CHAPTER 1

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biosphere: all life on earth
ecosystem: all of the living organisms & nonliving things
community: all of the living organisms in an area
population: all of the individuals of a specific species in an area

emergent properties: properties that emerge at a bigger/more complex level

eukaryotic cell: membraned-closed organelles

prokaryotic cell: lacks a nucleus and membrane-enclosed organelles
gene expression: process by which a gene is expressed and a product is formed

genome: human genome has 3 billion nucleotides

proteome: set of all proteins

feedback regulation: accumulation of a product causes the creation of that product to slow down
(negative) or speed up (positive)
examples: mammalian milk secretion (positive) mammalian birth (positive) platelet creation,
insulin secretion (negative)

domains: three main domains (bacteria, archaea, eukarya)

prokaryotic domains: bacteria & archaea

homologous: same position/embryonic origin but not same function (flipper of whale + human
arm)
analogous: different structures/positions but same function (butterfly wing + bird wing)

model organisms: escherichia coli, drosophila melanogaster

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CHAPTER 2
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calorie: the amount of heat required to raise the temperature of one gram of water by 1 degree
Celsius
kilocalories: the actual “calorie” on food packages
evaporative cooling: when an object evaporates, it gets cooler because the highest-energy
molecules evaporate first
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CHAPTER 3
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hydronium ion: H3O+
pH of human blood: 7.4 (basic) – pH range must be between 7 - 7.8
ocean acidification: carbon dioxide dissolves in the ocean and reacts with water to form
carbonic acid
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CHAPTER 4
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urea: CO(NH2)2

structural isomers: arrangement of an atom in the structure is different

cis-trans isomers: arrangement around a double bond is different (cis = same side, trans =
opposite sides)

enantiomers: isomers that are mirror arrangements of each other, contain an asymmetric carbon
(carbon attached to four different groups of atoms)
examples: ibuprofen comes in two different enantiomers and the S version is 100 times more
effective

hydroxyl group: OH– group, alcohols

carbonyl group: C=O- group, ketones/aldehydes
carboxyl group: C=O-O-H group, carboxylic acids

CHAPTER 5
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dehydration reaction: two molecules come together and a water molecule is taken
hydrolysis: a molecule is broken with the addition of water

polymers: usually 40-50 monomers

disaccharide: two monosaccharides with a glycosidic linkage

starch: storage polymer for plants, indigestible for humans because it contains fiber, contains
beta linkages and can’t be broken down

glycogen: storage polymer for humans, stored in muscles & liver and is broken down when the
body needs it

cellulose: structural polymer for plants, found in plant cell walls

chitin: structural polymer for animals, found in exoskeletons

saturated fatty acids: saturated with hydrogen, solid at room temperature, unhealthy
unsaturated fatty acids: not saturated with hydrogen, liquid at room temperature, healthy, kinks
because of double bonds
trans fats: unsaturated fatty acids that are saturated, very unhealthy
phospholipid: similar to fat molecule but only has two fatty acids
steroids: carbon skeleton with four fused rings

proteins: 20 main proteins

amino acids: can be hydrophobic (nonpolar) or hydrophilic (polar), acidic or basic
acidic amino acids: usually have negatively charged side chains due to a carboxylic acid group
basic amino acids: usually have positively charged side chains

secondary protein structure: alpha helix and beta pleated sheets

sickle cell disease: normal amino acid is glutamic acid, wrong substitution is valine
protein denaturation: changes in pH, temperature, can cause denaturation

x-ray crystallography: passes an x-ray through the atoms of a crystallized molecule to determine
the 3-D structure of a protein

nucleotide: composed of a pentose (five-carbon sugar), a nitrogenous base, and 1-3 phosphate
groups
pyrimidine: six-membered, cytosine/thymine/uracil
purine: six-membered fused to five-membered, adenine/guanine
DNA: semiconservative & anti-parallel

transfer RNA (tRNA): brings amino acids to ribosome during synthesis

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CHAPTER 6
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robert hooke: first person to see dead cells through microscope

light microscope: visible light passed through the lens and through glass lens, which refract so
small objects can be seen

magnification: ratio of an object’s image size to its real size

resolution: measure of an object’s clarity – minimum distance that two points can be separated
and distinguished as two separate points
contrast: difference between light and dark areas

electron microscope: forces a beam of electrons through the object

scanning electron microscope (SEM): good for the 3-D surface of a cell
transmission electron microscope (TEM): good for cross-sections

