SBI4U

Unit One - Biochemistry

Bonding

Ionic Bonds

  • dissociate easily in water

  • one or more electrons transferred between atoms with an electronegativity of greater than 1.7

  • results in cation and anion

  • soluble

Covalent Bonds

  • share electrons between atoms

  • three types:

    • polar

      • unequal sharing of e- pairs

      • EN between 0.41 and 1.7

      • eg. H2O

    • nonpolar

      • equal sharing of e-

      • electronegativity of less than 0.4

      • eg. H2, O2, N2, CO2, CH4

    • amphiphilic

      • some larger molecules have parts that are polar and parts that are nonpolar

      • eg. fatty acids

    • Note - like dissolves like, so polar dissolves polar, nonpolar dissolves nonpolar

Electronegativity

  • determines the strength of the bond

    • F (fluorine) has the highest EN (highest “pull” of e-)

  • has to do with the distance between valence e- and nucleus

  • even though e- are being shared, one element may have a stronger “pull”

  • can lead to the formation of polar molecules

  • the shape of molecules is related to their polarity

Intermolecular Forces (aka van der Waals Forces)

  • Hydrogen bonds

    • attractive force between a partially positively charged hydrogen atom and a partially negative charge in another molecule

    • eg. forces between water molecules

  • Other van der Waals Forces

    • weak, momentary attractions of one molecule to the nuclei of another molecule

    • eg. London dispersion forces, dipole-dipole forces

Chemical Reactions

Dehydration Reaction (aka Condensation)

  • Removal of an OH and H to join smaller molecules and make H2O

    • eg. occurs naturally in plants, including sugarcane and sugar beets, from which we refine the sugar into pure table sugar

Hydrolysis Reaction

  • Adding water as OH and H splitting a larger molecule

    • eg. happens in digestion in your stomach under the influence of the enzyme lactase

Neutralization Reaction

  • Between acids and bases to form water and salt

    • eg. digestion - pancreas releases sodium bicarbonate and it is added to the small intestine to increase pH

Redox Reaction

  • Electrons are lost from one atom and gained by another

    • eg. Aerobic Cellular Respiration: burning of fuel/glucose to produce energy

  • LEO - Lose Electrons Oxidation

  • GER - Gains Electrons Reduction

Water

Polar Covalent Bonds

  • Oxygen has a higher EN than hydrogen

Hydrogen Bonds

  • Electrons spend more time near the O than the H

Cohesion

  • Water molecules are attracted to other water molecules

Adhesion

  • Water molecules attach to other polar molecules

Capillary Action

  • Adhesion and Cohesion working together

  • Climbs inside tubules up to 90m

Surface Tension

  • Water molecules bond with their neighbours beside and below them

  • BUT there are more bonds at the surface

Lower Density Solid

  • Water expands when freezing and becomes less dense

  • This is why ice floats

  • Life persists when lakes freeze over because the ice stays on top

Spring/Autumn Turnover

  • The turnover and shifting of water throughout a body of water

  • Warm water stays on top, cold water sinks

  • Oxygenates the deep water and releases sulfurous gases

High Heat of Vaporization

  • Intenseheat and exercise may generate 1L of sweat per hour and 600 calories burned per litre of sweat evaporated

  • When sweat evaporates, it pulls the heat with it, cooling us down

High Heat Capacity

  • Large amounts of heat are required to raise the temperature of water

  • This is one of many reasons why rising ocean temperatures are so dangerous and concerning

Universal Solvent

  • Ionic and Polar substances dissolve in water

Properties Summary: (WILL BE ON THE TEST)

  • Low density solid

  • Universal solvent

  • High heat capacity

  • Heat of vaporization

  • Adhesion/cohesion

  • Capillarity

  • Surface tension

The Carbon Chemistry of Life

Carbon Chains

  • Carbon atoms are the backbone of biochemistry

  • Carbon atoms form the basis of the most complex molecules due to their ability to make 4 bonds, allowing for single, double, and triple bonds (as well as combinations of these bonds)

Functional Groups

  • Commonly found in large molecules

  • React in predictable ways

  • Include amino (NH2), carboxyl (COOH), carbonyl (CO), hydroxyl (OH), peptide (CHON), phosphate (PO4)

Macromolecules

  • Carbohydrates

  • Lipids

  • Nucleic Acids

  • Proteins

Carbohydrates

  • CHO - made up of carbon, hydrogen, and oxygen

  • Monosaccharide - Disaccharide - Polysaccharide

Monosaccharides

  • CHO 1:2:1

  • Soluble (polar alcohols - OH)

  • eg. glucose (C6H12O6), fructose

  • Energy is readily available and easily transported

Disaccharides

  • Condensation (aka dehydration) reaction occurs when two monosaccharides combine, creating a disaccharide and H2O

  • Hydrolysis uses H2O to break disaccharides back down into monosaccharides

  • Glycosidic bond

  • Transportable energy in plants and animals

  • eg. sucrose, maltose, lactose

Polysaccharides

  • Enzymes that digest α linkages can’t hydrolyze β linkages

  • The cellulose passes through the digestive tract as “insoluble fibre”

  • Many herbivores, from cows to termites, have symbiotic relationships with microbes that have enzymes to digest cellulose

Polysaccharides - structural

  • β-linkages have alternating orientation of monosaccharides

  • examples:

    • cellulose: long fibrous strings for structural support in plant cell walls

    • chitin, embedded in proteins, forms arthropod exoskeletons and is used to make strong and flexible surgial thread

Polysaccharides - storage

  • α gycosidic linkages have uniform orientation of monosaccharides

    • glycogen - glucose

  • eg. organelles called leukoplasts store energy in plant roots as starch (amylose, amylopectin)

Summary - Carbohydrates

  • Functions: energy transport and storage, structural support

  • Structure: monosaccharides - polysaccharides

  • eg. glucose, lactose, starch, glycose, cellulose

  • Functional groups: hydroxyl, carbonyls (aldehydes and ketones) (CARBONYLS ONLY SOMETIMES)

  • Gycosidic bonds

Lipids

  • CHO(P)

  • No monomers and no polymerization

  • Nonpolar (hydrophobic)

Monoglycerides - Diglycerides - Triglycerides

  • Glycerol

  • Fatty acid(s)

  • Ester bond

  • Essential unsaturated fatty acids are not synthesized in the human body and must be supplied in the diet

    • eg. Omega-3 fatty acids

      • Omega-3 fatty acids have one of their carbon-carbon double bonds at the 3rd carbon atom at the end of their carbon chain

Fat Functions

  • Store energy

  • Insulate

  • Cushioning

  • Nerve impulse transmission

Phospholipids

  • Form cell membranes

  • Amphiphilic

    • polar head (hydrophilic)

    • nonpolar tail (hydrophobic)

Other Fats

  • Messengers (hormones)

    • blood pressure

    • sexual characteristics

    • growth

  • Protection

    • waxy layer on leaves and fruit prevents invaders from entering tissue, dehydration

Summary - Lipids

  • Functions - energy storage, membranes, messengers

  • Structure - straight chains (fatty acids) and rings

  • eg. testosterone, cholesterol, beeswax

  • Functional groups - carboxyl, hydroxyl

  • Ester bonds

Nucleic Acids

  • CHONP

  • DNA - deoxyribonucleic acid

  • RNA - ribonucleic acid

Nucleodies - monomers

Bonding

  • Covalent bonds

  • Phosphodiester bonds

  • H- bonds

Proteins

  • CHON(S)

  • Amino acids (monomers) - dipeptide - polypeptide

Amino Acids

  • R group

    • 1-20

    • eg. glycine, alanine

    • Polar, nonpolar, electrically charged

Dipeptides

  • Polymerization (anabolic)

  • Condensation (catabolic)

  • Breaking apart (hydrolysis)

Protein Functions

  • Enzymes - catalyze reactions

    • eg. lactase

  • Antibodies - fight invaders

    • eg. viruses

  • Hormones - chemical messengers

    • eg. insulin

  • Hemoglobin - transports O2 in RBC

  • Movement - actin, myosin, etc.

