Metabolism
• Chemical reactions of life
– forming bonds between molecules
• dehydration synthesis
• synthesis
• anabolic reactions
– breaking bonds between molecules
• hydrolysis
• digestion
• catabolic reactions
That’s why
they’re called
anabolic steroids!
Examples
 dehydration synthesis (synthesis)
enzyme
 hydrolysis (digestion)
enzyme
• Enzymes work by decreasing the potential
energy difference between reactant and
product
Catalysts
• So what’s a cell got to do to reduce
activation energy?
– get help! … chemical help…
ENZYMES
Call in the
ENZYMES!
G
• As a result of its involvement in a reaction, an
enzyme permanently alters its shape.
Enzymes vocabulary
substrate
• reactant which binds to enzyme
• enzyme-substrate complex: temporary association
product
• end result of reaction
active site
• enzyme’s catalytic site; substrate fits into active site
substrate
enzyme
active site
products
Properties of enzymes
• Reaction specific
– each enzyme works with a specific substrate
• chemical fit between active site & substrate
– H bonds & ionic bonds
• Not consumed in reaction
– single enzyme molecule can catalyze thousands or
more reactions per second
• enzymes unaffected by the reaction
• Affected by cellular conditions
– any condition that affects protein structure
• temperature, pH, salinity
• If a patient in a hospital was accidentally given
an IV full of pure water they would be fine
because pure water is neutral so it can’t hurt
us.
Managing water balance
• Cell survival depends on balancing water
uptake & loss
freshwater
balanced
saltwater
Aquaporins
1991 | 2003
• Water moves rapidly into & out of cells
– evidence that there were water channels
• protein channels allowing flow of water across cell
membrane
Peter Agre
Roderick MacKinnon
John Hopkins
Rockefeller
Do you understand Osmosis…
.05 M
.03 M
Cell (compared to beaker)  hypertonic or hypotonic
Beaker (compared to cell)  hypertonic or hypotonic
Which way does the water flow?  in or out of cell
• Cellular respiration is only done by
heterotrophs because autotrophs can make
their own energy.
What does it mean to be a plant?
• Need to…
– collect light energy
ATP
• transform it into chemical energy
– store light energy
glucose
• in a stable form to be moved around
the plant or stored
– need to get building block atoms
from the environment
CO2
• C,H,O,N,P,K,S,Mg
– produce all organic molecules
needed for growth
• carbohydrates, proteins, lipids, nucleic acids
N
K P
…
H2O
• The purpose of fermentation is to produce a
small amount of energy when cells don’t have
access to oxygen.
Alcohol Fermentation
pyruvate  ethanol + CO2
3C
NADH
2C
1C
NAD+ back to glycolysis
 Dead end process
 at ~12% ethanol, kills
yeast
 can’t reverse the
reaction
Count the
carbons!
bacteria yeast
recycle
NADH
Lactic Acid Fermentation
pyruvate  lactic acid

3C
NADH
O2
3C
NAD+ back to glycolysis
 Reversible process
 once O2 is available,
lactate is converted
back to pyruvate by the
liver
Count the
carbons!
recycle
NADH
animals
some fungi
• Plants use water only as a means of keeping
their cells full and holding the plant itself
upright.
ETC of Photosynthesis
Chloroplasts transform light energy into
chemical energy of ATP

generates O2
use electron carrier NADPH
• The second step of photosynthesis is called
the dark reactions because it only happens in
the dark.
Light: absorption spectra
• Photosynthesis gets energy by absorbing wavelengths of light
– chlorophyll a
• absorbs best in red & blue wavelengths & least in green
– accessory pigments with different structures absorb light of
different wavelengths
• chlorophyll b, carotenoids, xanthophylls
Why are
plants green?
From Light reactions to Calvin cycle
• Calvin cycle
– chloroplast stroma
• Need products of light reactions to drive
synthesis reactions
– ATP
– NADPH
ATP
thylakoid
stroma
• Diagram how a gamete with 3 chromosomes
could be produced with two maternal
chromosomes and one paternal chromosome.
(there isn’t anything wrong in this statement)
• One trait = one gene
• All proteins are made of enzymes.
Proteins
• Most structurally & functionally diverse group
• Function: involved in almost everything
–
–
–
–
enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
• signals (insulin & other hormones)
• receptors
– defense (antibodies)
– movement (actin & myosin)
– storage (bean seed proteins)
• Structural homologies only exist in animals,
never in plants.
• When the environment changes all species
living in it will change to adapt to it.
• Whales lost their hind limbs because they
stopped using them.
Homologous structures
•
•
•
•
Similar structure
Similar development
Different functions
Evidence of close
evolutionary relationship
– recent common ancestor
Analogous structures
 Separate evolution of structures
similar functions
 similar external form
 different internal structure & development
 different origin
 no evolutionary relationship

