Copy of General Biology I

✅ 01: Biology & Learning

01: Biology & Learning

Tuesday, September 2

I. Memory and Learning

→ CC types of memory

→SEQ process of memory formation and learning

→SEQ long-term potentiation

II. Workshop Organization

→ SEQ workshop components

I. Memory and Learning

A. Nervous System

Consists of circuits or neurons and supporting cells

B. Nerve Plasticity

Ability of the nervous system to be modified after birth

Brain is dynamic → can be remodeled

Most remodeling occurs at synapsis

↳junctions between neurons

Changes are activity dependant

C. Memory

anatomical/physiological event occurring synapses dependent on neuronal plasticity and activity

Short-Term Memory (STM)

Info stored for a short time → seconds to minutes

Limited capacity (-7)

Released if irrelevant (not used)

Long-Term Memory (LTM)

Activated when info needs to be retained

As far as we can tell, infinite duration/capacity

Cannot use directly → retrieved to STM

Use It or Lose It

High activity → many connections

Low activity → lose connections

Multiple active synapses → stronger response at all synapses

Memory ≠ Learning

Learning: use of knowledge/experiences (memory) to decrease likelihood of negative outcome

Aka → you do better as a result of learning

Memory: which parts of fence are electrified

Learning: never attacking the same spot twice

Goals of Workshop

• Improve ability to form memories

• Use memories to learn and problem solve

• Develop learning skills/techniques

• Know GB content

D. Long-Term Potentiation

Lasting increase in the strength of synaptic transmission - physiological changes

Facilitates memory and retrieval

Activity dependent

Learner needs to use information

Use of information is a sorting process

Use → important → retained

Not used → unimportant → discarded

Discarded = no synapses formed

(see photos)

Facilitated by:

• Organization-associations aid in memory formation

• Chunking - learning sets of related info rather than just one thing at a time
  ↳Helps w/ memory and retrieval 0 easier to recall chunks

• Activity - practice = learning

II. Workshop Organization

Workshop weekly Practice Questions

Graded → old exam question, exact same format

“Reality check” → not, graded, self-assessment

Exams: 3x per semester

Same question format as PDs

Exam Guide

1st level & 2nd level → outline

Outcomes → learning outcomes (potential exam questions)

Organizers → how to practice

Verified correct &

✅ 02: Foundations of Biology

02: Foundations of Biology

Thursday, September 4

I. Themes in Biology

→ CC, SEQ levels of organization

II. The Scientific method

→ SEQ process fo science

III. Basic elements of Chemistry

→ CC chemical bonds

IV. Emergent Properties of Water

→ CC properties of water

I. Themes in Biology

A. Evolution

Unifying idea of biology - all living organisms are modified descendants of common ancestors

“Nothing in biology makes sense except in the light of evolution.” - T. Dobzhansky, 1972

B. Emergent Properties

Properties the results from arrangement and interaction of parts within system

The whole is more than just the sum of its parts

Ex. the pieces of a bike can’t get you anywhere, but the whole becomes a method for transportation (emergent property)

C. Levels of Biological Organization

1. The Biosphere

2. Ecosystems

3. Communities

4. Populations

5. Organisms

6. Organs and Organ Systems

7. Tissues

8. Cells

9. Organelles

10. Molecules

II. The Scientific Method

A. Introduction to Science

Science from Latin “to know”

Method of inquiry - finding natural explanations for natural phenomena

Limited to observable and measurable structures and process

Systematic methods of investigating natural world - hot haphazard

Language of Science

Hypothesis: testable proposed explanation for observations based on available data; an educated guess; Ex: A light doesn't work because the bulb is dead.

Prediction: Expected outcome when you test hypothesis; Ex: If the bulb is dead, then the light will work when I replace it.

Theory: broad explanation with significant support, leads to new hypotheses and accurate predictions; Ex: Earth revolves around the sun.

Law: statement of what always occurs under certain circumstances; observable pattern, not explanatory - “what” not “why;” Ex: conservation of energy

The Scientific Process

III. Basic Elements of Chemistry

Table 2.1 Elements in the Human Body

Oxygen, Carbon, Hydrogen, Oxygen → 96.3% of Body Mass

(see photos)

A. Electrons

Atoms made of protons (+), neutrons (/), electrons (-)

Electrons (e-)

Subatomic particles

-1 charge, 1 unit of negative charge

Move rapidly around atomic nucleus

Potential Energy

Energy (E) that a material possesses due to its location or structure

Can be used to do work - capacity to cause change

Once used, work has to be done to restore

Electrons and Potential Energy

e- located in distinct shells

Have potential E due to distance from nucleus

Further from nucleus → higher E

Absorb E to move to higher shell

Release E when fall to lower shell

Valance Electrons

Valence Shell - outermost shell

Valence electrons occupy valence shell

H and He - up to 2 e- in valence shell

All others - up to 8 e- in valence shell

Electrons Summary

Subatomic particles, carry a -1 charge

Surround atomic nucleus in discreet regions called shells

Contain E based on their location

Why so much on Electrons?