    • muscles, cilia, flagella

  • Support - collagen, elastin, keratin

    • tendons, ligaments, hair, horns, nails, feathers, quills

  • Nutrient Storage - albumin, amandin

    • amino acids for developing plant/animal embryos

Protein Organization

  • Primary

    • sequence of amino acids coded by DNA (peptide bonds)

  • Secondary

    • α helix and β sheet (H- between polar R’s)

  • Tertiary

    • 3D shape is globular or fibrous (various bonds)

  • Quaternary

    • 2 or more polypeptides join (becomes a functional protein)

Proteins Denature

  • Nonfunctional

  • Bonding in the tertiary structure is disturbed

  • Caused by:

    • Temperature

    • pH

    • Salt concentration

Summary - Proteins

  • Functions - transport, movement, messengers

  • Structure - 20 different amino acids - polypeptides

  • eg. enzymes, hemoglobin, anitbodies, hormones

  • Functional groups - amine, carboxyl

  • Bonds - peptide

EVERYTHING ABOVE THIS POINT IS ON THE UNIT ONE QUIZ

Cell Membranes

Types of Cells

  • can be prokaryotic

    • eg. bacteria cells

  • can be eukaryotic

    • eg. plant and animal cells

Eukaryotic Cells

  • organelles are the cell parts

  • the amount of each type of organelle varies by cell type

    • eg. muscle cells contain many mitochondria

    • eg. white blood cells contain many lysosomes

    • eg. pancreatic cells that make insulin contain a lot of rough ER

The Cell Membrane

Functions

  • maintain cell shape

  • allows some things to enter/exit (semi-/selectively permeable)

  • commication with other cells

  • show cell identity

Fluid Mosaic Model

  • flexible

  • made of many different parts

  • phospholipid bilayer with protein embedded throughout

  • molecules are attracted to each other but float freely

Phospholipids

  • form a bilayer spontaneously

  • hydrophilic heads associate with water inside and outside of the cell

  • nonpolar tails form hydrophobic inner layer

Carbohydrates (part 2!!!)

  • markers that identify the cell

  • glycoproteins

    • “person specific” so the immune system can recognize “invaders”

      • eg. sometimes transplants are rejected because of these markers

  • glycolipids

    • “tissue specific” so cells stop multiplying and stay put

      • eg. metastasized tumors ignore these markers

Cholesterol

  • contributes to the fluidity of the membrane

  • reduces membrane fluidity at moderate temperatures, but at low temperatures hinders solidification

Globular Proteins

  • receptors for communication

  • transport substances in and out

  • speed up reactions

  • anchors cells and their parts

  • two types

    • integral

      • embedded in protein

    • peripheral

      • attached to surface

Fibrous Proteins

  • form a cytoskeleton to maintain cell shape

  • shape is closely tied to function

Passive Transport

  • small particles diffuse across a membrane from high concentration to low concentration until an equilibrium is reached

Osmosis

  • the diffusion of water across a membrane

Simple Diffusion

  • movement of molecules from an area of [high] to [low] across a membrane

  • small molecules (O2, CO2)

  • nonpolar molecules only (steroids, amino acids)

Facilitated Diffusion

  • requires a specific protein channel

  • moves down concentration gradient

  • requires no energy

  • large, polar molecules (glucose, fatty acids, amino acids)

  • ions require channel proteins (K+, Cl-, Na+, H+)

Solutions

  • solvent - substance that dissolves the solute (eg. water)

  • solute - substance that dissolves in the solvent

Hypotonic

  • lower concentration of solute than inside the cell

  • in animal cells, this is dangerous - the cell may burst

  • in plant cells, the cell membrane pushes against the cell wall

    • Turgor pressure increases = turgid (firm, healthy)

Hypertonic

  • higher concentration of solute than inside the cell

  • in animal cells, the cell shrinks and becomes flaccid

  • in plant cells, the cell membrane tears away from the cell wall

    • Plasmolysis - rupture of the membrane occurs, killing the cell

Isotonic

  • equal concentration of solute inside and outside of the cell

    • EQUILIBRIUM

Active Transport

  • the movement of particles from an area of low concentration to an area of high concentration (against the concentration gradient)

  • uses ATP (cell energy)

    • eg. a toxic substance outside of the cell will actively be pumped out

    • eg. micronutrients need to be brought into the cell no matter how low the concentration is

Carrier Proteins

  • certain membrane proteins use ATP (cell energy) to change their shape, allowing particles to be taken in or out against natural diffusion

Endocytosis

  • the cell membrane folds around a substance, bringing it into the cell

  • this folded membrane becomes a vacuole

  • two types

    • phagocytosis

      • cell “eating” - taking in solids

    • pinocytosis

      • cell “drinking” - taking in liquids

  • receptor-mediated endocytosis

    • substances attach to membrane receptors

    • this causes the membrane to fold inward creating a coated vessicle

      • eg. LDL (cholesterol) uptake, glucagon, prolactin, insulin, GH, LH

        • these are all hormones

Exocytosis

  • vacuoles containing wastes, to be removed or cell products (eg. proteins) for export

  • the vacuole approaches the cell membrane, fuses with it, expelling the contents

Enzymes and Energy

Enzyme

  • biological catalyst that speeds up a chemical reaction without being consumed in the reaction

Active Site

  • a pocket or groove in an enzyme that binds to a substrate

Substrate

  • a substance that is recognized by and binds to an enzyme

Anabolic Enzyme

  • pulls molecules together

Catabolic Enzyme

  • pulls molecules apart

Induced-Fit Hypothesis

Enzymes

  • are somewhat flexible, changing shape to better accommodate a substrate

  • bind to one or more substrates (enzyme - substrate complex)

  • convert the substrate(s) into one or more products

  • ready to be reused as soon as products leave the active site

  • break down between 100 and 40 million molecules per second

Activation energy is lower when enzymes are present

  • (the energy needed to start the reaction)

Cofactors and Coenzymes

  • cofactors must bind to an enzyme for it to work

  • cofactors include magnesium, manganese, iron, copper, zinc, calcium, cobalt

  • coenzymes (NAD+, NADP+, and FAD derived from vitamins) act as electron carriers

Factors Affecting Enzyme Activity

Temperature

  • enzymes @ low temperatures - inactive

  • enzymes @ high temperatures - denatured

pH

  • different enzymes have different levels of ideal pH

  • too basic or too acidic for any given enzyme results in inactivity and denaturation

Concentration

  • enzymes have a certain amount of “work” that they can do (some can break down 100 substrates per second, others can do 40 million)

Allosteric Regulation

  • Competitive Inhibitors

    • interference by a molecule (inhibitor) binding to the active site and blocking the substrates

  • Non-Competitive Inhibitors

    • a molecule bonds to another place on the enzyme causing a change in the shape of the active site

Unit Two - Cellular Respiration

Energy

Metabolism

  • Laws of thermodynamics

    • energy can be transferred and transformed, but it cannot be created or destroyed (First Law).

    • during every energy transfer or transformation, some enrgy is unusable and is often lost as heat (Second Law).

Energy of Life

  • energy stored in sugars (glucose) and other fuels (fatty acids) is needed to perform work.

  • thousands of reactions occur - catalyzed by a specific enzyme.

Food to Fuel

  • chemical energy → chemical energy

  • food → ATP

ATP

  • adenosine triphosphate

  • contains:

    • ribose

    • adenine

    • 3 phosphate groups

Using ATP

  • glucose is the primary energy source of almost all living things

  • it is the energy currency of the cell

    • small packets of “useable” energy

  • ATP → ADP+P, + energy released to drive anabolic reactions

  • ADP+P, + energy from catabolic reactions → ATP

Mitochondria

Mitochondrial Structure

  • Outer membrane - allows transport of small molecules directly in/out

    • contains transport proteins known as PORINS, which allow movement of ions

  • Inner membrane - contains a variety of enzymes such as ATP synthase

  • Cristae -folds in the inner membrane to increase surface area

  • Matrix - fluid within the mitochondrion

  • Intermembrane Space - the space between the membranes

Functions

  • Important site of cellular respiration (Kreb’s Cycle + Electron Transport Chain)

  • Hear muscle cells, liver cells, and oocytes (egg cells) contain the most mitochondria

  • Other functions:

    • role in immunity

    • calcium ion balance

    • programmed cell death

    • stem cell regulation

Mitochondrial DNA

  • The egg cell contains the mother’s mitochondria only. Sperm cell carries only the father’s DNA.

