terms

Terms and Concepts to Understand

Introduction:

emergent property
cell types

prokaryotic
eukaryotic

scientific method (hypothetico-deductive thinking)

observation
questions
hypothesis
prediction
tests

evolution

three domains (fig. 1.11)

bacteria
archaea
eukarya

six kingdoms

prokaryotes

eubacteria
archabacteria

eukaryotes

protista
fungi
plantae
animalia

classifying life (fig. 1.10)

kingdom
phylum
class
order
family
genus
species

Small molecules and water:

atom

proton
neutron
electron

element

atomic number
atomic mass (mass number)

dalton

Atomic symbols

H - hydrogen
C - carbon
O - oxygen
N - nitrogen
Ca - calcium
P - phosphorus
K - potassium
S - sulfur
Na - sodium
Cl - chlorine

unit of charge
isotope

radioisotopes

behavior of electrons

shells and energy levels
orbitals
valence electrons

molecules
chemical reactions

importance of valence electrons
nucleus unchanged
reactants
products
chemical equilibria

chemical bonds

ionic bond

ions

cation
anion

covalent bond

single bond
double bond
triple bond

compounds

shapes of molecules

important examples (fig. 2.17)

H₂O
CH₄

polarity of covalent bonds

partial unit charge

partial positive
partial negative

polar Vs non-polar covalent bonds

weak interactions

hydrogen bond
van der Waals interaction
hydrophobic interaction

hydrogen bonding and water, fig.3.1
properties of water

cohesion

surface tension

adhesion

water as a solvent

interaction of solutes with water

hydrophilic molecules

ionic molecules, e.g. fig.3.7
polar molecules, e.g.fig. 2.16

hydrophobic molecules

hydrocarbons

molarity (Moles/Liter)

mole
molecular weight

dissociation of water

hydrogen ion, H⁺ (hydronium ion, H₃O⁺)
hydroxide ion, OH^-
pH = -log[H⁺]
acid Vs base

Chemistry of Carbon and Macromolecules:

Valence of H, N, C and O (fig. 4.3)
some simple organic chemistry

hydrocarbons
functional groups (table 4.1)

methyl
hydroxyl

alcohols

carbonyl

aldehydes
ketones

carboxyl

carboxylic acids

ionized vs. non-ionized

amines

ionized vs. non-ionized

phosphate
sulfhydryl

isomers (fig. 4.6)

structural isomers
geometric isomers
optical isomers

polymers (fig. 5.2)

monomers
oligomer
dehydration (condensation) synthesis
hydrolysis

carbohydrates

monosaccharides

general formula - C_nH_2nO_n
straight chain Vs ring form (fig. 5.4)
polar and hydrophilic
glucose

alpha Vs beta

disaccharide (fig 5.5)

glycosidic linkage
eg., sucrose

polysaccharide

storage polysaccharides

starch (amylose) and glycogen (fig. 5.6)

alpha glucose
often used as energy reserve
often branched

cellulose (fig. 5.8)

beta glucose
structural role
cellulose microfibrils and role of hydrogen bonds

derivative carbohydrates, eg. chitin

proteins

amino acids (table 5.15)

side chains (R groups)

non-polar (hydrophobic)
polar
charged

polypeptide (fig. 5.16)

peptide bond
N terminus (amino end)
C terminus (carboxyl end)

protein structure (conformation) (fig.5.24)

primary structure (amino acid sequence)
secondary structure (fig. 5.20)

role of hydrogen bonds
alpha helix
beta-pleated sheet

tertiary structure

side chain interactions (fig. 5.22)

hydrogen bonds
ionic interactions
hydrophobic interactions
disulfide bond

quaternary structure (fig. 5.23)

subunits (eg. hemglobin and collagen)

role of chaperone proteins (fig. 5.26)
denaturation (fig. 5.25)

nucleic acids

nucleotide (fig.5.29)

phosphate
nitrogenous base

purine

adenine
guanine

pyrimidine

cytosine
thymine
uracil

5 carbon sugar

phosphodiester bonds
DNA

nitrogenous bases

A,T,C,G

deoxyribose

RNA

nitrogenous bases

A,U.G,C

ribose

lipids

triglycerides (fig. 5.10)

