all of biochem

molecule

molecule

substances composed of two or more covalently bonded atoms

elements that make up the chemical foundation of life

CHNOPS - carbon, hydrogen, nitrogen, oxygen, phosphorus, sulfur

intramolecular forces

forces within molecules that hold atoms together: covalent bonds or ionic bonds

electronegativity

property of how strong an atom attracts electrons,

polar covalent bond

unequal sharing of electrons

non-polar covalent bond

when two atoms of similar electronegativities equally share electrons

intermolecular forces

between molecules and determine how same type molecules interact, weaker than intramolecular forces, responible for attracting molecules but will break with enough force

hydrogen bond

involves hydrogen atom and oxygen/nitrogen atoms, aqueous environments, hyrdophilic

hydrophobic

non-polar that don’t form hydrogen bonds

functional group

cluster of atoms that always behave in a certain way, contains ONPS

structural formulas

show how the atoms are bonded together

macromolecule

large complex molecules composed of repeating units of smaller molecuels, linked by covalent bonds

polymers

long chain like substances that make up macromolecules

monomers

a molecule that can be bonded to other identical molecules to form a polymer

types of macromolecules

carbs, lipids, protien, nucleic acids

carbohydrates

contain CHO, (CH₂O)_{#carbon atoms,} usually polar, sugars and starches

monosaccharides

single carbon based monomer stuctures, simple sugar with 3 to 7 carbon atoms, glucose, fructose, galactose, energy

disacchardies

two monosaccharides joined by glycosidic linkage, surose, lactose, energy

glycosidic linkage

a type of ether bond that joins a carbohydrate (sugar) molecule to another group, which may or may not be another carbohydrate

condensation reaction

forms glycosidic linkage, one monomer gives up hydroxyl group and other hydrogen, requires energy

hydrolysis reaction

how glycosidic linkage is broken, water is split into hydroxyl group and hydrogen, releases energy

polysaccharides

long chains of carbohydrate molecules, composed of several smaller monosaccharides, glycogen, starch, cellulose, storage, support/structure

function of carbs

energy, storage, support/stucture

functional groups of carbs

hydroxyl and carbonyl

triglycerides

lipid molecules formed from one glucerol molecule bonded by ester linkages to three fatty acid molecules

ester linkage

formed between the oxygen molecules of glycerol and the hydroxyl molecules of fatty acids

fatty acid

hydrocarbon chain ending in a carboxyl group

saturated

no double bonds between carbon, straight line, solid

unsaturated

monounsaturated (one double bond between carbond) or polyunsaturated (more than one double bond), bent, liquid

phospholipids

main components of cell membranes, similar to triglycerides but phosphate group replaces third fatty acid

steriods

lipids composed of four attached carbon based rings, used for sending signals and membrane fluidity, differ based on functional groups

waxes

lipids made of long carbon based chains, used for protection, solid

functions of lipids

long term energy(tri), membranes(phospho), sending signals(steriods), protection(wax)

functional groups of lipids

hydroxyl, carboxyl,

dual nature of phospholipids

they have a polar head and non polar tail which creates a hydrophobic interior and the basics of a cell membrane when placed in water. the tails move together and the hydrophilic heads move outwards facing the water

proteins

macromolecules composed of amino acids and linked by covalent bonds, made of polypeptides

amino acid

orgainic molecules composed of central carbon atom bonded to an amino group, carboxyl group, hydrogen, variable R group

functions of protein

• transport

• structural support

• mobility

• signals/hormones (regulating cellular processes)

• defence (antibodies)

• speed up reaction

type of linkage in proteins

covalent bonds called peptide bonds, form between carboxyl group and amino group

polypeptides

polymers composed of many amino acids linked by colvant bonds, protiens are composed of one or many polypeptides, vary in number and sequence of amino acids

levels of organization in proteins

• primary - linear sequence of amino acids

• secondary - hydrogen bonding contributes to an alpha helix or beta pleated structure

• tertiary - 3D folding based on hydrophobic and hydrophilic interactions

• quaternary - multiple polypeptides joining more than one polymer chain of amino acids

denaturation

breaking of many of the weak linkages, or bonds (e.g., hydrogen bonds), within a protein molecule that are responsible for the highly ordered structure of the protein in its natural state and is caused by extreme temp changes and chemical exposure.