Bond and Reactions

Properties Depend on Atomic Structure

Element, # valence e-, # e- to fill valence shell, #covalent bonds (single, double, or triple)

(see photos)

B. Formation of Molecules

Molecule: a compound of 2 or more atoms held together by chemical bonds

Chemical formula tells:

What type of atoms

How many of each

Ex: H₂O - 2 hydrogen, 1 oxygen

Emergent Properties of Compounds

Sodium (super dangerous) + Chlorine (super dangerous) = Sodium chloride (table salt)

Characteristics can differ from those of component elements

C. Chemical Bonds

Result of how atoms share electrons

“Want” (most stable with) a full valence shell

Will share, donate, or accept e- to achieve

Potential E stored in chemical bonds

Electronegativity

Measure of atom’s affinity for e-

Atoms in a molecules attract electrons to varying degrees

More electronegative → more strongly pulls e- towards itself

D. Types of Bonds and Interactions

Covalent Bond

sharing e- between atoms

Results in a full valence shell for each

Strongest type of bond (under biological conditions)

Ex: Hydrogen (H₂) → H:H; H-H

Nonpolar Covalent Bonds

Same or similar electronegativity → e- shared equally

Ex: O₂

Polar Covalent Bonds

Unequal electronegativity → unequal e- sharing

Causes partial (+) or (-) charges (𝜍 = partial charge)

Ionic Bonds

Highly unequal electronegativity → e- lost or gained → ion: charged atom

Like changes repel, opposites attract

Bond formed by attraction between anion (-) and cation (+)

Ex: Na & Cl

Salts

Compound formed by ionic bonds - form crystals

Dissolve in water

Van der Waals Interactions

(Relatively) short-lived, (relatively) weak interactions due to electron position and motion

Areas with partial (+) and (-) charges interact

Strong in large numbers

Includes many different interactions - London dispersion forces, hydrogen bonds

Hydrogen Bonds

Type of Van der Waals

Partial charges result when H binds to electronegative atom (e.g. O or N)

𝜍+ (on H)tends to associate with 𝜍- (on electronegative atom)

Resulting interaction is called a hydrogen bond

IV. Emergent Properties of Water

A. Hydrogen Bonds

Water is a polar molecule (due to polar covalent bonds)

→ Forms H bonds with each other

(see photos, Pearson fig 3.2)

B. Consequences of H-bonds

Cohesion: attraction between water molecules

Adhesion: attraction between water molecules and other substances

Moderates temperature - high specific heat

Expands when frozen - ice floats

“Universal” solvent - anything polar will dissolve aka hydrophilic (but not nonpolar - hydrophobic)

✅ 03: Biological Molecules

03: Biological Molecules

Tuesday, September 8

I. Biological Importance of Carbon

→ CC functional groups

II. Biological Macromolecules

→ SEQ Process fo Polymerization

→ CC Classes of Biological Molecules

I. Biological Importance of Carbon

A. Intro to Carbon

Organic compounds (C bonded to C or H)

The study of carbon compounds (the chemistry of life)

Cell ~70-90% H₂0, most of the rest is C-based compounds

Carbon can form 4 bonds bonds (complex molecules)

B. Hydrocarbons

Organic molecules of only C and H

Ex. Methane CH₄

Nonpolar, unchanged (nonionic)

↳hydrophobic

Can contain functional groups

↳replace one or more H

C. Functional Groups

Key to molecular function

Replace H with something else

6 Key Groups

1. Hydroxyl Group (-OH)

• Oxygen bound to hydrogen

• Alcohols, end in -ol

• Polar, hydrophilic

Ex. ethanol, alcohol in beverages

2. Carbonyl Group (=O)

• C with double covalent bond to O

• Polar, hydrophilic - but not all polar molecules are equal

Ex. acetone, the simplest ketone propanal, an aldehyde

3. Carboxyl Group (-COOH)

• C with double bond to O and single bond OH

• Can release proton (H⁺) → acidic (carboxylic acids)

• Polar, hydrophilic, important part of amino acids

Ex. acetic acid, which gives vinegar its sour taste

Ionized form of (-COOH) found in cells

4. Amino Group (-NH₂)

• N bound to 2 Hs

• Proton (H⁺) acceptor - basic

• Important component of amino acids

E. glycine, an amino acid (carboxyl group)

5. Phosphate Group (-PO₄H₂)

• O bonded to phosphorus (P), bonded to 1 O, 2 OHs

• 1 double bond present

• Can release 1 or both H+
  ↳Exists ionized and nonionized

• Acidic, hydrophilic, found in P and nucleic acids

E. glycerol phosphate, which takes part in many chemical reactions in cells

6. Methyl Group (-CH₃)

• C bonded to 3 H, all single bonds

• Nonpolar, hydrophobic

• In DNA, effects gene expression

Ex. 5-Methyl cytosine, a component of DNA that has been modified by addition of a methyl group

II. Biological Macromolecules

A. Macromolecules

Large molecules - thousands of atoms

Monomers: identical or similar building blocks

Polymers: produced by linking monomers

All polymers are macromolecules, not all macromolecules are polymers

Dehydration Reaction (Synthesis)

Dehydration reaction: synthesizing a polymer

Dehydration removes a water molecules, forming a new bond

Enzyme: dehydrogenase

*-ase = enzyme

Hydrolysis

Breaking down a polymer

Adds water molecule, breaking a bond

Enzyme: hydrolases

B. Carbohydrates

Made of C, H, and O

Approx. ratio of CH₂O

Fuel and structural

Monosaccharides

Single sugars

Monomer of carbohydrates

Usually 3-6 carbons

Ex. glucose C₆H₁₂O₆

Polysaccharides

Polymer of hundreds-thousands of monosaccharides

Connected by glycosidic linkage

Two Main Functions in Cells

1. Storage - starch, glycogen

2. Structure - cellulose, chitin

C. Lipids

Diverse, hydrophobic, NOT polymers

Do NOT dissolve in water

Dissolve in nonpolar solvents

Ex. chloroform

Three important lipid families

1. Fats

2. Phospholipids

3. steroids

Lipid Synthesis

Often dehydration reaction results in ester linkage

Glycerol

One of three dehydration reactions in the synthesis of a fat

Fats

Most abundant lipid-energy storage → contain 9 cal/gram carbs/proteins = 4 cal/g

Structure: glycerol + 1, 2, 3 fatty acids

Glycerol: 3 carbon alcohol 3 -OH groups

Fatty Acid: unbranched hydrocarbon, ~14 -22C carboxyl group

Phospholipid

Glycerol + 2 fatty acid phosphate group

Amphiatic: has hydrophobic and hydrophilic traits

Fatty acid “tails” + phosphate “head”

