ketone, aka sugars

biologically important carbohydrates

have 3-7 Cs (triose, tetrose, pentose, hexose)

monosaccharides definition

single hexose units

disaccharides definition

two conjoined monosaccharides

glucose

monosaccharide

-universal cell food

-found in honey and maple syrup

fructose

monosaccharide

-found in all sweet fruit and corn

galactose

monosaccharide

-found in milk only

sucrose

disaccharide

-cane or table sugar

-composed of a glucose and a fructose

maltose

disaccharide

-found in dark grains

-composed of two glucoses

lactose

disaccharide

-found in mammal milk

-composed of a glucose and a galactose

hexose polymers

fructose: fructans

galactose: galactans

the 2 glucose polymers

two glucose polymers

starches and celluloses

starches

-animals (glycogen)

-plants (starch)

-purpose: glucose storage

-amylase: enzyme that breaks up glucose for use

celluloses

-purpose: structural material

-used by plants to build bark, wood, leaves, etc

cellulase

enzyme that breaks down cellulose into glucose, made by bacteria

lipids definition

esters that are made of an alcohol called glycerol and 1-3 large carboxylic acids (aka fatty acids)

glycerol

3 carbon alcohol

fatty acids

large 10-28 C carboxylic acids

basic lipid

mono acyl glyceride

saturated vs unsaturated lipids

saturated: no double bonds, solid

unsaturated: has double bonds, liquid

double bond in saturation

double bond has the potential to absorb hydrogen, double bonds create kinks that make it harder for molecules to stick together (liquids)

lipids biological significance

building blocks of cell membranes, used for long term energy storage, high energy density

carbs vs fats energy storage

carbs are used for short term energy short falls, fat is used longterm to prevent starvation

amino acid definition

monomers of proteins, all have the same generic structure

amino acid structure

R group can be anything

number of amino acids used by living things

20

three R group categories

nonpolar, polar uncharged, charged

charged R groups

can be negative or positive, can switch between neg and pos from pH shifts

dipeptides

two amino acids joined together by a peptide bond

peptide bond

proteins definition

amino acid polymers

three structural levels of proteins

primary, secondary, tertiary

primary structure

amino acid sequence

secondary structure

hydrogen bond interactions between amino acids in the protein chain, leads to simple 2D or 3D shapes

types of hydrogen bond interactions

alpha helices and pleated sheets, polar parts stick together with h bonds

tertiary structure

complex 3D structures produced by R group interactions, determines a proteins functional properties

quaternary structure

two or more proteins joined to form a superstructure, Ex: hemoglobins

protein denaturation

process by which external physical factors disturb the 3D structures of a protein, protein is not broken

important denaturing factors

excessively high temperatures (cause vibrations), excessive pH (alkaline or acidic), excessive salinity

biological significance of denaturation

denatured proteins are usually altered for the worse, can be reversible or irreversible

common example of denaturation

cooking

nucleotide generic structure

phosphate-pentose-nitrogenous base

two pentose variations

ribose or deoxyribose

ribose vs deoxyribose structure

deoxy is missing an OH

two nucleotide base types

purines and pyrimidines

five biologically important types of nucleotides

adenine (A)- both

thymine (T)- deoxy

uracil (U)- ribo

cytosine (C)- both

guanine (G)- both

hydrogen bond nucleotide combos

nucleotides can selectively h-bond thru their bases

A-T, A-U, C-G

important single nucleotides

ATP and C-AMP

ATP (adenosine triphosphate)

P-P-P-pentose-base

second bond is loaded with energy and wants to break to form energy

C-AMP (cyclic AMP)

C-AMP diesterase- enzyme that breaks up C-AMP

caffeine stops the process (anti relaxant)

enzymes definition

protein catalysts

catalysts and their properties

chemical factors that change reaction rates without being used up in the process, usually speed them up, no reaction direction is favored, they are selective

energy model of catalyst

less activation energy is needed with catalyst

lock and key model of enzymes

substrate is shape compatible with the binding site

substrate imitators

agonists-trigger at least a partial enzyme response

antagonists- bind to binding site, but trigger no enzyme response

substrate binding

authentic substrates, agonists, and sometimes antagonists weakly bind to binding site and may release and reattach repeatedly

competitive competition mechanism

overwhelming amount of antagonists surrounds and outcompetes the substrates, enzyme is activated by dramatic increase of substrates

allosteric regulation mechanism

allosteric site is a secondary binding site that influences the primary binding site, secondary substrate binds to secondary binding site and activates the primary binding site

substrate cleavage mechanism

chops the substrate to stop an enzyme response, ex: pesticide sprays shut down acetylcholinesterase to make muscles constantly contract, acetylcholine doesn't get chopped so reaction never stops

substrate negative feedback mechanism

an enzyme produces its own competitor to limit itself and slow down reaction, reaction continues once competitor is absorbed by cells