ap bio <3

unsaturated fatty acid

fatty acid w unsaturated carbon chain (double bond between carbons in the chain), usually liquid, plants and fish

saturated fatty acid

fatty acid w fully saturated carbon chain (no double bonds), solid at room temp, animals

glycerol

C3H8O3, lipid monomer that links other lipids, usually fatty acid chains

protein monomer

amino acids, have amino and carboxyl groups and R functional group (determines function)

carbohydrate monomer

monosaccharide

nucleic acid monomers

nucleotides, phosphate group, pentose sugar, and nitrogenous base

lipid functions

barriers (cell membranes), energy storage

carbohydrate basic formula

(CH2O)n

carbohydrate functions

energy storage, structural support

phospholipid

lipid monomer type, negative charged phosphate head, two nonpolar fatty acid chains, amphipathic (diff spots are polar vs nonpolar)

polarity of water =

unequal sharing of electrons, resulting in partial pos charge in hydrogens and partial neg in oxygen, hydrogen bonding with other charged molecules

cohesion

same types of molecules bind together (usually weaker bonds)

adhesion

different types of molecules bind (stick) together (usually weaker bonds)

surface tension

air is less dense and nonpolar, less binding to water molecules, more binding cohesion, water sticks together and resists force

capillary action

adhesion to the sides of the container and cohesion to adject water molecules allow water to climb against gravity, thinner tube goes higher (pressure differential encourages climb)

specific heat

amount of heat that must be absorbed or lost for 1g of the substance to change temp by 1 deg C

specific heat of water is high bc...

hydrogen bonds between molecules take energy to break, in order to heat water (move molecules faster) those bonds need to be broken

bc specific heat of water is ..., it is good for...

high, cooling and regulating internal temps (resists temp change)

breaking hydrogen bonds ... energy

requires/absorbs (endo)

making hydrogen bonds... energy

gives off/releases (exo)

water ... when freezing bc...

expands, molecules orient themselves in matrix position that is more spread out to balance charges

hydration shells

water molecules gathered around a charged particles after dissolving it, all molecules should be oriented specifically

acids

increase H+ or H3O+ (hydronium) concentration

bases

increase OH- concentration (decrease H+)

bufferes

stabilize pH by minimizing effects of strong acids and bases

standard deviation

how much data points differ from the mean

x bar =

mean

n =

number of data points

higher standard deviation...

lower reliability

standard error

represents uncertainty, sample size and variability (smaller standard error, more likely mean is accurate generalization)

error bars

usually 2SEM, show the standard error, overlap = no statistical significance

hydroxyl

OH, polar, makes hydrophilic

amino

-NH2, often in bases, in amino acids with carboxyl

carboxyl

-COOH, carboxylic acid group (dissociates into acid in water), in amino acids with amino

methyl

-CH3, nonpolar, binds to cytosine to promote gene expression

euchromatin

open, methylated DNA

heterochromatin

closed, wrapped around histones, unmethylated

phosphate

-PO4 2-, negative charge = hydrophilic, in phospholipids and nucleotides

sulfhydryl

-SH, crosslinked molecules, when bound S-S

carbohydrate bond

glycosidic bond

disaccharides

2 bonded monosaccs, maltose, sucrose, lactose

polysaccharides

staches, glycogen, cellulose - long term energy storage and structure

cellulose

plant cell walls

peptidoglycan

bacterial cell walls

chitin

fungal cell walls, arthropod exoskeletons

lipid bond

ester bond

hydrogenation

artificially adding hydrogen to carbon chains in fats to saturate them

endomembrane system pathway

synthesize protein in ER, go inside ER, vesicle to golgi, absorbed thru cis face, packaging and tagging, exit thru trans face, vesicle to membrane (fuse w membranes along the way)

smooth ER

manufactures and replenishes the lipids (phospholipids mostly) consumed in the cell

cholesterol

animal sterol, produced in liver, stabilizes membrane

testosterone and estradiol

hormones (steroids), 4 ring structure

protein based hormones

bind to receptors on cell membrane, don't acc enter, trigger internal signalling

lipid based hormones

because membrane also lipid, can enter the cell itself, trigger signaling once inside of the cell

waxes

lipids, alcohol chain and fatty acid chain, insulate from water loss

protein functions

literally everything, cell functions, catalysts (enzymes), cell communication, structure (histones, cytoskeleton?), transport (motor proteins)

protein synthesis location

ribosomes, proteins the will be in the cytosol synthesized in free ribosomes, proteins secreted or in plasma membrane synthesized in bound ribosomes (er)

protein function determined by...