Steroids

3 6-C rings, 1 5-C ring

Differ in functional groups

Ex. cholesterol, sex hormones

D. Proteins

Monomers = amino acids

All have same basic structure

20 Amino Acids in Cellular Life

Can be:

• Nonpolar: hydrocarbon side chains

• Polar: hydroxyl groups

• Charges: acidic or basic

Polypeptides

Many (100+) AA’s joined in linear sequence by peptide bonds

Not protein yet; requires correct shape

Effect of Protein Unfolding

Denature: loss of proteins native structure

Lose structure → lose function

Protein Functions

Basically everything: structure, signaling, enzymes, defense, transport

E. Nucleic Acids

Polymers of nucleotides

2 classes

• DNA: deoxyribonucleic acid

• RNA: ribonucleic acid

Store and transmit genetic information

✅ 04: Origins of Life

04: Origins of Life

I. Process of Abiogenesis

Chemical evolution hypothesis: Life from non-living

1. Abiotic synthesis of monomers

2. Formation of organic macromolecules

3. Formation of protocells

4. Origin of self-replicating molecules

A. Abiotic synthesis of monomers

First life developed from non-living organic molecules

→abiogenesis

Those molecules had to form spontaneously

→Abiotic synthesis

4 Requirements for Abiotic Synthesis

1. Very little free O₂ in atmosphere (favors bond formation)

2. Source of E (Lightning, UV radiation)

3. Inorganic Building Blocks: (Ions, H₂O, Atmosphere: CO₂, CO, H₂, N₂, NH₃, H₂S, CH₄)

4. Time (earth formed around 4.5 billion years ago. Life began around 3.5 billion years ago)

2) Oparin-Haldane hypothesis (1920’s)

• Conditions of early earth favored spontaneous formation of simple organic molecules

• Molecules accumulated in oceans & formed “organic soup”

• Prebiotic (primoridial) soup

Test of hypothesis: Miller and Urey (1953) Apparatus, Stimulate conditions

Experiment repeated: Nucleic acid bases

All aa

Lipids, Sugars, ATP

Iron-Sulfer World Hypothesis

• Hydrothermal vents

• Protected

• Hot H20, CO, minerals

Abiotic Synthesis Hypotheses

2 general ideas - differ in “where”

1. Oparin-Haldance Hypothesis: 1920s, life formed near Earth’s surface - shallow water

2. Iron-Sulfur Hypothesis: recent hypothesis, life formed at deep sea vents

B. Abiotic Synthesis of Organic Macromolecules

1. Clay/Rock surfaces

Can form on clay or rock surfaces

Metal ions (Zn²⁺, Fe²⁺) catalyze polymerization

Experimentally: Polypeptides, Polynucleotides, Vesicles

1. Lab

Drip AA solution onto hot rocks -> Polypeptides

C. Formation of Protocells

Vesicle: fluid-filled compartment surrounded by membrane-like structure

Spontaneously forms from lipids in water

1. Vesicle

2. Fluid filled compartments

• Membrane

• Form when hydrophobic molecules added to H2O

2) Montmorillonite

• Soft clay form volcanic ash

• Early Earth

• Ions catalyze vesicles formation

Conclusion of experiment: Montmorillinite greatly increases rate of vesicle self-assembly

Protocells

Aggregates of abiotically produced organic macromolecules

Vesicle with many attributes of living cells:

• Maintain internal chemical environment different from external environment

• Divide in ½ when large

• No mechanism of heredity

Electrical potential across surface

Absorb materials → osmotic swelling

Unique internal chemical environment

Divide if sufficiently large

BUT: No mechanism of heredity

D. Appearance of Self-Replication

In living cells…

Genetic information stored in DNA

Info from DNA is Transcribed into mRNA

Info from mRNA is Translated into protein

DNA → RNA* → Protein

*Thought that RNA was the first nucleus acid in living things

RNA World Hypothesis

1. Pre-biotic earth

• RNA molecules that could catalyze:

I. Synthesis of RNA -> Replicate itself

II. Peptide bond formation -> Protein synthesis

1. RNA with catalytic properties

2. Hypothesis

• RNA (single stranded) was 1st genetic material

• Evolved into DNA (double stranded)

ADVANTAGE OF DNA: More stable & better at storing genetic information

The first replicating systems used RNA to store AND copy genetic information

Limited role for polypeptides

DNA incorporated later

Ribozymes

RNA molecules with enzymatic properties

E.g. Cleave RNA; Catalyze RNA polymerization

(see photos)

II. History of Life

Divisions

• Rocks and Fossils

A. The First Cells

Prokaryotes - no nucleus, or organelles

EX: Stromatolites

• Fossils of microorganisms

• Layers of bacteria & sediment

• Earliest direct evidence of life

Anaerobic - did not use oxygen

Heterotrophs (1st) - obtain organic molecules from the environment for Energy

Fermentation

• Anaerobic (without oxygen) breakdown

2) photosynthetic autotrophs (2nd)

• Energy from sunlight to produce food from simple inorganic molecules

• Cyanobacteria

- O2 revolution (Rapid increase of atmospheric O2 around 2.4 billion years ago)

3) Aerobes (3rd)

• Aerobic respiration (Uses O2)