cytology: study of cell structure

cell fractionation: spinning the cell through a centrifuge to separate its components – at low
speeds, the cell contains large parts and the opposite is also true

prokaryotic cells: contain organelles suspended in cytosol that are not membrane-bound, the
DNA is a big jumbled mess with no nucleus protecting it (this is called a nucleoid)

nuclear envelope: a double membrane, encloses the nucleus

nuclear lamina: netlike array of proteins for structure & organization with pore complexes
scattered all over the nucleus

smooth ER: synthesis of lipids/fats/oils/steroids, detoxification of poisons, calcium ion storage

golgi apparatus: consists of stacks of sacs (called cisternae) – has two sides, the cis side and
the trans side
cis side: usually near the ER and is packaging
trans side: usually away from ER and is receiving & transporting

autophagy: hydrolytic enzymes recycle their cells’ own genetic material (phago = eat, auto =
self, autophagy = self eat)

vacuoles: food vacuoles (phagocytes), contractile vacuoles (pump excess water out of the cell)
central vacuole: contains the cell sap (nutrients and inorganic ions – potassium and sodium)

endosymbiont theory: mitochondria & chloroplasts merged with normal prokaryotic cells

mitochondria: smooth outer membrane, convoluted inner membrane – divides mitochondria into
two parts (intermembrane space, mitochondrial matrix)
mitochondrial matrix: contains mitochondrial DNA

chloroplasts: stacks called thylakoids - each individual is called a granum, fluid outside the
thylakoids is called the stroma

peroxisome: an organelle that converts O2 to H2O2 for a variety of functions – breaking down
fats, detoxification of alcohol and other substances

glyoxysomes: convert fatty acids to sugar in the fat-storing tissues of plant seeds

microtubules: found in all eukaryotic cells, hollow rods made of tubulins — tubulins are dimers
(made of alpha tubulin & beta tubulin)
-function: shapes & supports the fell and guides vesicles from ER to cis side of Golgi apparatus

centrosomes: microtubules grow out from this in animal cells, within the centrosome is a pair of
centrioles, my help organize microtubules
centrioles: composed of nine sets of microtubules arranged in a ring

flagella vs cilia: flagellum are larger, usually occur once per cell, and have an undulating motion
rather than a rowing motion of cilia

motile flagella and cilia: have a group of microtubules arranged in a specific fashion - 9 doublets
of microtubules in a ring + 2 single microtubules in the center (9+2)

non-motile cilia: have a 9+0 arrangement of microtubules

basal body: anchors microtubules to the cilium or flagellum and has a 9+0 arrangement,
becomes a centriole inside the egg of many animals

dyneins: large motor proteins that assemble microtubules and produce the movements of
flagella & cilia, ‘walk’ along the microtubules of the doublers w/ ATP as an energy source

microfilaments: thin solid rods that can be called actin filaments as they are built from molecules
of actin, bear tension in the -cytoskeleton — network gives the outer plasma layer of the cell
(cortex) a gel consistency

actin: helps with movement & cytoplasmic streaming (circular movement of cytoplasm within
cell)

intermediate filaments: keratin filaments, only found in cells of some animals (vertebrates
included), reinforce s
hape in nuclear lamina

cell wall: much thicker than plasma membrane, made up of a primary cell wall (thin), middle
lamella (sticky pectins), secondary cell wall (strong and durable matrix)

wood: mostly secondary walls

ECM: mostly glycoproteins (proteins covalently bonded to carbohydrates)

collagen: most abundant glycoprotein in the ECM of animal cells (40% total protein), embedded
in a network made of proteoglycans

proteoglycans: protein core with lots of carbohydrate — can be 50-96% carbo)

fibronectins: attach cells to the ECM by binding to integrins — cell-surface receptor proteins

cell junctions: gap junctions, tight junctions, desmosomes, plasmodesmata

plasmodesmata: channels that connect cells & cytosol

tight junctions: plasma membranes are pressed very tightly together, prevents leakage of ECM
fluid (skin cells)

desmosomes: fasten cells into strong sheets, attach muscles to each other — muscle tears
involve rupture of desmosomes

gap junctions: membrane proteins that surround a pore, communication between cells in heart
muscle

