Enzymes are necessary because they cause reactions to

Enzymes are necessary because they cause reactions to happen.

Metabolism • Chemical reactions of life – forming bonds between molecules • dehydration 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.

substrate Enzymes vocabulary • 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, p. H, 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 water channels • protein channels allowing flow of water across cell membrane Peter Agre John Hopkins Roderick Mac. Kinnon 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 CO 2 • C, H, O, N, P, K, S, Mg – produce all organic molecules needed for growth • carbohydrates, proteins, lipids, nucleic acids N K P … H 2 O

• The purpose of fermentation is to produce a small amount of energy when cells don’t have access to oxygen.

Alcohol Fermentation pyruvate ethanol + CO 2 3 C NADH 2 C NAD+ back to glycolysis § Dead end process § at ~12% ethanol, kills yeast § can’t reverse the reaction Count the carbons! 1 C bacteria yeast recycle NADH

Lactic Acid Fermentation pyruvate lactic acid 3 C NADH 3 C NAD+ back to glycolysis § Reversible process § once O 2 is available, lactate is converted back to pyruvate by the liver Count the carbons! O 2 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 u generates O 2 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 u similar external form u different internal structure & development u different origin u no evolutionary relationship u 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 u not closely related u 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 are simple organisms with no tissues or organs.

• Dermal Plant TISSUES – epidermis (“skin” of plant) – single layer of tightly packed cells that covers & protects plant • Ground – bulk of plant tissue – photosynthetic mesophyll, storage • Vascular – transport system in shoots & roots – xylem & phloem

Basic plant anatomy 3 • root – root tip – root hairs • shoot (stem) – nodes • internodes – buds • terminal or apical buds • axillary buds • flower buds & flowers • leaves – mesophyll tissue – veins (vascular bundles)

• Plants actively move water up their trunks.

Transport in plants • H 2 O & minerals – transport in xylem – Transpiration • Adhesion, cohesion & Evaporation • Sugars – transport in phloem – bulk flow • Gas exchange – photosynthesis • CO 2 in; O 2 out • stomates – respiration • O 2 in; CO 2 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 H 2 O potential – water flows in from xylem cells • increase in pressure due to increase in H 2 O causes flow On a plant… What’s a source…What’s a sink? can flow 1 m/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 (2 n) Anther Microsporangium Microsporocytes (2 n) Mature flower on sporophyte plant (2 n) MEIOSIS Microspore (n) Ovule with megasporangium (2 n) Generative cell Tube cell Male gametophyte (in pollen grain) Ovary Pollen grains MEIOSIS Germinating seed Stigma Megasporangium (n) Embryo (2 n) Endosperm (food supply) (3 n) Surviving megaspore (n) Seed coat (2 n) Antipodal cells Polar nuclei Synergids Egg (n) Female gametophyte (embryo sac) Pollen tube Zygote (2 n) Nucleus of developing endosperm (3 n) Egg nucleus (n) Sperm (n) FERTILIZATION Discharged sperm nuclei (n) Pollen tube Sperm Pollen tube Style

Growth of the pollen tube and double fertilization Pollen grain 1 If a pollen grain germinates, a pollen tube grows down the style toward the ovary. Polar nuclei Egg Stigma Pollen tube 2 sperm Style Ovary Ovule (containing female Gametophyte, or Embryo sac) Micropyle 2 The pollen tube discharges two sperm into the female gametophyte (embryo sac) within an ovule. 3 One sperm fertilizes the egg, forming the zygote. The other sperm combines with the two polar nuclei of the embryo sac’s large central cell, forming a triploid cell that develops into the nutritive tissue called endosperm. Ovule Polar nuclei Egg Two sperm about to be discharged Endosperm nucleus (3 n) (2 polar nuclei plus sperm) Zygote (2 n) (egg plus sperm)