• Lots of energy from food -> ATP (they can make way more ATP)

• Major advantage over fermentation

B. Autotrophy

Use E from sunlight - made own food (big advantage)

1st released S₂

Later, released O₂ by splitting H₂O (cyanobacteria)

Oxygen Apocalypse

~2.5 bya

Rise in atmospheric O₂ due to oxygenic photosynthesis

Killed off most organisms

Banded iron formation

Then Aerobes Took Over

Deal with O₂ via aerobic respiration

Bonus: higher ATP yield

Most life today is aerobic

C. Origin of eukaryotes

1. Appeared ~2 billion years ago

2. More complex

• Cells with membrane-bound nucleus and organelles

1. Endosymbiotic theory - How Eukaryotes arose from prokaryotes

The Endosymbiotic theory

• Primary Endosymbiosis

1. A prokaryote was engulfed

Endosimbiosis -> A mutual and obligate relationship between host and endosymbiont

4) Multicellular eukaryotes

• 1.7 Billion years ago: Microscopic

• 600: Million years ago: Large, Soft bodied, diverse

• 535-525 Million years ago: Cambrian explosion. Rapid evolution of animals

• 500 Million years ago: Colonization of land. Fungi, Plants, & land animals

TREE OF LIFE VISUAL

III. Chemistry and Biology

1. Memory

2. Biological Molecules

✅ 05: Cell Structure

1. Cellular Characteristics & Diversity

2. Cells

3. Smallest unit that carries out all activities associated with life

• Order

• E processing

• Regulation/Homeostasis

• Growth & development

• Reproduction

• Response to stimuli

1. Types of organisms

3. All cells have a common ancestor (Tree of life)

LUCA = Last universal common ancestor

3 Domains

• Bacteria

• Archea

• Eukarya

Prokaryotes (prok) = Domains, Bacteria, & Archaea

Eukaryotes (euk) = Domain Eukaryote

4. Evolution of prok and euk

Cell Size

• Prok = 1 - 10 um

• Euk = 10 - 100 um

Cell size is limited by SA: vol

PM

• Boundary

• Everything must cross

SA: vol

• Determines how efficiently cell can exchange materials with env

-> Maximum SA:vol

	1 length box	5 length box
Total surface area	6	150	750
Total volume	1	125	125
SA: vol	6	1.2	6
Significance	Small cell Large SA:vol PROK	Large cell Small SA:vol NO GOOD	Large cell with endomembrane system Large SA:vol EUK

B. Prokaryotes

1. Single-celled

2. 1st appeared around 3.5 bya

4. Generalized structure of a prokaryotic cell

C. Eukaryotes

1. Single- & multi-celled

2. 1st appeared around 1.8 bya

3. Domain eukarya

4.Generalized structure of Eukaryotic cell

II. Components of Eukaryotic Cells

1. Endomembrane System

• Membrane = Lipid bilayer

• Closed Compartments (organelles)

Interact with each other through:

Direct physical continuity or vesicles (Lumen, Budding, Fusion)

1. Plasma membrane (PM)

2. Encloses cell contents

3. Selectively permeable

• Regulates passage

2. Nucleus

1. DNA (genetic material)

2. Nuclear envelope

• 2 concentric membranes

• Nuclear pores

1. Nucleolus

• RNA & proteins

• No membrane

• Synthesizes ribosomes

3. Endoplasmic reticulum (ER)

1. ER membrane continuous with the outer membrane of the nuclear envelope

2. ER lumen (internal space)

• Single internal compartment

1. Rough ER (RER)

• Ribosomes attached to outer surface

Polypeptides made of ribosomes -> Through translocon (=pore) into RER lumen -> Folded & modified -> Transport vesicle (w/proteins) buds off RER membrane -> Vesicle inserted into target membrane

1. Smooth ER (SER)

• No ribosomes

• Continuous w/RER

• Primary of lipid synthesis

• Glycogen breakdown -> Regulates blood glucose

• Detoxifying enzymes

- Add -OH groups -> More soluble

- Ex: Alcohol and drug abuse

- Liver cells produce more SER

- Increased rate of drug breakdown

- Increased tolerance

4. Golgi apparatus

1. Stacks of membranous sacs (cisternae)

Each has own lumen

1. Protein modification

2. Each stack has

1. cis face

• Closest to nucleus/ER

• Receives transport vesicles from RER

2. Medial cisternae

• Vesicles move through

• Modification

3. Trans face

• Closest to PM

• Transport vesicles (exit and & transported)

5. Lysosomes

1. Sacs of hydrolytic enzymes

2. Ex: Phagocytosis

6. Vacuoles

1. Large vesicles

2. Variety of functions depending on the cell

• Ex: Storage, H20 balance

B. Ribosomes

1. No membrane

- not organelles

1. Produced by nucleolus

2. Exit nucleus through nuclear pores -> Enter cytoplasm

3. 2 types

• Free in cytoplasm

• Bound to RER

1. Protein synthesis

C. Mitochondria and chloroplasts

1. Mitochondria

• All euk

• Aerobic respiration

1. Chloroplasts

• Only photosynthetic euk (plants and algae)

✅ 06: Membranes and Transport

1. Membrane Structure

   