fats vs. oils
ester linkage
glycerol
fatty acids (fig.5.11)

saturated Vs unsaturated

role in energy storage

compared to hydrated carbohydrate

phospholipid (fig. 5.12)

polar head (hydrophilic head)
hydrophobic tail(s)
interactions with water (fig 5.13)

phospholipid bilayer
micelle

steroids, eg. cholesterol

Metabolism:

metabolism

anabolism
catabolism

Energy

kinetic energy
potential energy

first law of thermodynamics
second law of thermodynamics

entropy (S)

chemical equilibrium
free energy (G)
change in free energy (kcal/mole) (fig. 6.5)

exergonic reaction

change in free energy < 0
spontaneous

endergonic reaction

change in free energy > 0
non-spontaneous

at equilibrium

change in free energy = 0

role of adenosine triphosphate(ATP)

hydrolysis is exergonic (fig. 6.8)
phosphorylated intermediate (fig. 6.9)
ATP cycle (fig. 6.10)

reaction rates

activation energy (fig. 6.12 & 13)

catalyst
enzyme (fig. 6.15)

substrate
enzyme-subtrate complex
product
binding site (fig. 6.14)

induced fit
active site
specificity

speeds up reaction rate

typically 10⁶ to 10¹² X's (depending on enzyme)

factors effecting the rate of enzymatic reactions

substrate concentration
temperature
pH

co-factors

coenzyme

certain vitamins

coupled reactions (eg. fig 6.9)
inhibition of enzyme activity (fig 6.17)

competitive

reversible Vs irreversible

non-competitive

regulation of enzyme activity

allosteric enzymes

allosteric sites

effects on protein conformation
inhibition Vs activation

control of metabolic pathways (eg. 6.19)

feedback inhibition (negative feedback)

Cells and Membranes:

microscopy

light microscope - .2 um resolution
electron microscope - 2 nm resolution
size of things (fig. 7.1)

cells

eukaryote: 10 - 100 um
prokaryote: 1 - 10 um

organelles
proteins

surface area : volume ratio

small Vs large cells (fig. 7.5)
consequences for cell

prokaryotic cells (fig. 7.4)

plasma memebrane
nucleoid
ribosome
cell wall
outer membrane
capsule
flagellum

eukaryotic cells (fig. 7.7 & 7.8)

cytoplasm
cytosol
ribosome
organelles
endomembrane system (fig 7.16)

endoplasmic reticulum (f.g 7.11)

site of membrane synthesis
rough ER Vs smooth ER

nucleus (fig. 7.9)

nucleoplasm
nuclear envelope

inner membrane
outer membrane
pores

nucleolus

site of ribosome synthesis

relationship to rough ER

Golgi apparatus (fig. 7.12)

transport vesicle
lysosome (fig 7.14)

plasma membrane

endocytosis (fig. 8.19)

phagocytosis
pinocytosis
receptor mediated endocytosis

exocytosis

energy processing organelles

mitochondria
chloroplasts
theory of endosymbiotic origin

possess chromosome like bacteria
replication by division
have ribosomes
can make protein

cytoskeleton

polymers with repeating protein subunits (table 7.2)
microtubules

tubulin dimer
rapid assembly and disassembly
role in movement

of vesicles (fig. 7.21)
cilia and fagella (fig. 7.23)

microfilaments

actin monomers
role in movement (fig. 7.27)

intermediate filaments

plant cell walls (fig. 7.28)

primary cell wall
secondary cell wall
plasmodesmata

extracelluar matrix 9fig. 7.29)

Intercellular junctions (fig. 7.30)

tight junction
desmosome
gap junction

selectively permeable
fluid mosiac model (fig. 8.2)
phospholipid bilayer (fig. 8.1, fig. 8.4)

hydrophilic heads
hydrophobic tails
some phospholipids have carbohydrate attached
no "flip-flop"
great lateral mobility

protein (fig. 8.6)

integral protein
peripheral protein
some have carbohydrate attached
no "flip-flop"
considerable lateral mobility (Fig 8.5)
role of membrane proteins (fig. 8.9)

cholesterol (fig.8.4)

can "flip-flop"

asymetry of membrane (fig. 8.8)

orientation of proteins
location of carbohydrates

phospholipid bilayer is generally permeable to:

hydrophobic molecules, especially small non-polar molecules

eg. O₂,CO₂

small polar molecules

eg. glycerol

phospholipid bilayer is generally not permeable to:

polar molecules the size of glucose or larger
charged molecules

eg Na⁺, Cl ^-, K⁺

transport proteins (fig. 8.14)

channels

two way
selective
often controled by cell, i.e. opened or closed

carriers

two way
selective
often controled by cell, i.e. can be turned on or off
coupled transport

diffusion

simple Vs facilatated
effect of concentration gradient

osmosis

osmotic pressure

hypertonic
hypotonic
isotonic

osmosis and cell shape (fig. 8.11)

lysis
turgid

active transport

requires energy and carriers
some hydrolyze ATP

eg. sodium-potassium pump (fig 8.15)
electrochemical gradient (fig. 8.17)

cotransport (fig. 8.18)

Glycolysis and Respiration:

oxidation

oxidizing reagent

reduction

reducing reagent

coupling of oxidation and reduction
NAD⁺(oxidizing reagent, fig. 9.4)
NADH (reducing reagent, fig. 9.4)
FAD (oxidizing reagent)
FADH₂ (reducing reagent)
substrate level phosphrylation

eg. fig 9.7

chemisomotic synthesis (fig. 9.14)

H⁺ ions and the electrochemical gradient
ATP synthase (inner mitochondrial membrane)

metabolism of glucose

glycolysis

location - cytosol
pyruvate - end product w/ 3 carbons
yeild

2 ATP
2 NADH

reveiw structure of mitochodria (fig 7.17)

inner membrane
outer membrane
matrix

conversion of pyruvate to acetyl CoA

location - mitochondria
coenzyme A
release of 2 CO₂per glucose
yeild 2 NADH

Krebs cycle (citric acid cycle)

location - matrix
citric acid
release of 4 CO₂ per glucose
yeild

2 ATP
6NADH
2 FADH₂

oxidative phosphorylation

location - mitochondria (fig. 9.15)
electron transport chain
oxidation of NADH and FADH₂ to NAD⁺ and FAD
reduction of O₂ to H₂O
production of electrochemical gradient

location of gradient

chemiosmotic ATP synthesis

yeild 34 ATP (maximum)

summary - fig 9.16

yeild - 38 ATP

fermentation

oxidation of NADH to NAD⁺
location - cytosol
yeild per glucose - 2 ATP
in yeast (fig. 9.17)

CO₂ and ethanol production

in humans (fig. 9.17)

lactate production
cycle of Cori

fermentation Vs oxidative phosphorylation in muscle cells

central role of glycolysis and respiration in all metabolic pathways

in catabolism (fig. 9.19)
in anabolism

control of metabolism

allosteric regulation (eg., fig 9.20) (Feedback regulation)

alloseric activator - positive feedback
allosteric inhibitor - negative feedback

Photosynthesis:

electromagnetic radiation

photon
wavelength (in nm)

energy inversely proportional to wavelength
visible light

used for photosynthesis

role of NADPH

compare to NADH

review structure of choloroplast (fig. 10.2)

outer membrane
inner membrane
thylakoid
stroma
thylakoid space

pigments

Photoexcitation (fig. 10.10)
3 fates of excited electron in pigment

return to ground state and

energy lost as heat or flouresence (fig. 10.10), or
most energy transfered to another pigment molecule (fig. 10.11)

electron lost from pigment (fig(10.11)

absorption spectra (fig. 10.8)
action spectra (fig. 10.8)
photosynthetic pigments

chlorophyll a
chlorophyll b
carotenoids

photophosphorylation (figh 10.16) (light reactions)

role of thylakoid membrane
photosystem I & photosystem II

energy absorbing "antenna complex"
location of photosynthetic pigments
reaction center

oxidation (splitting) of water

photosystem II
production of O₂
replaces electrons at reaction center

electron transport chain (electron carriers in membrane)
reduction of NADP⁺ to NADPH
production of electrochemical gradient

high [H⁺] inside thylakoid

ATP synthase and chemiosmosis
cyclic Vs non-cyclic photophosphorylation

Calvin-Benson cycle (dark reactions)

coupling of light and dark reactions (fig 10.4)
location - stroma
rubisco

catalyzes CO₂ fixation
slow turnover rate

fig. 10.17

carbon fixation

first stable molecule is a C₃

reduction and sugar production

requires ATP and NADPH from light cycle

regeneration of C₅

requires ATP

photorespiration

O₂ not CO₂ is substrate for rubisco
C₃ Vs C₄ plants

bundle sheath cells
mesophyll cells

CAM plants

Cell communication

local regulators

autocrine (signal molecule binds the cell that secreted the molecule)
paracrine
synaptic signal

hormonal (endocrine)
overview of cell signaling (fig. 11.5)
some important types of receptors