Mitochondrial Eve

  • The ancestor of all Homo sapiens sapiens

  • Your mitochondrial DNA is your mother’s mother’s mother’s mother’s…

Aerobic Cellular Respiration

Overview

  • Who

    • almost all cells (plants, animals, fungi*, protists)

  • What

    • C6H12O6 + 6O2 → 6CO2 + 6H2O + 36ATP

  • Where

    • cytoplasm and mitochondria

  • When

    • energy is needed at all times

  • How

    • chemical reactions catalyzed by enzymes

      • glycolysis

      • Oxidation of Pyruvate

      • Kreb’s Cycle (AKA Citric Acid Cycle)

      • Electron Transport Chain (ETC)

Generating ATP

1) Substrate level phosphorylation

  • occurs during glycolysis and the Kreb’s Cycle

  • requires enzyme and substrate

2) Oxidative Phosphorylation

  • using electron carriers such as NADH and FADH2

  • requires a membrane with a concentration gradient

Electron Carriers

  • coenzymes involved in redox reactions

    • NADH - nicotinamide adenine dinucleotide

    • FADH2 (electrons at a lower energy level)

  • can generate ATP!

    • NADH - 3 ATP

    • FADH2 - 2 ATP

High Energy Electrons

  • reduction reactions = gaining electrons (NADH has been reduced)

  • oxidation reactions = losing electrons (NAD+ has been oxidized)

LEO the lion says GER

- Lose Electrons Oxidation, Gains Electrons Reduction

  • the electron carriers are produced during glycolysis and the Kreb’s Cycle, then they drop off their electrons at the Electron Transport Chain

Glycolysis

  • ATP is made by substrate level phosphorylation in the cytoplasm

  • NADH made in the cytoplasm must pass electrons into mitochondria. Only 2 ATP can be generated from each of these NADH.

Oxidation of Pyruvate

  • Remember TWO pyruvate are produced during glycolysis

  • For each pyruvate:

    • a carboxyl group is removed as a CO2

    • a NAD+ is reduced to NADH

    • Coenzyme A changes the molecule to Acetyl CoA

  • Results in a total of:

    • 2 CO2

    • 2 NADH

    • 2 Acetyl CoA

Kreb’s Cycle (Citric Acid Cycle)

  • Occurs in the matrix of the mitochondria

  • For each Acetyl CoA:

    • 3 NADH

    • 1 FADH2

    • 1 CO2

  • For each glucose two Acetyl CoA have been made

  • This cycle will run twice

Electron Transport Chain (ETC)

  • each NADH generates 3 ATP

  • each FADH2 generates 2 ATP

  • oxygen drives the ETC as the ultimate e- acceptor, this results in the production of water (H2O)

Anaerobic Respiration and Fermentation

  • If no oxygen is available, cells can obtain energy through anaerobic respiration

  • Following glycolysis is the process of fermentation

Fermentation

  • Not efficient - results in far fewer ATP than aerobic respiration

  • There are two primary fermentation processes:

    • lactic acid fermentation

    • alcohol fermentation

Lactic Acid Fermentation

  • This happens in muscle cells during rapid and vigorous exercise, muscle cells may be depleted of oxygen. They then switch from respiration to fermentation

  • The pyruvate formed during glycolysis each gain a hydrogen from NADH

  • glucose → pyruvate → lactic acid and energy

  • This replaces the process of aerobic respiration so that the cell can have a continual source of energy in the absence of oxygen

  • This shift is only temporary - cells need oxygen for sustained activity

  • Vigorous exercise - lactic acid builds up in the tissue, causing a burning, painful sensation

Alcohol Fermentation

  • Occurs in yeasts, some other fungi, plants, and some bacteria

  • Pyruvate formed during glycolysis is broken down to produce alcohol and CO2 and is released (used to form ATP)

  • The pyruvate made during glycolysis loses another carbon making CO2

  • glucose → pyruvate → alcohol + carbon dioxide + energy

Controlling Metabolic Pathways - the Fate of Pyruvate

  • Aerobic respiration: pyruvate -> oxidation -> Kreb’s, products to ETC

  • Anaerobic respiration: pyruvate -> fermentation

  • After glycolysis, if needed, pyruvate can be made into:

    • lipids: pyruvate + acetyl CoA -> fatty acids + glycerol-> lipid

      • Ex. wax, oil, hormones or fat storage (when excess glucose)

    • proteins: pyruvate -> amino acids -> protein

      • Ex. enzymes, membranes

  • *** cannot make the essential amino acids we must get from our diet

Unit Two - Photosynthesis

Plant Processes

6CO2 + 6H2O → C6H12O6 + 6O2

Photosynthesis Equation

Light Reactions and Dark Reactions

  • Endothermic

  • Requires enzymes found in chloroplasts

Anabolic Reactions

  • Plants literally make their own food

  • Synthesize:

    • Proteins - enzymes, membrane transport

    • Lipids - cuticle, hormones, energy stored in seeds

    • Starches - energy stored in roots

Catabolic Reactions

  • Plant cells also need to perform cellular respiration

    • last unit — think glycolysis, Kreb’s cycle, ETC

Leaves

  • Thin

    • efficient diffusion of gases (H2O, O2, CO2)

  • Large Surface Area

    • maximizes sun exposure

  • Waxy Cuticle

    • protection

Chloroplasts, Pigments, and Light

Chloroplasts

  • Palisade mesophyll has a high concentration of chloroplasts

    • Upper layer of the mesophyll in a leaf cross section

  • Also found in guard cells

Chloroplast Structure

  • Thylakoid

    • membrane-bound sac

  • Granum

    • stack of thylakoids (pl. grana)

  • Lamella

    • joins grana together

  • Stroma

    • fluid inside the chloroplast

Light

  • Packets of energy called photons

  • Travels as waves but also acts like particles

  • Light can be transmitted, reflected, absorbed by leaves

Visible Spectrum

  • The longer the wavelength, the less energy it has

    • shorter wavelengths have more energy

  • Leaves contain an assortment of pigments to absorb a broad range of wavelenths (colours of light)

  • When photons are absorbed, the energy causes an electron to jump to a higher energy level

Absorbtion Spectrum

  • Each pigment molecule absorbs only specific wavelengths and reflects the others

Pigment Molecules

  • Hydrophilic rings

  • Hydrophobic chains (C-H) embedded in the thylakoid membrane

  • The protein must contain a specific amount of energy to be absorbed by electrons in the double bonds

Antenna Pigments

  • Increase the effective use of available energy

  • Absorb light of various wavelengths

  • Pass energy on to Chlorophyll A

Light Reactions

  • Require water

  • Produce ATP and NADPH (electron carrier), which go to the dark reactions

  • Occurs in the thylakoid membrane of chloroplasts

  • Photons of light are absorbed by pigments in Photosystem II → excited electrons from Chlorophyll A are boosted to a higher energy level and move to a protein that pumps H+ into the thylakoid using the electron’s energy → the electron arrives in Photosystem I

  • Photons of light are absorbed by PSI pigments and the boosted electron travels to Ferredoxin, then reduces NADP+ → NADPH

    • NADP+ + H+ → NADPH

  • Water (H2O) supplies electrons to PSII and releases O2

  • The concentration gradient created by pumping H+ into the thylakoid leads to the facilitated diffusion of H+ back to the stroma through ATP synthase and the production of ATP

Non-Cyclic Photophosphorylation

  • When the light reactions include both PSI and PSII, it is called non-cyclic because the electrons travel one way to NADPH and more electrons are supplied by water

    • produces ATP, NADPH

    • includes p680, p700 (pigment molecules)

    • releases O2 from H2O

Cyclic Photophosphorylation

  • PSI can function without PSII. It provides extra ATP for the dark reactions and other reactions that occur in the chloroplast

    • p700 (PSI) only

    • H+ pumped into the thylakoid

    • produces ATP

Summary:

  • Location: thylakoid (inside of the chloroplast)

  • Input: water

    • gets broken down into H+, O2, and e-

  • e- are energized by the light hitting the pigments

    • sent to NADP+ → NADPH

    • energy from e- pumps H+ across

  • ATP synthase (enzyme)

    • uses concentration gradient of H+ to assemble ADP + Pi → ATP

Dark Reactions: Calvin Cycle

  • Called the Melvin Calvin Cycle

  • Anabolic - reverse Kreb’s Cycle

  • Does not need light

  • Depends on the products of the light reactions

  • Inputs - CO2, ATP, NADPH

  • Occurs in the stroma of chloroplasts

Stages of the Dark Reactions

  • Carbon fixation

    • RuBP binds with CO2 using Rubisco (enzyme)

  • Synthesis of PGAL (aka G3P)

    • addition of ATP and NADPH

  • Regeneration of RuBP

    • addition of ATP

Calvin Cycle

  • CO2 enters the Calvin Cycle from the top right and bonds with RuBP

  • There is enough G3P made after 6 cycles to produce one glucose

    • remember G3P from glycolysis???