sequence of amino acids and R group interactions (20 diff R groups)

protein bond

peptide bonds

genetic code

triplet code of codons and which amino acids they relate to

primary protein structure

linear, chain of amino acids

secondary protein stucture

hydrogen bonding between near R groups, alpha helices and beta pleated sheets

tertiary protein structure

3D shape stabilized by R group interactions, hydrophobic, disulfide bridges, ionic bonds, folded into shape, for some proteins final

quaternary protein structure

association of multiple peptides (multiple subunits), usually weaker bonds, only some proteins

denaturation

protein unraveling (degrading) due to change of environment (temp, pH, etc)

2 types of nucleic acids

DNA (deoxy), RNA (ribo)

pyrimidines

cytosine, thymine, uracil (t in rna), single rings

purines

adenine, guanine, double rings, larger

nucleic acid bonds across the helix

A - T (2 h bonds) G - C (3 h bonds)

nucleotide bonds

phosphodiester bonds

antiparallel orientation

sides of double helix run in opp directions, count from carbon bound to base clockwise

5 things all cells share

cell membrane, genetic material, ribosomes, cytoskeleton, cytosol

cytoskeleton

support and mobility, microtubules (thick) microfilaments (thin), cilia and flagella, motor protein highway

golgi apparatus

enter the cis face, out the trans face, transport vesicles and motor proteins carry, golgi gives chemical tags

free ribosome

makes proteins that stay in the cytosol

bound ribosomes

make proteins that go to plasma membrane and outside of cell

phagocytosis

lysosomes break down invasive particles, food vacuoles with hydrolytic enzymes

autophagy

lysosomes break down old parts from the cell itself

amphipathic

have both hydrophobic and hydrophilic regions

functions of membrane proteins

transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to extracellular matrix

passive transport

transport across the cell membrane with the concentration gradient, no energy required (diffusion, osmosis, facilitated diffusion)

active transport

transport across the cell membrane against the concentration gradient, requires cell energy as ATP (endocytosis, exocytosis, sodium-potassium pump)

dynamic equilibrium

the state in which a substance is evenly dispersed and movement is uniform

selective permeability in the cell membrane

smaller, nonpolar molecules diffuse through faster than larger, polar molecules; certain molecules can go thru and others can't

facilitated diffusion

passive transport with transport protein channel (bind loosely to molecule, carry it thu) (aquaporins)

sodium potassium pump

inside cell, 3 sodium ions bind to pump, shape change, ATP bind a phosphate (phosphorylation), shape change, sodium out, 2 potassium bind, shape change, dephosphorylation, shape change, potassium release, start over

membrane potential

difference in electric charge across a membrane (inside usually more negative)

electrochemical gradient

chemical gradient - concentration of molecules, and voltage gradient - pos charged ions outside cells attracted to neg charge inside cell, when cell pos repel

endocytosis

invagination caused by membrane budding off to the inside of cell containing smth (usually large molecules or large numbers of molecules) as a vesicle (ex: phagocytosis, phagosome) - lots of atp (motor proteins)

exocytosis

vesicles from cell merge with membrane and push contents to outside of cell (ex: neurotransmitters into synapse) - lots of atp

cotransport

technically active transport, 2 molecules have to be present at a transport protein to diffuse thru the protein - active bc another pump moves co-molecule against concentration gradient (usually to outside) to be present at the protein - co-molecule often allows shape change, enables transport

antiport

2 molecules moving in opposite directions thru the same pump

symport

moving in same direction, move together

water potential

takes pressure and solute concentration to predict where water will travel (% = %p + %s)

metabolism

complete set of organic chemical reactions in the body

catabolism (catabolic reaction)

break down of large into smth smaller (ex: hydrolysis, proteases, nucleases, etc)

anabolism (anabolic reaction)

building large molecules from smaller (ex: kinases, dna polymerase, etc)

exergonic reactions

lower activation energy, high energy reactant w/ low energy products, releases energy into environment (ex: cellular respiration first steps, glucose + oxygen gas high energy -> co2 + H20 low energy, releases energy)

endergonic reactions

higher activation energy. low energy reactant w/ high energy products, need to take in energy for the bonds (ex: photosynthesis, co2 + h20 low energy, need sun to make glucose + o2)

enzymes lower...