G-protein-linked receptors

receptor
G protein

inactive (GDP bound)
active (GTP bound)

tyrosine-kinase receptors
ligand gated ion channel
intracellular receptors, eg. steroid hormone receptor

Phosphorylation cascade (fig. 11.11)

role of protein kinases
role of protein phosphatases

second messengers

cAMP
Ca⁺²

The cell cycle and cell division:

cell division

mother cell
daughter cells

binary fission (cell division in bacteria)

circular DNA (chromosome)
attached to membrane (fig. 12.10)

chromosome structure in eukaryotes

chromatin

~50% DNA & 50% protein

linear
after replication

centromere
sister chromatids

cell cycle (fig. 12.4)

M phase (mitosis)
Interphase

G₁ (most variable in length)
S (synthesis)
G₂

G₀

examples of cell cycle times

fertilized frog egg < 1 hour
dividing cell in gut lining ~1 day
liver cell ~1 year
nerve cell - doesn't divide

mitosis (fig. 12.5)

prophase

chromosomes condense
nuclear envelopoe disappears
centrosomes

move to opposite poles
are microtubule organizing centers
form spindle apparatus

kinetochore
spindle fibers

made of microtubles
kinetochore fibers
polar fibers

metaphase

metaphase (equatorial) plate
kinetochore fibers pull on chromosomes

anaphase

centromeres splits
chromosomes move to opposite poles

telophase

spindle apparatus disappears
nucleus reforms
chromosomes decondense

cytokenesis
regulation of cell cycle

cell cycle check points

G₁ check point
G₂check point
M checkpoint

external signals

density dependent (contact) inhibition
anchorage dependence

Cancer

tumor

benign
malignant

metastasis

asexual reproduction
sexual reproduction, eg. fig. 13.3

diploid (2N)

homologous pairs of chromosomes

sex chromosome
autosome

haploid (N)

gametes

sperm
egg

fertilization
zygote

meiosis
meiosis I (reductive division) (fig. 13.6)

prophase I

tetrad
synapsis
crossing over between homologous chromosomes (fig. 13.9)

chiasmata
increases variety

metaphase I
anaphase I

tetrad splits (not centromeres)

telophase I

interkinesis

no DNA synthesis

meiosis II (most like mitosis) (fig. 13.9)

prophase II
metaphase II
anaphase II
telophase II

compare mitosis and meiosis (fig. 13.7)
variations in life cycles (fig. 13.4)

eg. human Vs Ulva

spore Vs gamete

Mendelian genetics:

Gregor Mendel
monohybrid cross (eg. fig 14.2)

parental generation
F₁ generation
F₂ generation
phenotypes

dominant Vs recessive
3:1 ratio of phenotypes in F₂ generation

genotype Vs phenotype
homozygous
heterozygous
gene

alleles

gene locus
law of segregation

segregation of alleles during gamete formation (meiosis)

Punnet square
test cross (eg., fig. 14.6)

use of homozygous recessive individual

probability

rule of multiplication
rule of addition

dihybrid cross (eg., fig 14.7)

chromosomal basis (eg., fig. 15.1)
recombinants phenotypes
9:3:3:1 ratio of F₂phenotypes

law of independent assortment
incomplete dominance (eg. fig. 14.9)
codominance

eg. ABO blood groups

multiple alleles

eg. ABO blood groups

I^A,I^Band i alleles

pleiotrophy
epistasis
polygenic trait

eg., height or weight in humans
quantitative (continuous)
normal distribution

expression of gene effected by

other genes
environment

inheritance in humans

pedigree
inheritance of recessive traits

eg. Tay Sachs

inheritance of dominant traits

eg. huntingtons disease

Chromosomal basis of inheritance:

sex linked inheritance

inheritance in flies

wild type
mutant phenotype

sex determination in flies (eg. white eyed trait, fig. 15.3)