  • *** check diagrams for more info ***

What Happens to Glucose?

  • Can be converted to pyruvate then processed aerobically to make ATP or anaerobically to make alchol, CO2, and ATP

OR…

  • pyruvate + acetyl CoA → fatty acids + glycerol → lipid

    • ex. wax, oil, hormones

  • pyruvate → amino acids → protein

    • ex. enzymes, membranes

  • starch (energy storage)

  • cellulose (support in cell wall)

Photosynthesis Summary

  • Light Reactions

    • produced ATP

    • produced NADPH

    • consumed H2O

    • produced O2 as byproduct

  • Calvin Cycle

    • consumed CO2

    • produced G3P (used to make sugar)

    • regenerated ADP

    • regnerated NADP

Plant Adaptations (C3, C4 and CAM)

C3 Plants

  • Use light reactions and dark reactions

  • Include about 85% of plant species

    • eg. wheat, rice, barley, oats, peanuts, cotton, sugar beets, tobacco, spinach, soybeans, most trees, and lawn grasses

C4 Plants

  • Hot and dry environment

  • PEP has a higher affinity for CO2 compared to RuBP so the stomata are open for less time but maximize the capture of CO2

  • PEP + CO2 → oxaloacetate

  • Mesophyll (the site of photosynthesis) surround the vein (bundle sheath cells)

CAM Plants

  • eg. cacti

  • Hot, dry environment

  • Stomata close during the day to limit water loss when transpiration is highest

  • Only light reactions occur during the day

  • Calvin Cycle using C4 path happens at night

Leaf Adaptations

  • When a leaf lives in temperate, dry, or extremely wet conditions

Hydrophyte

  • Lacks cuticle due to abundance of moisture

  • Stomata on top

  • Leaf shape is broad and requires support

  • Sclerenchyma

  • Roots are often reduced

  • Rapid Early Shoot Growth

Xerophyte

  • Thick waxy cuticle

  • Epidermis several cells thick

  • Small leaves

  • Leaf curled and pitted

  • Extensive shallow root system

  • Spines, hairs

Rates of Photosynthesis

  • C3 plants and C4 both show an increase in photosynthetic rate as temperature rises

    • limit at roughly 40C

    • drastic decline at higher temps, likely due to denatured proteins (enzymes)

  • C3 and C4 perform equally well at high CO2 levels but C3 plants have a much lower photosynthetic rate a low levels of CO2

  • As brightness of light increase, the rate of photosynthesis also increase, unitl it reaches a maximum and plateaus.

Unit Three - Molecular Genetics

DNA Structure and Replication

DNA

  • Deoxyribonucleic Acid

  • Double Helix structure

  • Watson + Crick discovered molecular structure

  • Polymer made up of repeating subunits called nucleotides

    • made from nucleoside and phosphate

  • DNA makes proteins (that’s it)

    • this concept is called the Central Dogma

      • DNA → RNA → protein

Names to Know

  • Chromosomes

    • long strands of DNA carrying many genes

  • Sister Chromatids

    • include a chromosome and its exact duplicate after being copied in interphase

  • Chromatin

    • DNA looks stringy during interphase as it is being “used” to make proteins

  • Genes

    • segments of DNA that code for a specific trait

  • Genome

    • includes all of the genes of a species

DNA Replication

  • Semiconservative replication means that the new DNA molecules contain ½ of the old (original) DNA strand and ½ new nucleotides

  • The original DNA molecule unzips down the middle, breaking the weak hydrogen bonds that hold the base pairs (A double bonds to T, C triple bonds to G)

  • New nucleotides bond to each template strand, building in the 5’ → 3’ direction using an enzyme called DNA polymerase

  • on the leading strand replication is continuous while on the lagging strand it is done in segments, both sides following the 5’ → 3’ rule

Fixing Errors

  • DNA polymerase enzymes fix any errors by replacing a non-complimentary base (ex. T-G). Errors are found because the hydrogen bonds can’t form if they are mismatched

  • At this point, the errors are about 1 per million base pairs

  • A complex of proteins and enzymes including DNA polymerase I and II read the newly formed DNA to find these uncommon errors

  • DNA polymerase II fixes the errors by first removing the incorrect segment and then replacing it with a correct segment (ligase helps out too)

  • These repair mechanisms help correct damage caused by UV radiations and chemicals, therefore preventing loss/change in function, or cancer

Telomeres

  • Segments of DNA found at the ends of chromosomes

  • Contain repetitive pieces of non-coding DNA which get shorter each time a cell divides

  • As the length of the telomeres shorten through each cell division, the risk of damaging valuable genes along the DNA increases

Protein Synthesis

  1. Transcription

  2. Translation

Beadle + Tatum: One Gene - One Enzyme Hypothesis

  • Each gene is unique and codes for the synthesis of a single enzyme

  • Later restated as the “One Gene - One Polypeptide Hypothesis” since it is true for many proteins

Central Dogma

  • Theory that staes genetic info flows in one direction from DNA to RNA to protein

    • DNA replication

      • DNA is copied to make more DNA

    • Transcription

      • DNA is used to create new RNA

    • Translation

      • RNA is used to create new proteins

DNA → RNA → PROTEIN

  • genes are DNA sequences that code for proteins

  • DNA triplet code → mRNA codon → amino acid

RNA

  • Single stranded

  • A, U, C, G

  • Nucleus or cytoplasm

  • Small segments for a single gene

DNA

  • Double stranded

  • A, T, C, G

  • Nucleus

  • Thousands of genes for many characteristics

Transcription of DNA

  • DNA is unzipped and rezipped

  • RNA polymerase copies along the template strand

    • A pairs with U, T pairs with A

    • C and G pair with each other

Stages of Transcription

  • Initiation

    • RNA polymerase binds to a promoter (a region rich in A’s and T’s) called a TATA box (eukaryotes) or a TATAAT box (prokaryotes)

  • Elongation

    • RNA polymerase continues to build in 5’ → 3’ direction

  • Termination

    • when the RNA polymerase reaches the termination sequence, it detaches

Processing mRNA Transcript

  • Introns (non-coding regions) are removed and Exons (coding regions) are spliced together

  • Cap is placed on 5’ end while Poly A tail is attached to 3’ tail (prevents degradation in the cytoplasm)

Types of RNA

  • mRNA

    • messenger RNA

  • tRNA

    • transfer RNA

  • rRNA

    • ribosomal RNA

Translation

  • mRNA and tRNA meet in the ribosome to read the instructions for making a protein

  • Each triplet code corresponds to an amino acid in the protein

  • The genetic code has a built-in safety (several different triplets code for the same amino acid)

Ribosomes

  • Made up of protein and rRNA

  • rRNA makes the peptide bonds between amino acids to link them into a polypeptide chain

Translating the Message

  • The 1st tRNA with AUG carries Met (an amino acid) into the P-site

  • The 2nd tRNA arrives in the A-site carrying the amino acid Trp

  • tRNA anticodons match up with mRNA codons

  • A peptide bond forms between amino acids

  • The 1st tRNA leaves from the E-site while the 2nd moves to P-site as ribosome shifts along mRNA

  • New tRNA enters A-site carrying Gly

Proteins

  • When the stop codon is reached, the ribosome subunits detach from mRNA

  • The polypeptide undergoes further processing before it’s a functional protein

    • Secondary

      • hydrogen bonds forming alpha helix or beta-pleated sheet

    • Tertiary

      • 3D shape arises as globular or fibrous due to disulfide bridges, ionic bonds between charged R-groups, and folding in of nonpolar R-groups

    • Quaternary

      • more than 1 polypeptide may be needed to make a protein functional

Epigenetics

  • Epigenetics = on top of genetics

  • Chemical modifications of chromosomal DNA and/or structures that change the pattern of gene expression without altering the DNA sequence

Human DNA Structure

  • Each cell in our body contains the same DNA

  • More than 2m of DNA in each cell

  • DNA is packaged into chromosomes and tightly wrapped up to fit inside of the cell

  • Humans have 46 chromosomes

All cells contain the same DNA, but gene expression patterns are different in different cells (eg. nerve cells, RBC, fat (adipose) cells)

The Epigenome is Changeable

  • At different times in life, different genes are needed

    • e.g. puberty

  • Cells are constatntly listening for cells to change what they are doing

  • Signals come from inside the cell, neighbouring cells, or the environment

Epigenetic Signals

  • Sperm and eggs contain epigenetic tags from parents

  • Embryonic cells can become anything

  • Epigenetic memory is important because cells wouldn’t know which instructions to follow