functional group of proteins

hydroxyl, carboxyl, amino

monomers of nucleic acids

nucleotides

polymers of nucleic acids

DNA and RNA

4 main types of chemical reactions

neutralization, oxidation-reduction, condensation, hydrolysis

acid

substance that produces hydrogen ions (pH under 7)

base

substance that produces hydroxide ions (pH over 7)

neutralization reaction

acid and base react together, base accepts hydrogen ions, produces salt and water

normal range of human pH

7.35 fo 7.45 (below 7 or aboive 7.8 is fatal)

alkalosis

blood pH over 7.5, dizziness and agitation, caused by breathing quickly or taking too many antiacids

acidosis

low blood pH, kidney disease or vomiting

buffers

substances the minimize changes in pH, give H2 when basic and take H2 when acidic

oxidation reactions

when a molecule loses electrons and becomes oxidized

OIL

reduction reactions

when a molecule accepts electrons and is reduced

RIG

example of a buffer system

carbonic acid - hydrogen carbonate ion buffer system is used when the blood is too basic.

example of redox reaction

cellular respiration used redox to oxidze sugar through small steps to slow the release of energy - stored in chemical bonds

condensation reaction

joins molecules covalently, produces water, requires energy

hydrolysis reaction

breaks apart large molecules, uses water, releases energy

activation energy

energy requires to begin a chemical reaction, large activation energy means slow reaction

catalysts

substances that speed up chemical reactions by lowering activation energy, proteins

enzymes

specifics proteins that acts as catalysts in organisms, made of long chains of amino acids, globular shapes with indents called active sites

active sites

pockets or indents on the surface of an enzyme

enzyme substrate complex

when active sites and substate join together

induced fit

slight cahnge to the shape of the enzyme to fit the substate

catalytic cycle

cycle of a enzyme

addtional moleules needed to catalyze a reaction

coenzymes and cofactors

what affects enzyme activity

temperature and pH change and how much substate is present because enzymes encouter them less frequently

inhibitors

molecules that interact with enzymes, they reduce the activity of the enzyme by interfering with its interaction with the substrate

activators

molecules that can bind to an allosteric site to cause an increase in enzyme activity

feedback inhibition

process where biochemical reaction are grouped and regulated

competitive inhibitior

interfers with the active sites so substrate cannot bind to enzyme

noncompetitive inhibitor

changes the shape of the enzyme so substrate cannot bind

nucleus

manages or controls all the cell functions in eukaryotic cell, membrance bound

cytoplasm

fills the interior of the cell except for nucleus

cytosol

liquid of the cytoplasm

nucleoplasm

fills the nucleus

nuclear membrane

phospholipid membrane bilayer barrier around the nucleus

nuleolus

site where ribosomes are made

ER

connects to the nucleus and has 2 parts

rough ER

membrane bound tubules and sacs associated with ribosomes, sites of protein synthesis, transports materials within the cell

ribosome

synthesises proteins for export from the cell or membrane formation

smooth ER

synthesises lipids and lipid containing molecules, packages proteins

endomembrane system

system for transortation and product processing, proteins are synthesized and modified

golgi apparatus

sorts packages and distributes lipids, manufactures macromolecules, produced lysosomes/pectin, closely packed and flattened sacs

peroxisomes

manufacture cholesterol and bile acids, off the ER

vesicles

transort materials ouside of cell and temportary storage of substances

vacuoles

large vesicles in plant cells, store water ion sugar amino acids and macromolecules

lysosomes

digests worn-out cell parts, food particles, and invading viruses or bacteria

mitrochondria

break down energy-rich molecules to convert stored energy into useable energy

cell wall

provides protection and supprt in plants and fungi, made of cellulose

cytoskeleton

innner network of protein fibres which provide structure and anchoring to cell membrane and organelles

microtubules

maintain shape, facilitate movement of organelles, cell division (spindle formation)

intermediate filaments

maintain shape, anchor organelles, form internal scaffolding of nucleus

microfilaments

maintain shape, muscle contractions, assits in cell division (cleavage furrow)

nuclear pores

regulate transport in and out of nucleus

cilia

move cells by a wave lengh movement, can sense things, sweep out debirs in respirary tract

flagella

tails and move cells with a whip like motion

fluidity of the cell membrane is affected by

• temperature (more mallable w/ temp)

• presence of double bonds (more double bonds more fluid)

• length of fatty acid tail (longer length less fluid)

• presence of cholesterol (more choesterol less fluid)

what does the fluid mosaic model feature in a cell membrane

semi-fluid phospholipid bilayer with proteins, non-polar proteins and non-polar bilayer come in contact with each other, other proteins and molecules float in/on bilayer, made of two leaflets that slide across each other