Seed structure Seed coat Epicotyl Hypocotyl Radicle Cotyledons (a) Common garden bean, a eudicot with thick cotyledons. The fleshy cotyledons store food absorbed from the endosperm before the seed germinates. Seed coat Endosperm Cotyledons Epicotyl Hypocotyl Radicle (b) Castor bean, a eudicot with thin cotyledons. The narrow, membranous cotyledons (shown in edge and flat views) absorb food from the endosperm when the seed germinates. Scutellum (cotyledon) Coleoptile Coleorhiza Pericarp fused with seed coat Endosperm Epicotyl Hypocotyl Radicle (c) Maize, a monocot. Like all monocots, maize has only one cotyledon. Maize and other grasses have a large cotyledon called a scutellum. The rudimentary shoot is sheathed in a structure called the coleoptile, and the coleorhiza covers the young root.

• 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 H 2 O 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

1 st 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 p. H • 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 punctures cell membrane virus-infected cell

3 rd 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 YY Y antigen 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 Y antigenbinding site on antibody Y Y Y Y Y Antibodies • Proteins that bind to a specific antigen 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 membrane infected cell destroyed perforin punctures cell membrane target cell membrane

• Blood and filtrate move in the same direction through the nephrons of the kidney and this helps conserve energy.

Osmotic control in nephron • How is all this re-absorption achieved? – tight osmotic control to reduce the energy cost of excretion – use diffusion instead of active transport wherever possible the value of a counter current exchange system

Summary why selective reabsorption & not selective filtration? • Not filtered out – cells u proteins – remain in blood (too big) • Reabsorbed: active transport – Na+ – Cl– amino acids u glucose u • Reabsorbed: diffusion – Na+ – H 2 O u Cl– • Excreted – urea – excess H 2 O u excess solutes (glucose, salts) – toxins, drugs, “unknowns”

• Neurons are at equilibrium at resting potential.

Nervous system cells § Neuron signal direction u a nerve cell dendrites cell body § Structure fits function many entry points for signal u one path out u transmits signal u 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 Gate – 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 The rest of the dominoes fall! + + channel open – – – + + + + – – – Na+ + – – – – + + + wave

Action potential graph 40 m. V 4 30 m. V 20 m. V 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 m. V Depolarization Na+ flows in – 10 m. V 3 – 20 m. V Repolarization K+ flows out 5 – 30 m. V – 40 m. V – 50 m. V – 60 m. V – 70 m. V – 80 m. V 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 u u u synapse u u Ca++ receptor protein neurotransmitter acetylcholine (ACh) muscle cell (fiber) We switched… from an electrical signal to a chemical signal 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 u neurotransmitter degraded or reabsorbed

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 bound protein stimulates the transcription of the gene into m. RNA CYTOPLASM Testosterone binds to a receptor protein in the cytoplasm, activating it. The hormonereceptor complex enters the nucleus and binds to specific genes. DNA NUCLEUS The steroid hormone testosterone passes through the plasma membrane. New protein The m. RNA is translated into a specific protein.

LE 11 -7 b Signal molecule Signal-binding site a Helix in the membrane Signal molecule Tyrosines Tyr Tyr Tyr Tyr Tyr Receptor tyrosine kinase proteins (inactive monomers) CYTOPLASM Dimer Activated relay proteins Tyr Tyr Tyr 6 ATP Activated tyrosinekinase regions (unphosphorylated dimer) 6 ADP P Tyr Tyr Tyr P P P Fully activated receptor tyrosine-kinase (phosphorylated dimer) P P P Tyr Tyr Tyr P P P 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 c. AMP Second messenger Protein kinase A Cellular responses

LE 11 -8 Signal molecule Receptor Activated relay molecule Inactive protein kinase 1 ATP P Active protein kinase 2 Pi de ATP sca Inactive protein kinase 3 ca PP ion Pi ADP t yla or Inactive protein kinase 2 ph os Ph Active protein kinase 1 ADP Active protein kinase 3 PP Inactive protein ATP Pi PP P P ADP 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 d. N 1. 0 N dt Population size (N) 1, 500 Exponential growth K 1, 500 Logistic growth 1, 000 d. N 1. 0 N dt 1, 500 N 1, 500 0 0 5 10 Number of generations 15