AP Biology Notes

Unit 1: Chemistry of Life

Unit 2: Cell Structure and Function

Unit 3: Cellular Energetics

Unit 4: Cell Communication and Cell Cycle

Unit 5: Heredity

Unit 6: Gene Expression and Regulation

Unit 7: Natural Selection

Unit 8: Ecology

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Unit 3: Cellular Energetics

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Enzymes

Extracellular Components

Extracellular components and connections between cells help coordinate cellular activities

Most cells synthesize and secrete materials that are external to the plasma membrane

These extracellular (outside plasma membrane) structures include

Cell walls of plants- major structural component of plant cells made of cellulose, also found in prokaryotes, protists and fungi (peptidoglycan)

Cell wall protects the plant cell, maintains its shape and prevents excessive uptake of water

Plant cell walls are made of cellulose fibers embedded in other polysaccharides and proteins

Layers

Thin Flexible Primary Cell Wall

Thick Secondary Cell Wall

In between plasma membrane and primary wall gives structural integrity

Middle lamella - material between cell walls

Plasmodesmatagaps in cell wall allowing for communication and movement of things between plant cells, rigid cell walls are restrictive unlike permeable membranes

Extracellular matrix (ECM) of animal cells instead of cell walls

Series of glycoproteins such as collagen (major), proteoglycans, and fibronectin make up ECM

Fibronectin connects collagen to integrin

Proteoglycans perform adhesion (glue)

Proteins bind to receptor proteins in the plasma membrane called integrins

Functions

Support

Adhesion

Movement

Regulation

Intercellular junctions physically connect cells, adhere interact or communicate through direct contact

Types

Plasmodesmatagap-like channels that perforate cell walls

Tight Junctions membranes of neighboring cells are pressed together preventing leakage of extracellular fluid in between cells (in stomach)

Desmosomes (anchoring junctions) fasten cells together into strong sheets--strongest function (muscle cells)

Gap junctions (communicating junctions) provide cytoplasmic channels between adjacent cells (heart cells), enable multiple cells to act as one

Photosynthesis

The most important reaction in all of nature, makes food

Converts solar energy into chemical energy

Directly and indirectly nourishes all living things

Autotrophs/Producers - organisms that produce their own food through photosynthesis

Algae (protist, eukaryotic organism), plants, cyanobacteria - first living organisms to perform photosynthesis

Heterotrophs/Consumers - must eat in order to obtain energy, eating products of photosynthesis

Energy (light, invested energy) + 6CO2 + 6H2O → C6H12O6 + O2

Opposite of cell respiration (which is exergonic, produces ATP), photosynthesis is endergonic

Water is oxidized to O2, CO2 is reduced → glucose

Photosynthetic part of a plant (organ): Leaf

Holes in leaf: stomata, where water evaporates (transpiration) and CO2 enters and O2 leaves

Creates transpirational pull from roots

Xylem are cells that water travels through

Plants want water to evaporate out of the plants, no transpirational pull without evaporation

Plant would dehydrate if too much water evaporated, need to balance transpiration

Increase transpiration and dehydration

Heat (temperature)

Dryness (humidity)

Wind

PHOTORESPIRATION

STOMATA CLOSE to balance out environment with the guard cells

Calvin Cycle cannot occur (no CO2) can’t make sugar

RuBisCo can ALSO fix O2 to RuBP in place of CO2 → cant produce G3P

Wastes NADPH and ATP

C3 Plants make 3-Carbon compound, PGA in the calvin cycle

C4 Plants live in dry conditions (midwest), have adaptations to prevent photorespiration → STORE CARBON DIOXIDE

Doesnt matter if stomata are closed or open

Used stored CO2,

C4 Plant

Uses enzyme PEP Carboxylase → pulls in CO2 stores carbon as 4 carbon molecule Oxaloacetate

Calvin cycle takes place in Bundle-sheath cell, but still have mesophyll cells

CAM Plant - the extremes (cacti, desert plants)

Store carbon as crassulacean acid, organic acid

CAM Plant opens stomata at night (when it cools down)

More stomata on bottom, if more on top plant would dehydrate

Guard cells: flank stomata, control if stomata are open, closed, where gasses enter and leave, (O2/CO2), water can evaporate out of the stomata → transpiration (transpirational pull)