  • Once a cell has gone down a particular path, epigenetics stops it from going back

  • Environmental signals may be direct (diet) or indirect (stress)

Nutrition and the Epigenome

  • Queen bees are genetically identical to worker bees apart from diet

  • Worker bees are sterile

  • Royal jelly results in the queen developing ovaries and a large abdomen for egg laying

DNA Winding

  • DNA is wound around histones (proteins)

  • Histones are wound around one another many times

  • DNA is condensed

Epigenetic Modifications

  • Histone modifications

  • Act to tighten or loosen DNA coils

  • Exposes or hides genes from the cell

Epigenome and Twins

  • Monozygotic twins have identical DNA sequences

  • BUT epigenomes can vary enormously

  • Over time environmental influences differ

  • The epigenome of twins diverge

Controlling Gene Expression

Regulation of Gene Expression in Eukaryotes

  • More complex because DNA is indisde the nucleus

  • Short term control

    • genes are quickly turned on or off in response to the environment and demands of the cell

  • Long term control

    • gene regulation in development and differentiation

  • Eukaryotic genes are regulated in units of protein-coding sequences and next to controlling sites

DNA Methylation

  • a biological process by which methyl groups are added to the DNA molecule

  • can change the activity of a DNA segment without changing the sequence

  • when a methyl group is in a gene promoter, it acts to repress gene transcription (turns the gene “off”)

Regulation of Gene Expression in Prokaryotes

  • prokaryote gene expression is typically regulated by an operon

  • an operon typically includes:

    • regulator gene - this codes for a DNA-binding protein that acts as a repressor

    • promoter - DNA sequence that binds RNA polymerase

    • operator - portion of DNA where an active repressor binds

    • structural genes - code for enzymes and proteins needed for the operon’s metabolic pathway

  • example - Lac Operon

Lac Operon

  • regulation of lactose metabolism

  • the repressor is normally boudn to the operator to turn “off” gene expression

  • in the presence of lactose, lactose binds to the repressor causing it to change shape so DNA polymerase can bind to the promoter to transcribe mRNA to make lactase enzymes

Mutations

  • Mutations of one or a few nucleotides can affect protein structure and function

  • Mutations aare changes in the genetic material of a cell or virus

  • Point mutations are chemical changes in just one base pair of a gene

  • The change of a singel nucleotide in a DNA template strand can lead to the production of an abnormal protein

  • If a mutation has an adverse effect on the phenotype of the organism the condition is referred to as a genetic disorder or hereditary disease

Types of Small-Scale Mutations

  • Point mutations within a gene can be divided into two general categories

    • nucleotide-pair substitutions

    • one or more nucleotide-pair insertions or deletions

  • Substitutions

    • a nucleotide-pair substitution replaces one nucleotide and its partner with another pair of nucleotides

    • silent mutations have no effect on the amino acid produced by a codon because of redundancy in the genetic code

    • missense mutations still code for an amino acid, but not the correct amino acid

    • nonsense mutations change an amino acid codon into a stop codon, nearly always leading to a nonfunctional protein

  • Insertions and Deletions

    • insertions and deletions are additions or losses of nucleotide pairs in a gene

    • these mutations have a disastrous effect on the resulting protein more often than substitutions do

    • insertion or deletion of nucleotides may alter the reading frame, producing a frameshift mutation

New Mutations and Mutagens

  • Spontaneous mutations can occur during DNA replication, recombination, or repair

  • Mutagens are physical or chemical agents that can cause mutations

Biotechnology

Genetic Engineering

  • manipulation of DNA

  • if you are going to engineer DNA and genes and organisms, then you need a set of tools to work with

Bacteria

  • unicellular prokaryotes

  • reporduce by binary fission

  • rapid growth

    • regeneration every ~20 minutes

    • 100 million colonoy overnight!

  • dominant form of life on Earth

  • incredibly diverse

Bacterial Genome

  • Single circular chromosome

    • haploid

    • naked DNA

      • no histone proteins

    • ~4 million base pairs

      • ~4300 genes

      • 1/1000 DNA in eukaryote

Transformation

  • Incorporation of foreign DNA

    • import bits of chromosomes from other bacteria

    • incorporate the DNA bits into their own chromosome

      • express new genes

      • transformation

      • form of recombination

Plasmids

  • Small supplemental circles of DNA

    • 5000 - 20,000 base pairs

    • self-replicating

  • carry extra genes

    • 2-30 genes

    • eg. genes for antibiotic resistance

  • can be exchanged between bacteria

  • can be imported from environment

How Can Plasmids Help Us?

  • A way to get genes into bacteria easily

    • insert new gene into plasmid

    • Plasmid is a vector for gene delivery

    • bacteria now expresses new gene

      • bacteria makes a new protein

  • biotechnology - plasmids are used to insert new genes into bacteria

How Do We Cut DNA?

  • Restriction enzymes

    • restriction endonucleases

    • discovered in 1960s

    • evolved in bacteria to cut up foreign DNA

      • “restricted” in the sequences they cut

      • protection against viruses and other bacteria

    • Action of Enzyme

      • cut DNA at specific sequences

        • restriciton site

      • symmetrical “palindrome”

      • produces protruding ends

        • sticky ends

        • will bind to any complementary DNA

    • Many different enzymes

      • EcoRI, HindIII, BamHI, SmaI

    • Cut DNA at specific sites

      • leave “sticky ends”

Sticky Ends

  • Cut other DNA with same enzymes

    • leave “sticky ends” on both

    • can glue DNA together at “sticky ends”

  • Overall: Sticky ends help glue genes together

Restriction Enzymes - Fighting HIV

  • Julio Montaner

    • created HAART therapy: a triple shot of restriction enzymes that attack infected cells

    • prevents the HIV virus from spreading and reducing the likelihood of AIDS

    • UN AIDS program distributes HAART therapy to reduce and treat HIV across the world

Why Mix Genes Together?

  • Gene produces protein in different organism or different individual

Copy (& Read) DNA

  • Transformation

    • insert recombinant plasmid into bacteria

    • grow recombinant bacteria in agar cultures

      • bacteria make lots of copies of plasmid

      • “cloning” the plasmid

    • production of many copies of inserted gene

    • production of “new” protein

      • transformed phenotype

  • DNA → RNA → protein → trait

Uses of Genetic Engineering

  • Genetically modified organisms (GMO)

    • enabling plants to produce new proteins

      • protect crops from insects: BT corn

        • corn produces a bacterial toxin that kills corn borer (caterpillar pest of corn)

      • extend growing season: fishberries

        • strawberries with an anti-freezing gene from flounder

      • improve quality of food: golden rice

        • rice producing vitamin A improves nutritional value

Engineered Plasmids

  • Building custom plasmids

    • restriction enzyme sites

    • antibiotic resistance genes as a selectable marker

Uses of Restriction Enzymes…

  • Now that we can cut DNA with restriction enzymes…

    • we can cut up DNA from different people, or different organisms, and compare it

    • why?

      • forensics

      • medical diagnostics

      • paternity

      • evolutionary relationships

      • etc.

Comparing Cut Up DNA

  • DNA fragments are compared by being separated by size

  • They are separated by:

    • run it through a gel

      • agarose

      • made from algae or seaweed

    • gel electrophoresis

Gel Electrophoresis

  • A method of separating DNA in a gelatin-like material using an electrical field

    • DNA is negatively charged

    • when it’s in an electrical field it moves toward the positive side

  • DNA moves in an electrical field

    • size of DNA fragment affects how far it travels

      • small pieces travel farther

      • large pieces travel slower and lag behind

Running a Gel

  • Fragments of DNA separate out based on size

  • Stain DNA

    • ethidium bromide binds to DNA

    • fluoresces under UV light

Uses: Evolutionary Relationships

  • Comparing DNA samples from different organisms to measure evolutionary relationships

Uses: Medical Diagnostic

  • Comparing normal allele to a diseased allele

    • eg. test for Huntington’s Disease

Uses: Forensics

  • Comparing DNA sample from crime scene with suspects and victim

  • DNA fingerprints

    • comparing blood samples on defendant’s clothing to determine if it belongs to the victim

      • comparing DNA banding pattern between different individuals

      • unique patterns

Unit Four - Excretory System

Introduction

Homeostasis

  • maintaining a steady internal state while the external is changing

  • receptor

    • these could detect changes in temperature, light, sound, blood pressure, salt concentration, and blood glucose (blood sugar)

  • control centre

    • this could be your brain!

