Biochemistry

capillary action

the process by which a plant takes up water against gravity without energy

cohesion

water forming hydrogen bonds with water molecules

adhesion

water forming hydrogen bonds with other substances
ex. water on glass

hydrophilic

attracted to water (polar)

hydrophobic

not attracted to water (nonpolar)

hydrocarbons

chains consisting of only carbon & hydrogen

trace elements

required by an organism, but only in minute qualities

isotopes

forms of an element with different numbers of neutrons

radioactive isotopes

used in medicine for diagnosis and treatment

chemical bonds

interactions between valence electrons of different atoms

nonpolar covalent bond

electrons are shared equally

Electronegativity

tendency to attract electrons in a covalent bond

polar covalent bond

one atom has more electronegativity, so unequal sharing forms areas of partial + and - charges

ionic bonds

bonds from attraction between oppositely charged ions

hydrogen bonds

weak bonds between +H of H2O and -O or N of another molecule, play a role in 3D shape of proteins and nucleic acids

van der waals interactions

weak connections because of uneven distribution of electrons, contribute to 3D shape

transpiration

movement of water molecules up thin xylem tubes and their evaporation from the stomata in plants, the H20 clings to each other by cohesion & to the walls by adhesion

specific heat

amount of heat required to raise/lower the temperature of a substance by 1 degree Celcius

solvent

dissolving the solute

solute

being dissolved by the solvent

solution

the solvent and the solute together

acids

excess H+ ions H+ > OH-

bases

excess OH- ions OH- > H+

pure water

pH of 7, H+ = OH-

buffers

substances that minimize changes in pH, accept H+ ions when hydrogen molecules are in excess & give H+ ions when hydrogen molecules are depleted, essential in living tissues (ex. blood)

carbonic acid (H2CO3)

buffer that moderates pH changes in blood plasma & the ocean

major elements in life

C, H, O, N, S, and P: carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus

organic compounds

contain C, most have H

carbon

forms large, complex, and diverse molecules, 4 valence electrons, forms up to 4 covalent bonds (single, double, or triple)

isomers

molecules that have the same formula but differ in arrangement, results in molecules that differ in biological activities

What do the properties of an organic molecule depend on?

depends on the carbon skeleton arrangement and the functional groups attached to it

functional groups

hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, phosphate, methyl

hydroxyl group

OH

carboxyl group

COOH

carbonyl group

CO

amino group

NH2

phosphate group

PO3

Sulfhdryl group

SH

methyl

CH3

hydroxyl group function

alcohols like ethanol & methanol, they help dissolve molecules like sugars

carboxyl group function

carboxylic acids like fatty acids & sugars, they have acidic properties because it tends to ionize, source of H+ ions

carbonyl group function

ketones like aldehydes such as sugars

amino group function

amines such as amino acids

phosphate group function

organic phosphates, like ATP, DNA, and phospholipids

sulfhydryl group function

in the amino acid cysteine, makes disulfide bridges in proteins to stabilize their structure, compounds end in -thoil

methyl group function

doesn't increase solubility, when it binds to DNA it can affect gene expression

polymers

long chain molecules made of repeating subunits called monomers
ex. starch, a polymer made of glucose monomers
ex. proteins, polymers made of amino acid monomers

What bond is stronger, covalent or ionic bonds?

covalent bonds are stronger

hydrolysis

when water is added to split large molecules, the reverse reaction of dehydration

dehydration synthesis

creating polymers from monomers, 2 monomers are joined by removing 1 molecule of water, requires energy & enzymes

carbohydrates

simple sugars (glucose, fructose, galactose) & polymers (starch) made from these & others subunits, all carbs exist in a ration of 1 carbon : 2 hydrogen : 1 oxygen ration (CH2O)

monosaccharides

the monomers of carbohydrates
ex. glucose and ribose

polysaccharides

polymers of monosaccharides
ex. starch, cellulose, glycogen

What happens when you change the structure of a molecule?

it changes the function

starch

glucose monomers with 1-4 alpha linkages that the body can digest

cellulose

glucose monomers with 1-4 beta linkages that the body can't digest

polysaccharide function

energy storage and structural support

starch function

storage polysaccharide found in plants
ex. potatoes

glycogen function

storage polysaccharide found in animals (vertebrate muscle cells & liver cells)

cellulose function

major component of plant cell walls

chitin

in exoskeleton of arthropods (lobsters & insects) & cell walls of fungi

lipids

hydrophobic molecules not made of polymers
ex. wax, oil, fat, steroids

fats (triglycerides)

made of a glycerol molecule and 3 fatty acid molecules

fatty acids

hydrocarbon chains, nonpolar & hydrophobic, a long hydrocarbon tail with a COOH group @ the head

saturated fatty acids

no double bond between carbons, tendons to pack solid @ room temp, linked to heart disease, produced by animals
ex. butter, lard

unsaturated fatty acids

have some double carbon bonds that result in kinks, liquid @ room temp, made by plants
ex. corn, olive oil

lipid function

energy storage, they hold 2x the calories per gram as carbs & protection and insulation, in mammals it's stored in adipose cells

phospholipids

make up cell membranes, have a hydrophilic (polar) head that includes a phosphate group, have 2 fatty acid tails that are hydrophobic

How are phospholipids arranged?

they are arranged in a bilayer that form the cell membrane, they have hydrophilic heads that point toward the cytosol/extracellular environment & the hydrophobic tails are in between

steroids

made of 4 rings that are fused together

cholesterol

a steroid that is a common component of cell membranes

estrogen and testosterone

steroid sex hormones

amino acids

central carbon bonded to a carboxyl group (COOH), an amino group (NH2), a hydrogen atom, and an R group (a variable group/side chain)

primary protein structure

unique sequence in which amino acids are joined

secondary protein structure

1 of the 2 3D shapes resulting from hydrogen bonding between members of the polypeptide backbone

alpha helix

coiled shape of protein

beta pleated sheet

accordion shape of protein

tertiary protein structure

complex globular shape resulting from interactions between side chains (ex. hydrophobic interactiosn, van der waals, hydrogen bonds, disulfide bridges)

How are globular proteins (ex. enzymes) held in position?

they're held in position by R group interactions

quaternary protein structure

the association of 2 or more polypeptide chains into 1 large protein

hemoglobin

globular protein w/quaternary structure because it's composed of 4 polypeptide chains

What disease stems from an abnormal hemoglobin resulting from a single amino acid substitution of valine in the 6th spot?

sickle cell disease

Denaturation

when a protein loses its 3D shape, due to pH, temp, or salt, and it loses it's biological function

What is the simplest hydrocarbon?

methane

characteristics of methane

nonpolar, not soluble in water, hydrophobic, stable, little attraction between molecules, gas at room temp

How can hydrocarbons grow?

by adding C-C bonds

geometric isomers

molecules that differ in arrangement around a C=C bond, but have same covalent partnerships

enentiomer (stereo) isomers

molecules that are mirror images of each other, left-handed and right-handed versions

thalidomide

one version of the molecule gives birth defects and one gets rid of morning sickness

functional group definition

components of organic molecules that are involved in chemical reactions

aldelhyde

if a C=O bond is at the end

ketone

if a C=O bond is in the middle

macromolecules

smaller organic molecules join together to form larger molecules

sugars

end in -ose & are classified by the number of carbons

6 carbons

hexose

5 carbons

pentose

3 carbons

triose

Do lipids form polymers?

no, they don't form polymers

ester linkage

a bond between OH & COOH

What is a name for a fat molecule?

a triacylglycerol