Mesophyll- part of a leaf that contains lots of photosynthetic cells

Cells contain chloroplast - double membrane, inside are pancake shaped discs called thylakoids, and stacks of thylakoids = granum

Fluid in membrane outside thylakoids called stroma

Two reactions:

Light Reactions - light (photo) inside the thylakoids

NADP+ and ADP + P, take H2O and oxidize it, produce NADPH, and ATP, O2 as a byproduct,

Light to make ATP - photophosphorylation

Calvin cycle (The Dark Reactions)- synthesis (builds molecule) inside stroma

Major reactant in cycle: CO2 reduced and given electrons/protons, creates glucose, given by NADPH gives CO2 the electrons/protons. Electrons - energy

Purpose of producing glucose?

Glucose is used for everything:

Sugar → cell respiration, used to make ATP to grow plant

Sugar = structure, cellulose (long chain of glucose)

Sugar = energy storage, starch

Light - electromagnetic radiation

Shorter wavelength -- high energy (UV, gamma, X ray)

Longer wavelength -- low energy (infared microwaves, radiowaves)

Different colors correspond with different wavelengths, visible light in the middle of spectrum

Chlorophyll a is the main photosynthetic pigment

Accessory pigments such as chlorophyll b broaden the spectrum used in photosynthesis

Xanthophylls - yellow

Carotenoids - orange

Reflect (bounce off) vs Transmitting (go through)

No light is absorbed by cell

Green light cannot be used by plant, would die

Plants absorb red and blue light the best

Color of sky depends on molecular composition of atmosphere

Spectrophotometer - put sample of light in, tells level of transmittance or absorption

Shoot green light through chlorophyll, high transmittance (low absorption)

Shoot blue light through chlorophyll, low transmittance (high absorption)

Absorption Spectrum - graph plotting a pigment’s light absorption versus wavelength

Larger spectrums,

Action Spectrum - profiles the relative effectiveness of different wavelengths of radiation in driving a process, totality of spectrums

Pigment - molecule that will absorb or reflect a wavelength

Color determined by what it reflects

Trees go dormant in winter, chlorophyll dies, only see carotenoids and xanthophylls (yellow + orange), not enough sunlight

Engelmann’s Experiment

Grew algae under different wavelengths

Grew aerobic bacteria on top of the algae, large growth on opposite sides of spectrum, none in green because algae isn’t photosynthesizing there

Plants not black because would absorb every wavelength, overheat, proteins denature

Chlorophyll has a Magnesium center (a vs. b has difference of one func. group)

Mg holds on to electrons, electrons from water and NADPH

Accepts unit of light - photon, excites electron, gives power to electron

Cellular Respiration

Alcohol fermentation (yeast)

Pyruvate converted to ethanol (2 carbon, releases CO2)

Brain cells = purely aerobic

Obligate anaerobes = die in the presence of O2 (bacteria), carry out fermentation/anerobic respiration

Denitrifying bacteria

Anaerobic respiration: use sulfates as final electron activity instead of O2 and substrate level phosphorylation not the electron transport chain

Glycolysis

Oldest process

Before mitochondria, glycolysis took place

Oldest prokaryotes used this for energy

Cell respiration

Regulated by feedback inhibition

When ATP builds up, pathway is turned off

Utilizes allosteric enzymes

Turns off Phosphofructokinase (first enzyme in pathway)

AMP turns back on, forces pathway on

Fats and proteins can also be used in cellular respiration (triglycerides), not just glucose and carbohydrates

Fats provide more energy than carbohydrates, therefore more ATP

Glycerol (3 carbon molecule) and three fatty acids

Monomers of fatty acids/glycerol can enter cellular respiration

Glycerol has the same amount of carbons as a glucose pyruvate, enters process at pyruvate oxidation no need for glycolysis, more energy

Beta Oxidation

Fatty acids from lipids need to break down long chains of carbons in order to enter cellular respiration

Breaks the fatty acid chain and breaks it down into two-carbon molecules

Feeds directly into the Kreb Cycle

If you don’t have enough carbs or lipids, or too much protein, protein can be used in cellular respiration

Proteins have an atom that cannot enter cellular respiration, have to get rid of nitrogen in order to enter, stomach and small intestines break down proteins into amino acids

The amino acids can go into cellular respiration

Deamination

The process by which the amino group (NH2) leaves the amino acid to enter cell respiration

Amino acid can enter multiple levels of the cellular respiration

Cellular Respiration refers to both aerobic and anerobic respiration but is mainly the aerobic respiration

Respiration usually tracked with glucose because it starts at the first step

Fermentation partial degradation of sugars that occur without O2

Keeps pyruvate happening?