  • effector

    • this could be a gland that makes a hormone or a muscle that contracts

Feedback Loops

Feedback Loops

  • Hormone signals and nerve impulses are used to communicate information from the control centre to the effectors

  • A feedback loop has three components that react to a stimulus and cause a response

Feedback Loop Components

1) A sensor or receptor must be able to detect the stimulus

  • a change in light levels or wavelength

  • a change in temperature

  • a change in sound intensity or frequency

  • a change in osmotic pressure

2) The control centre determines (with input from other systems) if a response is required

3) The effectors may include a variety of actions involving several systems

Feedback Loops

  • Negative

    • exhibits an effect that returns to steady state and response is turned off

    • similar to thermostat maintaining narrow range of temperature even as outside temperature is fluctuating

  • Positive

    • exhibits an effect that AMPLIFIES the response which is turned ON

    • similar to flicking the light on and leaving it on because it’s night

Positive Feedback

  • AUGMENTS response for continued stimulation

    • augments: make something greater by adding to it; increase

  • When the size of the baby stimulates labour and delivery, it is not a process that must be “returned to a steady state”

  • The “work” or “labour” refers to the dilation of the cervix (10 cm), which requires muscular contractions

  • Contractions must continue to be amplified gradually as the baby enters the birth canal prior to delivery

  • When babies begin to nurse, milk production is necessary to keep up with the demand

  • Suckling stimulates a feedback loop that will cause milk production and milk “let down” → therefore more stimulus, more production

  • The stimulus from the baby is sent to the hypothalamus using neurons

  • The hypothalamus tells the pituitary gland to release prolactin and oxytocin

    • prolactin: makes the mammary gland produce milk

    • oxytocin: causes milk “let down,” which releases the milk into the ducts

Thermoregulation

Thermoregulation

  • Homeotherms (aka endotherms) regulate body temperature

  • Poikilotherms (aka ectotherms) have a body temperature similar to their environment

  • Mammals have evolved to have a variety of adaptations that allow them to live in different environments

Osmoregulation

  • The process of actively regulating the osmotic pressure of bodily fluid and cells

  • Osmotic pressure - the pressure that results from a difference in water concentration (water concentration gradient) between two sides of a semi-permeable membrane

  • Across a membrane:

    • hyperosmotic = hypertonic

    • hypoosmotic = hypotonic

    • isosmotic = isotonic

Homeostasis

  • Osmoregulation keeps the organism’s water/solute levels balanced

  • Aquatic organisms need to regulate this much more since they are submersed in a watery environment

Human Excretory System

Parts of the Excretory System

Kidney - filters blood, removes waste (by producing urine), balances bodily fluids

Urinary Bladder - stores urine

Ureter - takes urine from kidneys to bladder

Urethra - takes urine out o the body from the bladder

Adrenal Gland - sends signals to balance salt/water and blood pressure

Renal Artery - takes blood to the kidney (from heart)

Renal Vein - takes blood away from the kidney (to heart)

Kidneys

  • Found just below the bottom of the ribcage by the spine

  • Consists of three layers:
    1) cortex
    2) medulla
    3) renal pelvis

  • Kidney tissue has an extensive blood supply to facilitate filtration of waste

    *look at “excretory systems diagrams” to see more*

  • Everyone has two kidneys, but you can live with just one

  • Living donor transplants

Ureter

  • Carries urine from kidneys to bladder

  • May become infected by bacteria (Urinary Tract Infection - UTI)

Bladder

  • Stores urine and releases it through a sphincter that can be consciously controlled

Urethra

  • Carries urine from bladder out of body

  • Prostate - male physiology

    • an early sign of an enlarged prostate or possibly cancer is difficulty passing urine

  • Skene glands - female physiology

Filtration

  • Waste produced from cells is collected by the blood

  • Blood is filtered by the kidneys

  • Filtrate contains both waste + valuable nutrients

Metabolic Waste

  • Uric Acid

    • produced from the breakdown of nucleic acids (DNA, RNA)

  • Urea

    • protein denaturation during metabolism

    • ammonia is toxic so it is combine with CO2 in the liver to make urea (less toxic)

    • 2NH3 + CO2 → urea

Nephron

  • Filtration

    • as blood passes through the glomerulus, small dissolved particles leak out of the capillary network and get collected by the Bowman’s Capsule

  • Reabsorption

    • the filtrate that entered the Bowman’s Capsule contains valuable substances needed by the body so active and passive transport will move these particles out of the nephron and back into the bloodstream that surrounds the proximal convoluted tubule, the Loop of Henle

  • Secretion

    • the filtrate in the distal convoluted tubule will receive more urea and uric acid from the capillaries through active transport; pH is modified as well by the movement of bicarbonate ions (HCO3-)

*see excretory system - diagrams for more

Kidney Functions

  • Water Balance

    • increase/decrease H2O output using hormone messaging

      • think ADH (comes later)

  • Blood pH Balance

    • maintain pH = 7.45 by using a bicarbonate buffer

  • Blood Pressure

    • regulates blood volume using hormone messaging

      • angiotensin, aldosterone (comes later)

Feedback Loops in the Excretory System

  1. High Na+ concentration detected in the bloodstream
    1b. the hypothalamus detects changes in osmotic pressure and signals the pituitary gland

  2. Pituitary gland (posterior lobe) stimulated to release ADH*

  3. ADH carried to kidney by the blood

  4. Increased reabsorption of water from kidney back into the bloodstream
    4b. H2O dilutes Na+ in the blood

  5. Lower Na+ concentration

This is a negative feedback loop to control water balance.

* ADH = Anti-Dieuretic Hormone (Dieuretics make you pee, so anti-dieuretics make you consere water so you don’t pee)

Regulating Blood Pressure (BP)

  • Two ways:

    • Angiotensinogen → Angiotensin → Vasoconstriction

      • Angiotensinogen is an inactive protein that is converted to active angiotensin when BP drops. Vasoconstriction will create more pressure.

    • Aldosterone → increase Na+ reabsorption → Osmosis

      • Released from the adrenal glands when BP drops

      • When more Na+ is reabsorbed from the nephron into the blood, water follows by osmosis, creating more pressure by increasing blood volume.

Regulating Blood pH

  • Our blood becomes more acidic when more CO2 from cell respiration forms carbonic acid in the blood

  • Likewise, a more acidic diet would also lower pH

  • These changes in [H+] are BUFFERED by a conjugate acid-conjugate base:

    • carbonic acid → bicarbonate ion + H+

  • This equilibrium can move to the left or right to balance pH

  • The kidneys help by removing ions from the blood so they can exit the body in the urine

Carbonic Acid/Hydrogen Carbonate Buffer System

CO2 + H2O → H2CO3 → H+ + HCO3

Carbon dioxide + water → carbonic acid → hydrogen ion → bicarbonate ion

  • CO2 carried in RBC

  • HCO3 dissolved in plasma as carbonic acid

  • CO2 dissolved in plasma

Hemodialysis

  • When our kidneys start to fail, we rely on a dialysis machine to stay alive

  • Blood is pumped into a Dialyzer

    • machine where a series of membranes filter out the metabolic waste

  • Dialyzer is filled with Dialysate Fluid

    • composed of acidified solution, bicarbonate, and purified water, as well as electrolytes

  • Dialysate balances the blood pH as well as electrolyte levels

Hemodialysis - Simplified

  • Blood removed from body

  • Blood goes through dialyzer membranes

  • Clean blood returned to the body

  • Communication system

  • 100 billion nerve cells in your brain alone

  • 2 main divisions to a vertebrate nervous system

  1. Central Nervous System (CNS)

    • Brain and spinal cord

    • Coordinating centre

  1. Peripheral Nervous System (PNS)

    • Nerves that carry info between the CNS and the rest of the organ systems

    • Somatic Nerve System:

      • voluntary (nerves you can control)

      • connected to skeletal muscles and skin

    • Autonomic Nerve System:

      • involuntary (nerves you can’t control)

      • connected to other organ systems (e.g. circulatory, digestive, respiratory)

Autonomic System

  • Sympathetic System

    • “Fight or flight” mode

      • involves cortisol and adrenaline

    • Increased heart rate, breathing rate, blood flow, blood pressure

    • Reduced digestion

    • Much harder on the body

  • Parasympathetic System

    • “Rest and digest” mode

    • Increased digestion

    • Resting HR, breathing rate, blood flow, BP

Stress

  • Activates the Sympathetic System (fight or flight)