2. Components

3. Phospholipids

4. Structure

• Amphipathic

• Cylindrial

1. Bilayers

2. Proteins

a. Peripheral

• Bound to surface

• Hydrophilic

b. Integral

c. Proteins determine most main functions

• Intercellular joining

• Cell-cell recognition

• Signal transduction

• MISSING

• MISSING

3. Carbohydrates

• Glycoprotein

• Glycolipid

B. Fluid-Mosaic Model

1. Fluid

2. Phospholipids move laterally in 1 layer

3. Factors that affect fluidity

4. Temperature

5. Fatty acid chain length

• Various lengths = more fluid

1. Degree of fatty acid saturation

• Saturated tails pack together -> less fluid

• Unsaturated tails prevent packing -> more fluid

1. Cholesteral

• At lower temps

- > Prevents solidification

- At higher temps

- > Prevents too much fluidity

2. Mosaic - > Proteins form patterns

a. Some proteins stay in place by:

- Extracellular matrix

b. Some proteins move laterally within one layer

1. Membrane Transport

2. Passive transport

• No metabolic E

• E from concentration ([]) gradient

• Diffusion

-> Tendency for substances to spread out into an available space

-> Net movement is down [] gradient (from high to low)

-> Continues until dynamic equilibrium is reached (no net charge)

1. Simply diffusion across a permeable membrane

• Movement of particles from high to low []

• No transport protein

1. Osmosis

• Simple diffusion of water of H20 across a membrane

1. Background

• Solvent: Dissolves other substances

• Solute: Dissolved substance

• H2O moves across membrane, solutes do not

• Tonicity: Ability of solution to cause a cell to gain or loose H20

-> Comparison of 2 solutions

Isotonic = Same [solute] = Same [H2O]

Hypertonic = Higher [solute] = Lower [H2O]

Hypotonic = Lower [solute] = Higher [H2O]

• Water moves from high [H2O] to low [H2O]

• Equalizes solute concentration on both sides of the membrane

1. Direction of osmosis (H2O moves across membrane, solutes do not)

Review of simple diffusion & osmosis

• Some materials cross

  • Gases: O2, CO2, N2

  • Small hydrocarbons (hydrophobic)

  • H2O (hydrophilic, but small & uncharged)

- Many cannot

Large Molecules: Too big

Polar molecules (ex: glucose): hydrophilic

Ions (H+): Charged, hydrophilic

Problem: Lipid bilayers too selective

Solution: Transport proteins

3. Facilitated diffusion

• Transmembrane protein

• Passive

- No metabolic E

- E from gradient []

1. Channel proteins do not change shape

• Do not change shape

• Hydrophobic AA

• Solutes pass through

• Ex: aquaporins

1. Carrier proteins

Bind to specific solute -> Protein changes shape -> "carries" substance through

B. Active transport

1. Cell supplies metabolic E (ATP)

2. Transport protein required

Transmembrane, changes shape

1. Works against [] gradient

-> Materials can be stockpiled

1. Ex: Sodium-potassium pump

2. Bulk Transport

• Large molecules

• Many molecules

• Vesicles

• Requires E input from the cell (ATP)

1. Exoxytosis

2. Vesicle fuses w/ PM & contents released

3. Wastes & secretory products

4. Adds lipids to PM -> Growth of PM

B. Endocytosis

Materials enter by vesicles from PM

1. Phagocytosis

• Cell ingests large particle -> Food vacuole -> Fuses with lysosome

1. Pinocytosis

• Fluid & dissolved materials -> vesicle -> contents transfer to cytoplasm

Draw and explain Figure 5.7

07: Metabolism

1. Metabolism & Energy

Energy flow through ecosystems.

Light E -> Photosynthesis -> Concerted into chemical energy resulting in oxygen produced

Then cellular respiration, transforms organic molecules into ATP (another form of chemical energy) -> some ATP turns into heat energy -> some heat energy leaves the molecule

(Cellular respiration can go back to photosynthesis in a chart)

1. Metabolism

2. Sum of all chemical reactions & E transformations in organism

3. Emergent property of life

• Arises from orderly interaction between molecules

1. 2 types of metabolic reactions

2. Anabolic = Synthetic

• Simple -> Complex

• Require E

1. Catabolic = Degradative

• Complex -> Simple

• Release E

4. Regulated Homeostasis

B. Energy (E)

1. Intro

2. Ability to do work

3. 2 forms

i. Potential = Stored

ii. Kinetic = Motion

1. Laws of Thermodynamics

i. E cannot be created or destroyed

ii. E can be converted from one form to another

E transformations are not 100% efficient

-> Lost as heat

Cannot perform work

Disperses into env

• Every energy transformation increases entropy (disorder)

• Low entropy = Ordered

• High entropy = Disordered

2. Energy & Life

1. Ultimate source of energy for most organisms?

• Radiant E from the sun

1. Direct source of E for heterotrophs

Food (Low entropy = Unstable E)

1. Cellular work

• Mechanical

• Transport

• Chemical

1. Free E = G (Gibbs)

• E from reaction that is available to do work

• Delta G = Change in system before and after reaction

3. Chemical reactions in cells

1. Exergonic (“E outward”)

i. Reactants have more potential E than products

E released

R -> P + E

ii. G in initial state > G in final state

Delta G is negative # (Loss of free energy)

iii. Spontaneous

• Goes from higher to lower free E

• Energetically favorable

• Does not equal Instantaneous

iv. Catabolic reactions

1. Endergonic reactions (“E inward”)

i. Reactants have less potential energy than products

Input of E required

R + E -> P

ii. G in initial state < G in final state

Delta G is positive # (Gain of free energy)

iii. Not spontaneous

iv. Anabolic reactions

C. ATP (adenosine triphosphate)

High E compound

1. Structure

2. Adenine = nitrogenous base

3. Ribose = 5C sugar

4. 3 phosphate groups (Pi)