activation energy

energy coupling

when the energy released from an exergonic reaction is used as the activation energy to fuel an endergonic reactions (es: breakdown of glucose to fuel atp production)

enzymes function by...

providing specific binding sites to line up where reaction will happen, apply stress/pressure to bonds (then rebond to others), microenvironment, maybe even directly participate

enzymatic pathway

series of multiple enzymes that trigger each other, eventually reach specific function

precursor molecule

molecule that has a similar shape and composition to another molecule, with small change will become that molecule

enzyme activity is affected by...

temperature, pH, concentration (substrate + enzyme)

saturation curve

graph that shows how at a certain substrate concentration all enzyme will constantly be working, so increasing substrate concentration does not increase activity

inhibitor

substance that stops enzyme from functioning properly

competitive inhibitor

molecules that mimic shape of substrate, occupy where substrate wants to go and doesn't let bind (can be outcompeted by substrate)

noncompetitive inhibitor (allosteric)

molecules that bind to a spot on the enzyme (not active site) and changes the enzyme shape, preventing substrate binding (effective even in increasing substrate concentration)

activator

substance that promotes enzyme functioning

allosteric activator

molecules that binds to spot on enzyme (not active) and stabilizes the active enzyme to promote binding of substrates

cooperactivity

when substrate binds to active site, stabilizes the enzyme to promote substrate binding

feedback inhibition

when a product of an enzymatic pathway then inhibits an earlier step in the pathway (to turn off), maximizes energy

cofactor

nonenzyme that binds to enzyme during reaction, essential for reaction (not all reactions)

metabolism

set of chemical reactions that a cell performs

chemical energy

potential energy available for release thru breaking chemical bonds

2nd law of thermodynamics

energy transfer increases disorder in the universe (higher entropy)

catabolic

pathways of degradation, break down complex molecules (high potential) and release energy, often exergonic (ex: cellular respiration)

anabolic

consume energy to build complex molecules from simpler molecules, often endergonic (ex: photosynthesis)

luciferase reaction is exothermic bc...

energy is released in the form of light

energy coupling

when the energy released from an exergonic reaction is used to fuel an endergonic reaction

phosphates for phosphorylation come from..

hydrolysis of ATP (performed by kinase) into ADP or cAMP

ATP structure

similar to nucleotide - ribose (pentose sugar), adenine, chain of 3 phosphate groups

cellular respiration (basic)

C6H12O6 + 6O2 = 6 H20 + 36 ATP, high pe reactants to low pe products, energy release used to make ATP molecules (high pe)

steps of cell communication

reception, transduction, response

target cell

cell with specific receptor that will bind a signal molecule and have a specific response to it

parasympathetic nervous system

relaxed, rest and digest, less airflow, less atp production + use, peristalsis, etc

sympathetic nervous system

fight or flight, danger, take in more oxygen, release glycogen and break down into glucose, make and use more atp, adrenaline and noradrenaline, etc

scaffolding protein

protein that holds phosphorylation cascade kinases in place to increase speed of reactions

how do signaling pathways begin and terminate

binding of ligand to receptor initiates signaling, activates transduction proteins, when transduction proteins deactivated, turn off

yeast mating factor

yeast cells exchange mating factors (signaling molecules), when mating factors different, will mate - varied genetic material makes more resilient offspring

phosphorylation cascade

series of kinases activating next kinase by phosphorylation

dephosphorylation

removal of added phosphate group by phosphatase

second messenger

smaller molecule in signaling pathway that diffuses thru cell quicker, allows for quicker signaling

Calcium ion and signaling

cell uses calcium ion pumps to create concentration gradient of Ca2+, when gated ion channel is unlocked by molecule, ions flood into the cell and cause voltage change, which opens voltage-gated pump/channel

paracrine

local signaling, short distance, secretory vesicle

endocrine

long distance signaling, in bloodstream, hormones

amplification

when 1 molecule in pathway activates many molecules in the next step, makes faster

specificity

property of ligands only activating response in certain target cells bc only certain cells express gene to create the receptor for that ligand

neuronal communication (basic)

electric signal sent down