  • Releases cortisol and epinephrine (adrenaline) - both hormones

  • Cortisol increases HR, BP, and breathing rate

  • Chronic stress leads to overactivation of the sympathetic system, wearing the body down over time

Neurons

  • Nerve cells that send electrochemical signals to each other and other parts of the body

  • A nerve is a bundle of many neurons

Reflex Arc

  • The simplest nerve pathway is called a reflex arc

  • Typically occurs in the spinal cord

  • Contains 5 essential components

    • receptor

    • sensory neuron (afferent)

    • interneuron

    • motor neuron (efferent)

    • effector

Sensory Neurons (Afferent Neurons)

  • unipolar

  • carry impulses from sensory receptors to CNS

    • e.g. photoreceptors in eyes (light), thermoreceptors in skin

Motor Neurons (Efferent Neurons)

  • multipolar

  • carry impulses from the CNS to effectors (muscles, organs, glands… AKA things that produce a response)

Interneurons

  • bipolar

  • connects sensory and motor neurons (found mostly in the CNS)

Nervous System - Communication

Nerve Cell Anatomy

  • Cell body

    • nucleus and majority of cytoplasm

  • Dendrites

    • projections of cytoplam that carry impulses toward the cell body

  • Axon

    • extension of cytoplasm that carries nerve impulses away from the cell body

  • Axon Terminal

    • impulses end and chemical is released

  • Myelin Sheath

    • insulated covering (fatty protein) over the axon of some nerves, “myelinated”

      • prevents loss of charge

  • Nodes of Ranvier

    • regularly occuring gaps between sections of the Myelin Sheath

Signal Transmission

  • Nerve impulses jump from one node to another - increases speed of the impulse

    • non-myelinated nerves carry impulses at a slower rate

    • axon diameter also effects speed

      • narrower = faster

  • Neurons in the brain have less myelination on the axons than those located in the spinal cord

    • axons in spinal cord are longer and therefore the signal needs to travel faster

  • Mass of less-myelinated neurons - gray matter - found mostly in the brain and inner section of the spinal cord

  • Mass of highly-myelinated neurons - white matter - found mostly in the peripheral NS (nerve system) and outer section of the spinal cord

Action Potential

  • Firing an action potential is an “all-or-none” response to a stimulus that has reached the THRESHOLD POTENTIAL

  • Threshold examples:

    • “just enough” pressure change on the skin

    • “just enough” temperature change to notice

  • If the threshold is not reached, the neuron does not fire an action potenital; even if there is a stimulus, it’s just not enough

Sodium Potassium Pump

  • Neurons maintain a resting potential by constantly moving Na+ out and K+ across the concentration gradient

  • When the threshold is reached, the cell opens Na+ channels and as those ions rush in, the cell is depolarizing

Neuron Communication

  • Once the electrical imulse reaches the axon terminal and hits the threshold, it releases chemicals called neurotransmitters

  • Neurotransmitter moves across the synapse

    • gap between the axon terminal of one neuron and the dendrite of another neuron

  • Neurotransmitters will bind to receptors of dendrites - when enough bind to receptors, it starts the action potential

Neurotransmitters

  • Acetylcholine

    • sent from motor neurons to the muscle and tissue

  • Glutamate

  • GABA

  • Dopamine

    • responsible for motor function, learning and memory, addiction

  • Serotonin

    • associated with happiness and pleasure

  • Epinephrine

  • Norepinephrine

SSRIs

  • Selective Serotonin Reuptake Inhibitors

  • Antidepressant and anit-anxiety medication

  • Prevents serotonin from going back to the axon terminal from the synapse

  • Allows serotonin to bind to receptor multiple times, eliciting more pleasure and happy feeling

Unit Four - Nervous and Endocrine Systems

Nervous System

  • Communication system

  • 100 billion nerve cells in your brain alone

  • 2 main divisions to a vertebrate nervous system

  1. Central Nervous System (CNS)

    • Brain and spinal cord

    • Coordinating centre

  1. Peripheral Nervous System (PNS)

    • Nerves that carry info between the CNS and the rest of the organ systems

    • Somatic Nerve System:

      • voluntary (nerves you can control)

      • connected to skeletal muscles and skin

    • Autonomic Nerve System:

      • involuntary (nerves you can’t control)

      • connected to other organ systems (e.g. circulatory, digestive, respiratory)

Autonomic System

  • Sympathetic System

    • “Fight or flight” mode

      • involves cortisol and adrenaline

    • Increased heart rate, breathing rate, blood flow, blood pressure

    • Reduced digestion

    • Much harder on the body

  • Parasympathetic System

    • “Rest and digest” mode

    • Increased digestion

    • Resting HR, breathing rate, blood flow, BP

Stress

  • Activates the Sympathetic System (fight or flight)

  • Releases cortisol and epinephrine (adrenaline) - both hormones

  • Cortisol increases HR, BP, and breathing rate

  • Chronic stress leads to overactivation of the sympathetic system, wearing the body down over time

Neurons

  • Nerve cells that send electrochemical signals to each other and other parts of the body

  • A nerve is a bundle of many neurons

Reflex Arc

  • The simplest nerve pathway is called a reflex arc

  • Typically occurs in the spinal cord

  • Contains 5 essential components

    • receptor

    • sensory neuron (afferent)

    • interneuron

    • motor neuron (efferent)

    • effector

Sensory Neurons (Afferent Neurons)

  • unipolar

  • carry impulses from sensory receptors to CNS

    • e.g. photoreceptors in eyes (light), thermoreceptors in skin

Motor Neurons (Efferent Neurons)

  • multipolar

  • carry impulses from the CNS to effectors (muscles, organs, glands… AKA things that produce a response)

Interneurons

  • bipolar

  • connects sensory and motor neurons (found mostly in the CNS)

Nervous System - Communication

Nerve Cell Anatomy

  • Cell body

    • nucleus and majority of cytoplasm

  • Dendrites

    • projections of cytoplam that carry impulses toward the cell body

  • Axon

    • extension of cytoplasm that carries nerve impulses away from the cell body

  • Axon Terminal

    • impulses end and chemical is released

  • Myelin Sheath

    • insulated covering (fatty protein) over the axon of some nerves, “myelinated”

      • prevents loss of charge

  • Nodes of Ranvier

    • regularly occuring gaps between sections of the Myelin Sheath

Signal Transmission

  • Nerve impulses jump from one node to another - increases speed of the impulse

    • non-myelinated nerves carry impulses at a slower rate

    • axon diameter also effects speed

      • narrower = faster

  • Neurons in the brain have less myelination on the axons than those located in the spinal cord

    • axons in spinal cord are longer and therefore the signal needs to travel faster

  • Mass of less-myelinated neurons - gray matter - found mostly in the brain and inner section of the spinal cord

  • Mass of highly-myelinated neurons - white matter - found mostly in the peripheral NS (nerve system) and outer section of the spinal cord

Action Potential

  • Firing an action potential is an “all-or-none” response to a stimulus that has reached the THRESHOLD POTENTIAL

  • Threshold examples:

    • “just enough” pressure change on the skin

    • “just enough” temperature change to notice

  • If the threshold is not reached, the neuron does not fire an action potenital; even if there is a stimulus, it’s just not enough

Sodium Potassium Pump

  • Neurons maintain a resting potential by constantly moving Na+ out and K+ across the concentration gradient

  • When the threshold is reached, the cell opens Na+ channels and as those ions rush in, the cell is depolarizing

Neuron Communication

  • Once the electrical imulse reaches the axon terminal and hits the threshold, it releases chemicals called neurotransmitters

  • Neurotransmitter moves across the synapse

    • gap between the axon terminal of one neuron and the dendrite of another neuron

  • Neurotransmitters will bind to receptors of dendrites - when enough bind to receptors, it starts the action potential

Neurotransmitters

  • Acetylcholine

    • sent from motor neurons to the muscle and tissue

  • Glutamate

  • GABA

  • Dopamine

    • responsible for motor function, learning and memory, addiction

  • Serotonin

    • associated with happiness and pleasure

  • Epinephrine

  • Norepinephrine

SSRIs

  • Selective Serotonin Reuptake Inhibitors

  • Antidepressant and anit-anxiety medication

  • Prevents serotonin from going back to the axon terminal from the synapse

  • Allows serotonin to bind to receptor multiple times, eliciting more pleasure and happy feeling