CHAPTER 7
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amphiphatic: hydrophilic & hydrophobic regions — phospholipids

fluid mosaic model: phospholipids & glycoproteins

membrane proteins: two major populations — integral & peripheral proteins, some can be
glycolipids but most are glycoproteins

integral proteins: embedded in the plasma membrane

peripheral proteins: loosely bounded to the surface of the membrane

CCR5 protein: a co-receptor that CD4 must bind to which helps HIV infect cells, drugs target this
instead of CD4

membrane permeability: lipid bilayer has a hydrophobic aspect, which makes it difficult for polar
molecules like glucose & water to pass through

transport proteins: aid specific ions & variety of polar molecules in crossing the membrane by
helping them avoid contact with the lipid bilayer

aquaporins: channel proteins that allow entry of up to 3 billion water molecules per second

passive transport: diffusion of a substance across a biological membrane because no energy

needed

osmosis: water diffuses across the membrane from region of higher free water concentration to
lower free water concentration

tonicity: ability of a surrounding solution to cause a cell to gain or lose water

isotonic: no net movement of water : plant cell becomes flaccid and plant wilts

hypertonic (more solutes): cell will lose water, plant cell will plasmolyze (plasma membrane pulls
away from cell wall), animal cell will shrivel

hypotonic: water enters cell faster, cell will swell and lyse, plant cell is turgid (preferred)

facilitated diffusion: ions & molecules that are polar are transported across membrane with the
help of transport proteins

ion gated channels: channels that let ions flow through but also respond to a stimulus - they
open their channel with the help of a stimulus

active transport: pumping a solute against its concentration gradient - which requires energy

electrogenic pump: a transport protein that generates a voltage across the cell,
sodium-potassium pump for animal cells

proton pump: main electrogenic pump for plant cells, transports protons (H+) out of the cell

sodium-potassium pump: 3 K+ ions pumped in for every 2 Na+ ions pumped out

membrane potential: -50 mV to -20 mV (more negative on the inside)

cotransport: coupling the passive diffusion of one substance with the active transport of another
substance (H+/sucrose in plant cells)

exocytosis: fusing vesicles to the cell membrane (by rearranging the lipid bilayers of the two
membranes and them fusing them) and transporting them out - can be used to export products
like insulin or neurotransmitters in nerve cells

endocytosis: the taking in of products in which there are three types - phagocytosis (cellular
eating), pinocytosis (cellular drinking), receptor-mediated endocytosis

receptor-mediated endocytosis: enables the cell to take in bulk quantities of substances like
cholesterol, which is found in Low-Density-Lipoproteins (LDL) and these LDLs bind to receptors
which then take them in

inherited disease familial hypercholesterolemia: high level of cholesterol in the blood because
receptor proteins are non-functional or missing

phagocytosis: cell engulfs a particle by extending pseudopodia around it and packaging it within
a food vacuole inside the cell - which will later be digested
pinocytosis: cell gulps small droplets of extracellular fluid into tiny vesicles formed by the
foldings of the plasma membrane
CHAPTER 8
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metabolic pathway: a molecule is metabolized (added/altered up to create a certain product)

catabolic pathway: degrading processes

second law of thermodynamics: every energy transfer increases the entropy of the universe
(entropy = a measure of molecular disorder)

spontaneous reaction: the process increases entropy - which should occur according to the 2nd
LAW

non-spontaneous reaction: the process does not increase entropy so it needs other input to
proceed

free energy: portion of a system’s energy that can perform work, negative means energy can be
used for work

gibbs equation: G = H - TS (H = change in system’s enthalpy or total heat energy, (S = change

in entropy), T = absolute temperature

equilibrium: state of maximum stability with respect to a chemical reaction - as reaction

proceeds toward equilibrium, free energy decreases - as reaction proceeds away from
equilibrium, free energy increases

exergonic reaction: energy-outward, a net release of free energy

endergonic reaction: absorbs free energy from its surroundings, G is positive which is
non-spontaneous

energy coupling: the use of an exergonic process (which naturally occurs) to drive an
endergonic process - used because a cell does three main kinds of work (chemical work,
transport work, mechanical work)

chemical work: synthesis of polymers, work with reactions

transport work: active transport

mechanical work: muscle cell contraction, beating of cilia, movement of chromosomes

breakdown of ATP into ADP: releases 7.3 kcal of energy and is spontaneous, phosphate bonds
are not high energy! The reactants have high energy relative to products and the release of
energy comes