Phosphate bonds (covalent)

store lots of potential E

2. Function

• Terminal Pi removed by hydrolysis reactions

= Exergonic

• Pi transferred to substrate

= E for endergonic reaction

E for endergonic reactions is from couples reactions

1. Enzymes

2. Activation Energy (EsubA)

• Chemical reactions involve breaking and forming bonds

• E is needed to start a reaction

-> Barrier that determines reaction rate

- Even exergonic —

B Function

1. Biological catalysts

• Speed up rate of reactions by lowering EsubA

• Are not used up

• Proteins, -ase

1. Act on specific substrate

EX: Sucrase splits Sucrose

1. Induced fit model

• Globular proteins

• Clefts/grooves

• Active site

Induced fit

Substrate binds

-> changed shape of enzyme

-> strain breaks bonds

Enzymes often work in “teams”

1. Metabolic pathway

Organized set of chemical reactions

• Series of defined steps

• Each step catalyzed by different enzyme

• Results in specific product

1. Redox reactions

2. Transfer of e-

3. Oxidation (“acted upon by oxygen”)

Loss of e- (s)

1. Reduction

Gain of e- (s)

Positive charge reduced

OILRIG= Oxidation is loss, reduction is gain

1. E- cannot exist in free state in cells

Must have both reactions -> Redox

Significance of e- transfer

-> Transfers R to an acceptor molecule

B. Movement of hydrogen atoms

C. Electron carriers

• Compounds that function as e- shuttles

• Easily reduced (accepted e-) or oxidized (lost e-)

• Reduced forms have higher potential energy

1. NAD

• NAD+ = Oxidized form

• NADH = Reduced form (has accepted 2 e- and 1 H+)

1. NADP

• NADP+ = Oxidized form

• NADPH = Reduced form

1. FAD

• FAD+ = Oxidized form

• FADH2 = Reduced form

Redox summery

• Metabolism involves moving e-

• Redox reactions are couples reactions that involve the gain and loss of e-

• E-acceptor compounds like NAD+ store and use E during metabolism

08: Photosynthesis

All life needs

• Source of energy

• Source of carbon

1. Introduction

2. Nutritional mods

3. Chemoheterotroph

E source = organic compound

C source - organic compounds

Consumers (feed on other organisms)

Glucose

1. Photoautotroph

E source = light

C source - CO2 (Inorganic)

Producer (can produce organic compounds)

Photosynthesis

Light energy + inorganic carbon source -> Chemical energy (organic)

B. Light

1. Properties

2. Waves

3. Photon

• Small particle of E

• E inversely proportional to wavelength

Shorter wavelength = more E/photon

Longer wavelength = less E/photon

2. Effect of photon on electron

Electron in ground state -> electron absorbs light energy -> electron energized (unstable)

-> electron returns to ground state

OR

-> electron leaves and is captured by acceptor (photosynthesis)

Oxidized (lost an electron, + charge) Reduced (gained electron, - charge)

Light and electrons are NOT the same thing

II. Structures

1. Plant organization

Leaves: Main site of photosynthesis -> Mesophyll cell -> about 30 structures that are chloroplasts: - Photosynthesis organelle - Eukaryotes (endosymbiosis)

1. Chloroplasts

   

Labeling

• Outer membrane

• Intermembrane space

• Inner membrane

• Thylakoid

• Thylakoid space

• Granum (stack of thylakoids)

• Stroma (fluid)

1. Photosynthetic pigments

2. Pigment

• Absorbs visible light

1. Photosynthetic

• Capture light E

• Embedded in thylakoid membranes

1. Chlorophyll

2. Structure

Head: Absorbs light E

Tail: Embedded in membrane

1. Ex: chlorophyll a

III. Process

1. Overview

2. Parts

3. Light dependent reactions (photo)

• In thylakoid membrane

1. Calvin cycle (synthesis)

• Light dependent

• In stroma

2. Overall reactions (Redox)

Reduction = Gain of H

Oxidation = Loss of H

Endergonic

B. Light dependent reactions

1. Convert light energy into chemical energy (ATP and NADPH)

2. Photosystems

• In thylakoid membranes

• Photosynthetic pigments

• Capture light energy

• PS I & PS II

1. Key points

• Electron flow (redox reactions)

• ATP & NADPH synthesis

2. Linear electron flow and synthesis of ATP and NADPH

• PS II captures light E

• Chlorophyll electron is excited

• Electron transferred to ETC (electron transport chain)

• Energy from electron pumps H+ across membrane and into space

• Facilitated diffusion of H+ provides E for ATP synthesis

• PS I captures light E

• Chlorophyll electron is excited

• Electron transferred to ETC

• NADP+ + H+ + electron (from ETC) —NADP+ reductase—> NADPH

• PS II ETC transfers electrons to PS I+

• PS II+ is extremely strong oxidizing agent -> Oxidizes H20 & takes electron

C. Calvin cycle

• Synthesis of carbs from CO2

• Does not require light directly

• Require NADPH & ATP

• Occurs in stroma (enzymes)

Phases

1. C fixation

RuBP + CO2 (inorganic) –Rubisco→ PGA (organic)

1. Reduction

• Synthesis of organic compounds

• ATP required

• NADPH required

1. Regeneration

• ATP required

• RuBP regenerated

09: Cellular Respiration

Cellular Respiration

I. Introduction to cellular respiration

A. Overview

1. Food: Source of E & C

2. Cellular Respiration

• Chem E in food → Chem E in ATP

• All cells: Prok & Euks

• Aerobic (O₂) or anaerobic (no O₂)
  

  

4. Key types of reactions

a. Redox

• Transfer of e⁻-

b. Dehydrogenation

• Catalyzed by a Dehydrogenase

• H atoms move from a substrate to an acceptor

• = Transfer of e⁻-

c. Substrate-level phosphorylation (SLP)