Don’t be fooled
by their looks!
Solving a similar problem with a similar solution
Convergent evolution
• Flight evolved in 3 separate animal groups
– analogous structures
Does this mean
they have a
recent common
ancestor?
Convergent evolution
 Fish: aquatic vertebrates
 Dolphins: aquatic mammals
similar adaptations to
life in the sea
 not closely related

Those fins & tails
& sleek bodies are
analogous structures!
• Bird and bat wings can only be described as
homologous structures, not as analogous
structures.
• The strongest evidence supporting the
endosymbiotic theory is that mitochondria
and bacteria are the same size and have a
similar shape.
• The primitive atmosphere had to contain
oxygen before life could evolve.
• Plants actively move water up their trunks.
Transport in plants
• H2O & minerals
– transport in xylem
– Transpiration
• Adhesion, cohesion &
Evaporation
• Sugars
– transport in phloem
– bulk flow
• Gas exchange
– photosynthesis
• CO2 in; O2 out
• stomates
– respiration
• O2 in; CO2 out
• roots exchange gases
within air spaces in soil
Why does
over-watering
kill a plant?
Ascent of xylem fluid
Transpiration pull generated by leaf
• Plants get food from the ground.
Pressure flow in phloem
• Mass flow hypothesis
– “source to sink” flow
• direction of transport in phloem is
dependent on plant’s needs
– phloem loading
• active transport of sucrose
into phloem
• increased sucrose concentration
decreases H2O potential
– water flows in from xylem cells
• increase in pressure due to increase in
H2O causes flow
On a plant…
What’s a source…What’s a sink?
can flow
1m/hr
Transport of sugars in phloem
• Loading of sucrose into phloem
– flow through cells via plasmodesmata
– proton pumps
• cotransport of sucrose into cells down
proton gradient
• Plants do not do sexual reproduction.
The life cycle of an angiosperm
Key
Haploid (n)
Diploid (2n)
Anther
Microsporangium
Microsporocytes (2n)
Mature flower on
sporophyte plant
(2n)
MEIOSIS
Microspore (n)
Ovule with
megasporangium (2n)
Generative cell
Tube cell
Male gametophyte
(in pollen grain)
Ovary
Pollen
grains
MEIOSIS
Germinating
seed
Stigma
Megasporangium
(n)
Embryo (2n)
Endosperm
(food
supply) (3n)
Sperm
Surviving
megaspore
(n)
Seed
Seed coat (2n)
Antipodal cells
Polar nuclei
Synergids
Egg (n)
Female gametophyte
(embryo sac)
Pollen
tube
Zygote (2n)
Nucleus of
developing
endosperm
(3n)
Pollen
tube
Egg
nucleus (n)
Sperm
(n)
FERTILIZATION
Discharged
sperm nuclei (n)
Pollen
tube
Style
• Ectotherms do not regulate their body
temperature in any way
• Most materials are transported through the
blood stream of mammals and into and out of
tissues by active transport.
Arranged as a Phospholipid bilayer
• Serves as a cellular barrier / border
sugar
H2O
salt
polar
hydrophilic
heads
nonpolar
hydrophobic
tails
impermeable to polar molecules
polar
hydrophilic
heads
waste
lipids
Proteins domains anchor molecule
• Within membrane
Polar areas
of protein
– nonpolar amino acids
• hydrophobic
• anchors protein
into membrane
• On outer surfaces of
membrane in fluid
– polar amino acids
• hydrophilic
• extend into extracellular
fluid & into cytosol
Nonpolar areas of protein
Many Functions of Membrane Proteins
“Channel”
Outside
Plasma
membrane
Inside
Transporter
Enzyme
activity
Cell surface
receptor
Cell surface
identity marker
Cell adhesion
Attachment to the
cytoskeleton
“Antigen”
Membrane Proteins
• Proteins determine membrane’s specific functions
– cell membrane & organelle membranes each have unique
collections of proteins
• Classes of membrane proteins:
– peripheral proteins
• loosely bound to surface of membrane