phosphorylated intermediate: recipient molecule with phosphate group bonded to it, this helps
couple exergonic & endergonic reactions

activation energy: initial energy to start a reaction and contort molecules so the bonds can
break, increased temperature can allow molecules to make it over activation energy

catalysis: an alternative for high temperature, process in which an enzyme speeds up a reaction

substrate: reactant enzyme acts on

enzyme-substrate complex: when the enzyme binds to the substrate

active site: a pocket on the enzyme where catalysis occurs

induced fit: the enzyme tightens its hold after the substrate bonds

temperature: up to a certain point, the temperature of an enzymatic reaction increases with

increasing temperature but after that temperature the proteins and bonds denature, 35-40
degrees Celsius

pH: optimal values for enzymes fall around 6-8 but there are exceptions like pepsin in the
stomach (acidic) and trypsin in the intestine (alkaline)

cofactors: nonprotein/non organic helpers for catalytic processes - ions of zinc, iron, copper

coenzymes: organic versions of cofactors

competitive inhibitors: reduce productivity of enzymes by blocking substrates from the active
sites

non-competitive inhibitors: do not directly compete with the substrate to bind to the enzyme at
the active site, but rather bind to another part of the enzyme which causes enzyme to change its
shape and throw off the substrate

sarin: binds to R group on serine, which is found in acetylcholine (nervous system

neurotransmitter), competitive inhibition

penicillin: blocks active site of an enzyme that bacteria use to make cell walls
allosteric regulation: a protein’s function is affected by the binding of a molecule to another site -
basically non-competitive inhibition for regulation reasons

cooperativity: one binding site on an enzyme causes an increase in catalytic activity for other
active sites (ex: increases affinity for oxygen)

feedback inhibition: metabolic pathway is halted by binding of end product to an enzyme that
acts early in the pathway

CHAPTER 9
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fermentation: catabolic process that degrades sugars to ATP without oxygen

aerobic respiration: most efficient - eukaryotic & many prokaryotic cells

cellular respiration: technically uses aerobic & anaerobic respiration

redox reactions: transfer of electrons from one electron to another, oxidation = loss of electrons
from one substance, reduction = addition of electrons to another substance

reducing agent: electron donor

oxidizing agent: electron acceptor

nicotinamide adenine dinucleotide (NAD+): electron carrier which is defied from niacin, can
cycle between NAD+ and NADH

dehydrogenases: enzymes that remove 2 electrons and 2 protons (pair of H+ atoms) from
substrate and give 2 electrons and 1 proton to NAD+, turning it to NADH

electron transport chain: molecules built into the inner membrane of eukaryotic cells

glycolysis: occurs in the cytosol and breaks glucose into two molecules of pyruvate

pyruvate oxidation: pyruvate enters mitochondria and is oxidized to acetyl CoA

citric acid cycle: glucose is broken down to CO2

oxidative phosphorylation: electron transport chain accepts electrons from NADH or FADH and
then combines these electrons with molecular oxygen & H+ to form water, transforms ADP to
ATP by adding inorganic phosphate, accounts for 90% of ATP generated by respiration
substrate-level phosphorylation: generates smaller amount of ATP, uses phosphate molecule
from organic group

—ENERGY USE PHASE—

glycolysis products: Glucose -> Glucose-6-Phosphate -> Fructose-6 -> Fructose 1, 6

Bisphosphate -> Glyceraldehyde 3-phosphate (G3P) and Dihydroxyacetone phosphate (DHAP)

glycolysis enzymes: hexokinase (transfers phosphate group to glucose),

phosphoglucoisomerase, phosphofructokinase (transfers phosphate group to fructose), aldolase
(cleaves sugar molecule into two 3-carbon sugars) , isomerase (converts G3P and DHAP to
each other)

—ENERGY PAYOFF PHASE—

glycolysis products: 1, 3-Biphosphate glycerate -> 3-Phosphoglycerate -> 2-Phosphoglycerate

-> Phosphoeonol-pyruvate (PEP) -> Pyruvate

glycolysis enzymes: triose phosphate dehydrogenase (G3P oxidized to form NADH, phosphate
group attached to oxidized substrate in exergonic), phosphoglycerokinase (phosphate group
transferred to ADP in endergonic), phosphoglyceromutase (relocates remaining phosphate
group), enolase (double bond forms in substrate by extracting H20), pyruvate kinase (phosphate
group transferred to ADP