X chromosome
Y chromosome
males are hemizygous

Barr body in mammals

X chromosome inactivation (eg., fig. 15.10)

sex linked inheritance in humans

eg. red-green colorblindness, hemophilia

linkage

chromosomal basis (fig. 15.1)
linked genes
effect of crossing over during meiosis (eg. fig. 10.20)

recombinants and parental types
recombination frequency (fig. 10.21)
effect of multiple crossovers

linkage map

sex determination (fig. 15.8)

sex chromosome
autosome

aneuploidy

trisomy eg, downs syndrome
monosomy
alteration in numbers of sex chromosome

XXY and XO are sterile
XYY and XXX are apparently normal

alterations of chromosome structure (fig. 15.12)

deletion
duplication
translocation
inversion

Molecular basis of inheritance:

Griffith experiment

Streptococcus pneumoniae

S strain
R strain

transformation (fig. 16.1)

Hersey -Chase experiment (fig16.2)

bacteriophage

³⁵S in protein in supernatant
³²P in DNA in pellet with infected cells

Chargaffs rules

[A] = [T] and [C] = [G]
the ratio of [A]:[T]:[C]:[G] constant within a species

Watson and Crick
chromosomal DNA - double helix structure (fig. 16.5)

double stranded

strands are complementary
each strand is directional

3' end
5' end

antiparallel

strands held together by base pairs which form H bonds (fig. 16.6)

complementary base pairs

A only pairs with T
C only pairs with G

replication of DNA

3 modes of replication considered

conservative
semiconservative
dispersive

Meselson-Stahl experiment (fig 16.9)

use of ¹⁴N and ¹⁵N
density gradient centrifugation

DNA poymerase

uses the monomers (fig. 16.11)

dATP (d=deoxy)
dTTP
dGTP
dCTP

template is read 3^' to 5^'
complementary strand made 5^' to 3^'
proof reading
error rate

without proof reading is 1 in 10⁴ base pairs
~1 in 10⁹ base pairs in humans with proof reading

origin of replication

prokaryote

1 site on each chromosome

eukaryote

many sites on each chromosome

replication fork (box 16.13)

leading strand

continuous synthesis

lagging strand

Okazaki fragments

primase

makes RNA primer

DNA ligase

joins Okazaki fragments

telomere

telomerase (fig. 16.19)

From gene to protein:

nature of the gene
one gene - one enzyme hypothesis (Beadle and Tatum)

Neurospora experiment (Fig 17.1)

one gene - one polypeptide hjypothesis
central role of transcription and translation in gene expression (fig. 17.2)
transcription & translation of mRNA in eukaryotes vs. prokaryotes

can be simultaneous in prokaryotes ((fig. 17.20)
in eukaryotes

transcription occurs in nucleus
translation occurs in cytoplasm

transcription (fig. 17.6)
transcription unit
RNA polymerase

DNA template strand read 3^' to 5^'
monomers

ATP
UTP
GTP
CTP

complementary RNA transcript

made 5^' to 3^'
base pairing rules same as in DNA except:

A in DNA pairs with U in RNA

promotor
initiation site (startpoint)
terminator and termination point
stages of transcription

initiation
elongation
termination

several types of transcripts

messenger RNA - mRNA
ribosomal RNA - rRNA
transfer RNA - tRNA
and other RNAs

genetic code

codon

3 bases
64 codons
codes for:

amino acids
start
stop

RNA maturation in eukaryotes (fig. 17.9)

primary transcript (pre-mRNA)

exon
intron

RNA splicing

removal of introns
role of spliceosome

translation of mRNA

ribosome (fig. 17.14)

composed of ribosomal RNAs & proteins
large subunit
small subunit

tRNA (fig. 17.12)

anticodon
amino acid attachment site
charged tRNA

aminoacyl tRNA sysnthetases ( fig. 17.13)

initiation (fig. 17.15)

reading frame

elongation (fig. 17.16)