• ex: cell surface identity marker (antigens)
– integral proteins
• penetrate lipid bilayer, usually across whole membrane
• transmembrane protein
• ex: transport proteins
– channels, pumps
Membrane carbohydrates
• Play a key role in cell-cell recognition
– ability of a cell to distinguish one cell from
another
• antigens
– important in organ &
tissue development
– basis for rejection of
foreign cells by
immune system
• In each of the following pairs the two terms
given mean the same thing and do the same
job.
– leukocyte; lymphocyte
– antigen; antibody
– B lymphocyte; T lymphocyte
– cytotoxic T cell; helper T cell
1st line: Non-specific External defense
• Barrier
• skin
• Traps
Lining of trachea:
ciliated cells & mucus
secreting cells
• mucous membranes, cilia,
hair, earwax
• Elimination
• coughing, sneezing, urination, diarrhea
• Unfavorable pH
• stomach acid, sweat, saliva, urine
• Lysozyme enzyme
• digests bacterial cell walls
• tears, sweat
•
Leukocytes:
Phagocytic
WBCs
Attracted by chemical signals released by damaged
cells
– ingest pathogens
– digest in lysosomes
• Neutrophils
– most abundant WBC (~70%)
– ~ 3 day lifespan
• Macrophages
– “big eater”, long-lived
• Natural Killer Cells
– destroy virus-infected cells
& cancer cells
Destroying cells gone bad!
• Natural Killer Cells perforate cells
– release perforin protein
– insert into membrane of target cell
– forms pore allowing fluid to
flow in & out of cell
natural killer cell
– cell ruptures (lysis)
vesicle
• apoptosis
perforin
perforin
punctures
cell membrane
cell
membrane
cell
membrane
virus-infected cell
3rd line: Acquired (active) Immunity
• Specific defense with memory
– lymphocytes
• B cells
• T cells
– antibodies
• immunoglobulins
• Responds to…
– antigens
• cellular name tags
– specific pathogens
– specific toxins
– abnormal body cells (cancer)
B cell
How are invaders recognized?
• Antigens
– cellular name tag proteins
• “self” antigens
– no response from WBCs
• “foreign” antigens
– response from WBCs
– pathogens: viruses, bacteria, protozoa, parasitic worms, fungi,
toxins
– non-pathogens: cancer cells, transplanted tissue, pollen
“self”
“foreign”
Lymphocytes
bone marrow
• B cells
– mature in bone marrow
– humoral response system
• attack pathogens still circulating in
blood & lymph
– produce antibodies
• T cells
– mature in thymus
– cellular response system
• attack invaded cells
• “Maturation”
– learn to distinguish “self”
from “non-self” antigens
• if react to “self” antigens, cells
are destroyed during maturation
Y
Y
Y
Y
Y
Y
Y
Y
Y
Y
antigen
Y
Y
– multi-chain proteins
– binding region matches molecular shape of antigens
– each antibody is unique & specific
• millions of antibodies respond to millions of
foreign antigens
– tagging “handcuffs”
• “this is foreign…gotcha!”
Y
Y
antigenbinding site on
antibody
Y
Y
• Proteins that bind to a specific antigen
Y
Y
Antibodies
Y
Y
variable
binding region
Y
Y
each B cell
has ~50,000
antibodies
Vaccinations
• Immune system exposed
to harmless version of pathogen
– stimulates B cell system to produce
antibodies to pathogen
• “active immunity”
– rapid response on future exposure
– creates immunity
without getting
disease!
• Most successful
against viruses
Attack
of
the
Killer
T
cells
• Destroys infected body cells
– binds to target cell
– secretes perforin protein
• punctures cell membrane of infected cell
– apoptosis
Killer T cell
vesicle
Killer T cell
binds to
infected cell
cell
membrane
infected cell
destroyed
perforin
punctures
cell membrane
target cell
cell
membrane
• Neurons are at equilibrium at resting
potential.
Nervous system cells
 Neuron
signal
direction