Aerobic respiration consumes organic molecules and O2 and yields ATP

Anerobic Respiration similar to aerobic respiration but consumes compounds other than O2

Glycolysis occurs whether or not O2 is present

PLANTS

All plants evolved from a type of green algae called carophycenes, but modern plants are different (derived character) they can live on land

Evolutionary History: chronologically

Bryophytes: mosses, first group to evolve

Pteridophyta: ferns

Vascular Tissue: next derived character (xylem= water transport, phloem=sugar transport)

Evolution of Seed Plants: (MAJOR)adaptation that allows plants to no longer rely on water to reproduce → reproduce on land more

Gymnosperms: use cones as a reproductive structure, rely on wind to carry pollen from cone to cone

Angiosperms (flowering plants): produce flowers (reproductive structure)

Alternation of Generations:

Every generation plants flip between haploid to diploid and then back

Sporophyte: (2n) goes through meiosis to make haploid spores

Gametophyte: (n) goes through mitosis to make gametes, create a diploid zygote

In ANGIOSPERMS, the sporophyte version is dominant whereas the gametophyte is extremely reduced

The Flower: used to reproduce in angiosperms, help from animals, wind, and insects to transport pollen, brightly colored to attract other animals/bugs to it

Nectar: sugary substance produced by flowers to attract birds and bees to consume, the pollen will stick to the animals so pollen can go from plant to plant

Contains both male and female reproductive parts (lilies) but most flowers are either male or female

Stamen: male reproductive part

Anther: structure that produces pollen, flower is the sporophyte, whereas pollen produced has two male gametophytes (sperm)

Filament: long stalk that comes out of the anther

Carpel (pistil): female reproductive part

Stigma: sticky part where pollens gets stuck (top)

Style: long tube that connects to the ovary

Ovary: contains the ovule (inner structure) which produces/contains the female gametophyte (egg)

Contains a lot of a small eggs, but one big giant egg with polar nuclei (two nuclei)

Sepals: leaves beneath the flower

Petals: colored part to attract organisms with pollen

Cross-Pollination: gives genetic variation, pollen of one flower goes to the carpel of another flower

Self-Pollination: staying within the same flower anther sperm goes directly into the stigma, no genetic variation → can survive on its own without other individuals in the population (e.g. polyploidy)

Double-Fertilization: (used in angiosperms) pollen goes from male anther to female stigma, it grows a pollen tube down the style into the ovary into the ovule

Essentially, two sperm from pollen enter the ovary and fertilize two eggs

One egg in ovule (big one) contains two nuclei (polar nuclei), two sperm (from pollen) go down the tube and into the ovule, one sperm will fertilize one egg to make a zygote. The other will fertilize the big egg, to have three nuclei (triploid → endosperm, functions as a food source for the developing embryo. The Ovule becomes a seed with the endosperm and embryo. The ovary around the seed becomes a fruit

Fruit: mature ovary used to disperse seeds (sporophyte embryos)

Fruit is made to taste good so herbivores eat fruit, they cannot digest seed, so they poop out seeds everywhere, seed gets fertilizer to grow into a new plant

You eat the endosperm which is the nutritious part of the nut/seed

Any type of flowering plant produces some sort of fruit

Embryo Development:

Germination occurs when mitosis of the seed occurs (begins to grow)

Cotyledons: first seed leaves upon germination

Monocot: one leaf (smaller angiosperms, orchids, grasses, lilies) VEINS RUN PARALLEL, with fibrous root systems, cannot grow that big without a lot of support

Dicots: two leaves, bigger angiosperms, has central tap roots to grow big, branching veins in leaves (maple trees, sunflowers, beans, etc.) BRANCHING VEINS

These are the two distinct and different types of angiosperms

Nitrogen: needed to make nucleic acids and proteins

Atmospheric N2 is the greatest nitrogen reservoir, but can’t do anything with that, you need to convert it