P site
A site

termination (fig. 17.17)
mRNA read 5' to 3'
protein made N-terminus to C-terminus
polyribosomes (fig. 17.18)

role of signal peptide (fig. 17.19)

directs protein synthesis to ER

mutations (fig 17.22)

point mutations

base pair substitutions

missense
nonsense

base pair substitution or deletion

frameshift

Control of gene expression:

control of transcription in prokaryotes

structural genes
polycistronic message
operon

promotor
operator
repressor
eg. typtophan operon (fig. 18.19)
eg. lac operon (fig. 18.20 & 18.21)

chromatin structure in eukaryotes (fig. 19.1)

nucleosomes ("beads on string")"
heterochromatin
euchromatin

gene control in eukaryotes (fig. 19.7)

most inportant is that control of transcription and translation are both very important

Darwin and Evolution:

includes - chapter 1 -pages 9-12.
1860 - Darwin publishes On the Origin of Species

natural selection

observation - all species have the potential for exponential growth
observation - most populations have relatively constant population size
observation - natural resources are limited
inference - overproduction of individuals of a species will create:

a struggle for existence
and only some will survive to reproduce

observation - individuals vary from one another
observation - that variation is heritable
inference - the individuals inheriting the best variations are most likely to survive (survival of the fittest)
inference - non-random ability to survive will lead to a gradual change in the population, i.e. the best variations will accumulate

influenced by the work of:

geologists , eg. Lyell

earth was older and had changed more then previously thought
fossils suggested evolution

Malthus

Essay on principle of population

human populations can grow exponentially
but resourses (eg. food) do not
hence resources will always be limited and there will be a struggle for exsistence

Earth is ~ 4.5 billion years old (fig. 26.3)

early atmoshere without O₂
first cells appear 3.5-3.8 billion years ago

heterotrophs
prokaryote-like

photosynthetic organisms that split water and produce O₂evolve later
O₂ begins to accumulate in atmosphere ~ 2.5 billion years ago

aerobic respiration becomes wide spread

first eukaryotes do not appear till about 2 billion years ago
first multicelluar organisms appear ~ 1 billion years ago

Evolution and populations:

population genetics

population

gene pool
gene (allele) frequency

frequency of homozygotes + 1/2 the frequency of heterozygotes

Hardy-Weinbreg equation (fig. 23.3)

p and q represent allele frequencies at a single gene locus with 2 alleles
p + q = 1
p²+ 2pq + q²= 1

p²= frequency of homozygotes of one allele
2pq = frequency of heterozygotes
q²= frequency of homozygotes of the other allele

Hardy-Weinberg equilibrium at a gene locus is favored by

random mating
large population
no mutations
isolated population (no immigration)
no natural selection

factors changing gene pool of population

mutation

essentially random

gene flow

essentially random

genetic drift (sampling error,eg., fig.23.4)

essentially random
bottlenecks (fig. 23.5)
founder effect
small populations most effected

non - random mating
natural selection

adaptive
non - random
modes of selection (fig. 23.11)

stabilizing selection
directional selection
disruptive selection

genetic variation and evolution

sources of new variation

mutation

can create new alleles
can cretae new genes (eg., fig. 19.3)

recombination during

meiosis (crossing over between chromosomes)
sexual reproduction

artificial selection can illustrate how selective forces can create new variations

ge, Brassica, fig. 20.3

how is variation preserved

environmental changes with time
habitat is not uniform

eg., clines (fig. 23.8)

selection may preserve variation

balance polymorphism (fig. 23.10)
heterozygote advantage, eg. sickled cell anemia

Speciation:

biological species concept

definition by Ernst Mayr (see table 24.1)

other definitions for species in table 24.1

morphological species

anagenesis (fig. 24.1)
cladogenesis (speciation, fig. 24.1)
types of speciation

allopatric speciation

e.g. Darwins finches

parapatric speciation
sympatric speciation

polyploidy (fig. 24.10)

adaptive radiation (evolutionary radiations)

e.g. Darwins finches, fig. 25.7
e.g. mammals after extinction of the dinosaurs

mechanisms of reproductive isolation

prezygotic

habitat isolation
behavioral isolation
mechanical isolation
temporal isolation
chemical (gametic) isolation

postzygotic

hybrid inviability
hybrid infertility

speciation Vs extinction