a nerve cell
dendrites
cell body
 Structure fits function
many entry points for
signal
 one path out
 transmits signal

axon
myelin sheath
dendrite  cell body  axon
signal direction
synaptic terminal
synapse
Cells have voltage!
• Opposite charges on opposite sides of cell
membrane
– membrane is polarized
• negative inside; positive outside
• charge gradient
• stored energy (like a battery)
+ + + + + + + + + + + + + + +
– – – – – – – – – – – – – –
– – – – – – – – – – – – – –
+ + + + + + + + + + + + + + +
How does a nerve impulse travel?
• Wave: nerve impulse travels down neuron
– change in charge opens
+ –
+
next Na gates down the line
• “voltage-gated” channels
channel
– Na+ ions continue to diffuse into cell
closed
– “wave” moves down neuron = action potential
Gate
The rest
of the
dominoes
fall!
+
+
channel
open
– – – + + + + + + + + + + + +
+ + + – – – – – – – – – – – –
Na+
+ + + – – – – – – – – – – – –
– – – + + + + + + + + + + + +
wave

Action potential graph
40 mV
4
30 mV
20 mV
Membrane potential
1. Resting potential
2. Stimulus reaches threshold
potential
3. Depolarization
Na+ channels open;
K+ channels closed
4. Na+ channels close;
K+ channels open
5. Repolarization
reset charge gradient
6. Undershoot
K+ channels close slowly
10 mV
0 mV
Depolarization
Na+ flows in
–10 mV
3
Repolarization
K+ flows out
5
–20 mV
–30 mV
–40 mV
–50 mV
–60 mV
–70 mV
–80 mV
Hyperpolarization
(undershoot)
Threshold
2
1
Resting potential
6 Resting
• The nervous and endocrine systems send
completely different kinds of messages so
they never work together.
Chemical synapse
axon terminal
 Events at synapse
action potential


synaptic vesicles

synapse


Ca++
receptor protein
neurotransmitter
acetylcholine (ACh)
action potential depolarizes membrane
opens Ca++ channels
neurotransmitter vesicles fuse with
membrane
release neurotransmitter to synapse 
diffusion
neurotransmitter binds with protein
receptor
 ion-gated channels open

neurotransmitter degraded or
reabsorbed
muscle cell (fiber)
We switched…
from an electrical signal
to a chemical signal
LE 11-4
Local signaling
Long-distance signaling
Target cell
Secreting
cell
Local regulator
diffuses through
extracellular fluid
Paracrine signaling
Electrical signal
along nerve cell
triggers release of
neurotransmitter
Endocrine cell
Neurotransmitter
diffuses across
synapse
Secretory
vesicle
Target cell
is stimulated
Blood
vessel
Hormone travels
in bloodstream
to target cells
Target
cell
Synaptic signaling
Hormonal signaling
• All hormones have the same types of effects
on cells, no matter what they are made of.
LE 11-5_3
EXTRACELLULAR
FLUID
Reception
CYTOPLASM
Plasma membrane
Transduction
Response
Receptor
Activation
of cellular
response
Relay molecules in a signal transduction
pathway
Signal
molecule
LE 11-6
Hormone
(testosterone)
EXTRACELLULAR
FLUID
Plasma
membrane
Receptor
protein
Hormonereceptor
complex
The steroid
hormone testosterone
passes through the
plasma membrane.
Testosterone binds
to a receptor protein
in the cytoplasm,
activating it.
The hormonereceptor complex
enters the nucleus
and binds to specific
genes.
DNA
The bound protein
stimulates the
transcription of
the gene into mRNA.
mRNA
NUCLEUS
New protein
The mRNA is
translated into a
specific protein.
CYTOPLASM
LE 11-7b
Signal
molecule
Signal-binding site
a Helix in the
membrane
Signal
molecule
Tyrosines
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
Receptor tyrosine
kinase proteins
(inactive monomers)
CYTOPLASM
Dimer
Activated relay
proteins
Tyr
Tyr
Tyr
Tyr
Tyr
Tyr
6
ATP
Activated tyrosinekinase regions
(unphosphorylated
dimer)
6 ADP
P Tyr
P Tyr
P Tyr
Tyr
P
P
Tyr P
Tyr
Fully activated receptor
tyrosine-kinase
(phosphorylated
dimer)
P Tyr
P Tyr
P Tyr
P
Tyr P
Tyr P
Tyr
Inactive
relay proteins
Cellular
response 1
Cellular
response 2
LE 11-10
First messenger
(signal molecule
such as epinephrine)
Adenylyl
cyclase
G protein
G-protein-linked
receptor
GTP
ATP
cAMP
Second
messenger
Protein
kinase A
Cellular responses
LE 11-8
Signal molecule
Receptor
Activated relay
molecule
Inactive
protein kinase
1
Active
protein
kinase
1
Inactive
protein kinase
2
ATP
ADP
Pi
P
Active
protein
kinase
2
PP
Inactive
protein kinase
3
ATP
ADP
Pi
Active
protein
kinase
3
PP
Inactive
protein
P
ATP
P
ADP
Pi
PP
Active
protein
Cellular
response
• All populations will increase continuously,
regardless of outside factors.
Survivorship curves
What do these graphs tell
about survival &
strategy of a species?
• Generalized strategies
Survival per thousand
1000
Human
(type I)
I. High death rate in
post-reproductive
years
Hydra
(type II)
100
II. Constant mortality rate
throughout life span
Oyster
(type III)
10
1
0
25
50
75
Percent of maximum life span
100
III. Very high early
mortality but the few
survivors then live long
(stay reproductive)
Reproductive strategies
• K-selected
– late reproduction
– few offspring
– invest a lot in raising offspring
• primates
• coconut
• r-selected
K-selected
– early reproduction
– many offspring
– little parental care
• insects
• many plants
r-selected
Logistic rate of growth
• Can populations continue to grow
Of course not!
exponentially?
no natural controls
K=
carrying
capacity
What happens as
N approaches K?
effect of
natural controls
Population growth predicted by the logistic model
2,000
dN
 1.0N
dt
Population size (N)
1,500
Exponential
growth
K  1,500
Logistic growth
1,000
dN
 1.0N
dt
1,500  N
1,500
500
0
0
5
10
Number of generations
15