Nitrogen-fixing Bacteria: take in N2 and convert it into ammonium (NH4)

Ammonifying Bacteria (detritivores):break down dead organisms (humus) and convert it into ammonium

Nitrifying Bacteria: convert ammonium into nitrates (NO3)

The plants can accept the nitrates and use those to build macromolecules

Nitrates are the key ingredient in fertilizer to nourish plants

Roots have lots of hair things to increase surface area for rate of exchange

Transport: movement of materials in a plant

Cell Level: nutrients from soil -> roots

Depends on water potential (ONLY USED TO MOVE WATER IN PLANTS, everywhere else it only depends on osmosis/diffusion) (pressure potential + solute potential)

The lowest the pressure can be is 0, the highest the solute potential can be is 0 (pressure is nonnegative, the solute is nonpositive)

Solute potential = -iCRT, C= concentration of solutes/molarity, more solute you have the more negative the potential becomes

Plant roots have lots and lots of sugar → really low water potential (0 pressure and high positive amount of solute), TAKES IN WATER

Since plant roots have low potential, roots will absorb water from the environment, soil has no pressure, and some low solute content, higher water potential in the soil (water moves high → low potential) so the water will move into the roots

Roots will gain pressure from the water, until the water potential on the outside EQUALs the pressure on the inside, (not when the pressure is 0 necessarily) so you add a specific amount of pressure to the roots to get the same water potential

Turgor Pressure: BEGINS movement of water up the plant that builds up in the roots forces the water up from this initial transaction

Xylem: system of tubes water moves up

Transpirational Pull (evaporation): FINISHES movement of water up the plant; pulls water through and up the plant, also works through cohesion (water stuck to water) and adhesion (water stuck to other things) as the top water molecules are pulled out the stomata, and pull up the rest through hydrogen bonding

Stomata: holes in leaves where water leaves that can open and close

Guard Cells: can open and/or close stomata

What causes an increase in transpiration rate (bad too much water loss):

Higher temperatures

Arid/dryer conditions

***Wind

→ causes guard cells to close stomata to preserve water

If O2 enters the calvin cycle instead of carbon dioxide will cause photorespiration (but C4 and CAM plants can store carbon dioxide)

Short distance: water from roots into xylem tubes (turgor pressure), or sugar from leaves into phloem (active transport)

Long distance: movement of water in xylem or sugar in phloem (sugar goes down to the roots to decrease water potential, but is built in the leaves through photosynthesis), phloem and xylem run side by side

Bulk Flow/Pressure flow/Translocation: water diffuses into phloem pushes sugar down using pressure into the roots

Xerophytes: desert plants that have adaptations for arid conditions (extreme CAM plants)

Only open stomata at night

Store water inside of them

Cacti needles are leaves without surface area, prevents water from evaporating as much (and protection from eaters)

Thick cuticle: feels waxy because the wax prevents water loss (wax = hydrophobic)

Stomata are always on the bottom of the leaves to prevent water loss

Plant Defenses/Immune Systems against Herbivores: physical and chemical defenses to prevent eating

Physical: thorns, trichomes (irritating hair things), prevent them from being eaten

Chemical: (poison ivy) release toxins

Chemicals in the saliva of an eating caterpillar causes a signal transduction pathway in the plant, plant releases volatile attractants to attract parasitoid wasps to kill the caterpillars and reproduce in them

Plant Defenses/Immune Systems against Pathogens: against organisms that can infect the plant

Virulent Pathogen: (viral lytic cycle) would kill the plant entirely

Avirulent Pathogen: the plant has a chance to defend itself and live (THIS defense system only works for this type of pathogen)

Gene-for-gene recognition:

R-genes: code for R-proteins that can activate plant immune system

Hypersensitive Response: causes cell and tissue death near the infection site → LOCALIZED, not across the entire plant, kill everything that is infected to save the rest of the plant, create changes in the cell wall of plant cells to confine the pathogen

Produced chemicals that can kill the specific pathogen

Systemic Acquired Resistance: spreads across the ENTIRE plant, causing the plant to become resistant to the virus (long term).

Salicylic Acid: chemical ligand that initiates SAR, (aspirin), spreads throughout the entire plant to make plant immune to that specific pathogen

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