• Transfer of Pi from a substrate to ADP

• Produces ATP

d. Decarboxylation

• CO₂ removed (diffuses out)
  

  

II. 4 Stages of aerobic cellular respiration

A. Glycolysis

1. Glucose enters cell via GLUT1

   • Carrier protein

   • Facilitated diffusion
     

2. Occurs in cytoplasm

3. 2 phases

a. E investment phase

• Starts with: Glucose (6C)

• Requires: 2 ATP

• Ends with: 2 molecules of G3P (each is 3C)

• Endergonic

b. E payoff phase

• Starts w/: 2 × 63P

• Yields: 4 ATP

• Ends w/: 2 × pyruvate

• Exergonic
  

B. Pyruvate Oxidation

1. Pyruvate

   • Enters matrix

2. Pyruvate dehydrogenase complex

   • 72 polypeptide chains (quaternary structure)

   • Catalyzes 3 reactions

3. Steps

a. Decarboxylation

• 2C compound produced

b. Dehydrogenation

• 2C compound oxidized

• NAD⁺ reduced to NADH

• Acetyl group produced

c. Coenzyme A

• Transferred to acetyl group

• Acetyl CoA produced
  

Reminder: For every 1 glucose, there are 2 pyruvates

C. Citric Acid Cycle

D. Oxidative phosphorylation

1. Electron Transport Chain (ETC)

a. Series of e-⁻ carriers

• Embedded in inner mem

b. Series of redox reactions

• Each carrier reduced & then oxidized

c. Overall: Transfer e⁻ from NADH & FADH₂ to O₂

2. Chemiosmosis

a. Diffusion of H⁺

b. ATP Synthase

• Transmembrane channel

• H⁺ diffusion causes rotation (E)

• Oxidative phosphorylation (synthesis of ATP by chemiosmosis)
  

  

Aerobic Cellular Respiration

O₂ reduced

= Terminal e-⁻ acceptor (TEA)

H₂O produced

If O₂ not available:

→ ETC stops

→ All steps of aerobic resp stop

→ No ATP

→ DEATH

III. Photosynthesis and Respiration

A. Similarities

• Double-membrane

• ETC & H⁺ gradient

• Chemiosmosis & ATP synthase

B. Major Differences

1. Mitochondria

• Source of e⁻ is organic molecules (food)

• Chemical E in food → Chemical E in ATP

2. Chloroplasts

• Source of e-⁻ is water

• Light E → Chemical E in ATP
  

  

🔴 EXAM 1 (lectures 1-9)

10: Cell Cycle

1. Genetic material

2. Introduction

3. Cell theory

• Cell is basic unit of life

• All life consists of 1 or more cells

• All cells come from other cells

1. Functions of cell division

• Prokaryotic and unicellular eukaryotic cells

-> New organism

• Multicellular eukaryotic cells

Growth and development

Tissue renewal and repair

Both distribute identical genetic material into daughter cells

Eukaryotic

• Nucleus

• Several, linear chromosomes

B. Chromosome

1. DNA molecule + protein

2. Gene

3. Informational units

Code for all proteins

1. 100s or 1000s / chromosome

2. Each at specific locus

3. Humans have around 20,000 genes

3. Chromatin

• Uncondensed chromosome

• Most of time during cell cycle

• Coils up and condolences during cell division

4. Chromatid

• Highly condensed chromosome

• Unique shape and size

• Centromere: constricted region where spindles attach

• Chromatid (1 chromosome) duplicates, and creates 2 sister chromatids (1 chromosome) held together by one centromere

C. Ploidy

The # of sets of chromosomes in a cell

1. Haploid = n

2. One set of chromosomes

= one copy of each chromosome

1. Gametes

= reproductive cells

= sex cells

One set of chromosomes

2. Diploid = 2n

1. Two sets of chromosomes

= 2 copies of each chromosome

1. Somatic cells

= body cells

1 copy from mom, 1 copy from dad

1. Homologous chromosomes

The 2 copies in a pair

Homomorphic

Humans

2n = 46

23 pairs

Human karyotype

Ex: Dogs

2n = 78

38 pairs

Haploid and diploid cells undergo mitosis

II. Phases of the cell cycle

An ordered series of events in the life of a cell

Generation time (T)

• One complete revolution

• Around 8-20 hours

1. Events of interphase

2. Introduction

3. Around 90% of cycle

4. Time between division

5. Not resting

6. Chromatin

2. 3 stages of interphase

1. G1

• Metabolic activity

• Growth, development, & normal function

• Prep for S phase

1. S phase

1. S = synthesis (replication)

- DNA and chromosomal proteins

- Still in form of chromatin

- Ploidy has not changed

2. Centrosomes duplicate

- pair of centrioles

- only in animal cells

- organize mitotic spindle

3. After replication

• Each chromosome

= 2 sister chromatids (exact copies)

• Centromere

Sister chromatids most closely attached

• Kinetochores

Proteins attached to each centromere

1. G2

• Short phase

• Now twice as much DNA

• Still chromatin

• Prep for mitosis

Metabolic activity

Protein synthesis

B. Events of M phase

Mitosis and Cytokinesis

Around 10% of cell cycle

Mitosis

Nuclear division associated with division of somatic cells

Continuous process:

• Prophase

• Prometaphase

• Metaphase

• Anaphase

• Telophase

Ploidy does NOT change! (if a cell is haploid and goes through mitosis, it will remain haploid. Same for diploid)

1. Prophase

2. Chromatin condenses

3. Nuclear envelope breaks down

4. Mitotic spindle begins to form

• Microtubules

• Extend from centrosomes

2. Prometaphase

Centrosomes

Move away from each other towards opposite poles

Spindle

- Continues to elongate

- Attached to kinetochores

3. Metaphase

• Chromosomes

Line up on metaphase plate

• Sister chromatids

Oriented towards opposite poles

4. Anaphase

Chromatids

• Separate at centromeres

• Move to opposite poles as microtubules shorten

-> Chromosomes

5. Telophase

• Chromosomes start to decondense

• Nuclear envelopes form

• Spindle depolymerizes

-> 2 nuclei genetically identical to each other & to original parent cell

Ploidy did NOT change!