The Brain

  • Composed of three main parts

    • cerebrum (forebrain)

    • cerebellum (hindbrain)

      • controls fine motor coordination

    • brainstem

      • connects brain to spinal cord

        • Medulla Oblongata - controls circulatory and respiratory system

Cerebrum

  • Composed of grey matter

  • The folds (fissures) create more surface area

    • allows faster and greater neural activity (more communication between neurons)

  • Most neural activity of the cerebrum occurs on the surface

  • Corpus Callosum

    • highway of axons that allows the left and right hemispheres to communicate

Lobes of the Cerebrum

  • Frontal Lobe

    • contains prefrontal cortex and motor cortex

  • Parietal Lobe

    • contains primary sensory cortex

  • Occipital Lobe

  • Temporal Lobe

Parts of the Cerebrum

  • Prefrontal Cortex

    • in front of frontal lobe

    • in charge of all planning, decision making, goal setting, time management

    • develops during high school

    • fully develops around age 18

  • Motor Cortex

    • coarse motor movement

  • Sensory Cortex

    • tactile (touch)

  • Frontal Lobe

    • thinking, personality, consciousness, inhibition

  • Temporal Lobe

    • long term memory, hearing

  • Parietal Lobe

    • sensory centre, where all sensory input is processed

  • Occipital Lobe

    • vision

Limbic System

  • AKA the Primitive Brain

  • Composed of white matter

  • Thalamus

    • relays sensory signals, regulates consciousness

  • Hypothalamus

    • controls all needs and processes requiring hormones including: thirst, huger, sleep, BP, fight or flight, sugar intake

  • Pituitary Gland

    • receives signal from hypothalamus to release hormones to regulate endocrine system

  • Hippocampus

    • short-term memory processing, spatial memory

  • Amygdala

    • emotional centre

What Protects the Brain?

  • Skull

    • first line of protection, composed of bone

  • Meninges

    • two membranes filled with cerebrospinal fluid

    • hold the brain and spinal cord in place, act as shock absorber

  • Blood-Brain Barrier

    • thin membrane between blood vessels and the brain

    • only water and small molecules like glucose and ions get through

    • keeps out substances that would be harmful to the brain

Concussions and CTE

Concussion

  • Traumatic force causes the brain to hit or bounce against the skull

  • Leads to shearing of the axons in the affected areas

  • Can have long-term effects

Chronic Traumatic Encephalopathy (CTE)

  • Caused by repeated traumatic blows to the head over a long period of time

  • Brain slowly degenerates over a long period of time

  • Changes to personality, mood swings, and memory loss

  • Can lead to dementia and early death

Vision

Parts of the Eye

  • Sclera

    • tough outer layer

  • Cornea

    • protects the eye and redirects light into the eye

  • Pupil

    • opening for light

  • Lens

    • thickens for “near” focus and flattens for “far” focus (made of protein that becomes cloudy with age - cataracts)

  • Iris

    • controls the amount of light entering the pupil

  • Retina

    • photoreceptor layer (rods and cones)

  • Macula

    • part of the retina that contains most of the cones

  • Optic Disk

    • optic nerve and blood vessels exit eyeball and there are no photoreceptors (blind spot - brain fills in the picture)

Note: the eye uses Rapid Eye Movement to determine changes in picture

The Retina

  • Photoreceptors are found in the retina

  • Rods - detect low levels of light, night vision

  • Cones - detect different wavelengths or colours, fine detail

    • detects Red, Blue, Green light

    • 6 million cone receptors

  • Sends signals along optic nerve

Vision

  • Optic nerve sends sensory input from the eye to the occipital lobe where it is processed

Hearing

Outer Ear

  • Pinna direct sound waves into ear canal

  • Sound waves vibrate the tympanic membrane (eardrum)

Middle Ear

  • Vibrations of sound are amplified by 3 tiny bones called with ossicles which tap on the cochlea

    • Ossicles:

      • hammer

      • anvil

      • stirrup

Inner Ear

  • Cochlea - spiral-shaped organ filled with fluid

    • vibration from the ossicles virbates the fluid inside and activates hair cells

    • the further the vibration goes in the cochlea, the higher the frequency of sound

    • input from the hair cells is sent to the auditory nerve

    • fluid in the cochlea also detects and determines your balance

Hearing

  • The auditory nerve sends sensory input from the cochlea to the auditory cortex in the temporal lobe where it is processed

Tinnitus

  • May be caused from damage to cochlea

  • Neurons will produce this noise if it does not detect a stimulus

Touch

  • Mechanoreceptors pick up touch stimulus

  • It is sent to sensory neurons which send signals to the spinal cord

  • The signal travels up the spinal cord to the thalamus which redirects the signal to the Primary Sensory Cortex

Homunculus

  • Map/model of where the most neurons are located in the body (LOTS in face, lips, HANDS)

Phantom Limb Syndrome

  • When amputees loose limbs, the signal to those dedicated neurons in the cortex disappears

  • To prevent itself from dying the neuron will connect to neurons belonging to another body part

  • Amputees can still feel their missing limb if they touch the other body part

Endocrine System

  • Hormones send messages throughout your body

  • The signal can establish a slow and sustained response to a stimulus

    • When would you want a slow and sustained response?

      • Going through a growth spurt, puberty

      • Breastfeeding baby

      • Responding to long term stressors

Glands

  • A gland is an organ which produces and releases substances that perform a specific function in the body

Hormones

  • Endocrine glands are ductless which means they secrete hormones directly into the bloodstream to be transported to target cells

  • Hormones from secreting cells (in glands) only bind to receptors on target cells. They will have no effect on other cells.

  • Chemical messengers (protein or steroid)

  • Participate in feedback loops

  • Stimulate or inhibit an action in the target or effector

    • secretion

    • synthesis

    • contraction

    • import/export

Protein Hormones

  • Water soluble

  • Travels in plasma to cell membrane

  • Attaches to receptor

  • Does not go through membrane

Steroid Hormones

  • Insoluble (because it’s a lipid)

  • Travels with protein (carrier) in plasma

  • Diffuses through cell membrane

Pancreas

  • Sugar regulation

    • Islets of Langerhans contain alpha and beta cells

    • beta cells secrete insulin

    • alpha cells secrete glucagon

  • When blood glucose is high, insulin increases glucose uptake into cells and stores glucose in the liver as glycogen

  • When blood glucose drops, glucagon releases glucose from storage (liver, muscles)

Thyroid and Parathyroid Gland

Calcium regulation

  • Calcitonin, secreted from the thyroid, causes the storage of calcium in the bones while parathyroid hormone prompts its release from storage where needed (for nerve and muscle functions)

  • Osteoporosis is a result of depleted bone density and leads to frequent fractures, affecting both men and women

The Master Gland

  • The pituitary gland is called the master gland because it sends out a wide variety of messages

  • The hypothalamus tells the pituitary gland what to do.

Pituitary Gland

  • The hypothalamus controls hormone secretion from the pituitary gland

    • Anterior Pituitary

      • receives releasing factors from hypothalamus, responds by secreting hormones

    • Posterior Pituitary

      • receives nerve signals from hypothalamus, causing it to release hormones

Thyroid Gland

  • Thyroid stimulating hormone from the pituitary stimulates secretion of thyroxine to increase metabolic rate

  • Hypothyroidism

    • not enough thyroxine released; makes you cold, tired, depressed, constipated, weight gain

  • Hyperthyroidism (Graves’ Disease)

    • thyroxine level is too high; autoimmune disease; enlarged thyroid (goiters), lacking iodine in diet, weight loss, warm, energetic

Growth Hormone

  • Regulation of growth and development

  • Released from anterior pituitary

  • Stimulates growth and development of tissues (bone and muscle)

  • Metabolism increases → protein synthesis increases for making the building blocks of cells

  • Rate of mitosis increases

Melanocyte Stimulating Hormone

  • Response to sunlight

  • Exposure to sunlight is the stimulus for MSH production and secretion from the anterior pituitary

  • Pigmentation provides protection from UV radiation which is a contributing factor in the development of skin cancer

ACTH

  • Sent from pituitary to adrenal glands in times of stress

  • Responses to stress (fight or flight)

    • Norepinephrine (=noradrenaline)

    • Epinephrine (=adrenaline)

      • Increased HR and BP, breathing rate and volume, bronchioles and pupils dialate, peristalsis slows, insulin is suppressed

    • Cortisol

      • reassigns energy partitioning to deal with stressors

      • negatively impacts immunity, mental health, physical breakdown of cells