6. Cytokinesis

• Cytoplasm divides into 2 daughter cells

• Cell organelles randomly divide between cells

• Each nucleus in interphase

1. Animal cells

• Cytokinesis = cleavage

• Cleavage furrow

• Contratile ring forms

Actin and myosin

Parent pinched into two

1. Plant cell

• Vesicles from golgi

-> line up at old metaphase plate

-> fuse

-> material forms cell plate

-> cell wall

Cell cycle summary

• Interphase

1. Non-dividing

2. Normal growth and function

3. Preps for cell division

• M phase

1. Cell division

2. Mitosis and cytokinesis

Occurs in haploid (n) and diploid (2n) cells

Daughter cells are identical to parent cells

Ploidy does not change

11: Meiosis

1. Introduction to heredity

Heredity

Transmission of traits from one generation to next

= inheritance

Variation

Differences between individuals

All this plays into genetics

1. 2 types of reproduction

1. Asexual

2. Single parent -> Offspring

Single celled organisms One cell -> Two cells	Multi-cellular organisms -> bud or fragment

1. Mitosis

• 2n parent -> 2n offspring

• n parent -> n offspring

1. Clones

• Identical genetic material

1. Advantages

• Rapid & low E

• No mate

• Many offspring

-> well-adapted to environment

2. Sexual

1. Parents (2n) -> offspring (2n)

Gamete (n) + Gamete (n) -> Zygote (2n)

How do 2n parents produce n gametes?

1. Meiosis

• One diploid cell -> -> four haploid cells

• Chromosome # is half (reduction division)

1. Offspring not clonal

2. Advantage -> genetic variation

Some offspring better able to survive change or stress

Meiosis & fertilization

• Always occur in sexual reproduction

(Meiosis has the chromosome number, fertilization restores diploid #)

• Alternate during life cycle

• Maintain constant chromosome #

B. Chromosomes

1. Homologous chromosomes (homologs)

• Pair of chromosomes

• Same shape & genes

• In a pair, 1 from mom & 1 from dad

1. Following replication, each chromosome consists of 2 sister chromatids

2. Humans

1. Somatic cells

• Diploid (2n)

• 46 chromosomes (=23 pairs)

• Produce somatic cells (2n) by mitosis

Somatic cell karyotype

• 22 pairs of autosomes

• 1 pair of sex chromosomes

1. Primordial germ cell

• Diploid (2n)

• 46 chromosomes (=23 pairs)

• Produce gametes (n) by meiosis

Gamete karotype

• 22 autosomes

• 1 sex chromosome

TABLE CC PRACTICE:

DRAW PRACTICE:

2n = 6

II. Stages of meiosis

• Interphase

• Meiosis I (P1 P1 M1 A1 T1)

• Interkinesis

• Meiosis II (P2 P2 M2 A2 T2)

1. Interphase (same as mitosis)

2. Chromosomes replicate

• S phase

• Chromatin

1. Each chromosome

• 2 sister chromatids (exact copies)

1. Humans

• 46 chromosomes

• = 92 chromatids

B. Meiosis I

-> Separates homologs

1. Prophase I

2. Synapsis

• Homologs align & pair

• Corresponding genes lined up

  

• Tetrad = 4 chromatids

  

1. Crossing-over

• Between non-sister chromatids

• Enzymes break and rejoin DNA molecules

1. Chromatin combines

2. Prometaphase I

1. Nuclear envelope fully broken down

2. Spindle completes & attached to kinetochores

End of prometaphase I in humans

# of Chromosomes? 46

# Chromatids? 92

# Tetrads? 23

3. Metaphase I

1. Tetrads

• Align on metaphase plate

  

1. Homologs

• Orient to opposite poles

MISSING

4. Anaphase I

1. Disjunction

• Homologs separate

1. Sister chromatids

• Remain attached

• Move toward same pole

1. Chromosomes act independently

• Each pole gets random mixture of maternal & paternal

• Depends on how tetrads lined up

1. Nondisjunction

• Error

• One or more homologs fail to separate

-> one pole gets both homologs

-> other pole had no chromosome for that pair

5. Telophase I & Cytokinesis

• Result in 2 haploid cells

• Each chromosome = 2 sister chromatids

End of telophase I in humans

# of Chromosomes in each nucleus? 23

# Chromatids? 46

# Tetrads in each cell? 0

C. interkinesis

• Between 1st and 2nd division

• Short

• No DNA synthesis

D. Meiosis II

-> separates sister chromatids

1. Prophase II and Prometaphase II

• Fast

• Spindle reforms

• No homologs -> no pairing

1. Metaphase II

• Chromosomes line up on metaphase plate

• Sister centromeres oriented to opposite poles and attach to spindles

1. Anaphase II

• Chromatids separate & go to opposite poles

• Each now a chromosome

1. Telophase II and Cytokinesis

• Chromosomes decondense

• Nuclear envelopes form

• 4 haploid cells (gametes)

In humans, each has 23 chromosomes

Overview of meiosis

III. Comparison of Mitosis and Meiosis

1. Types of cells

2. Processes

3. # of chromosomes & ploidy

12: Intro to Genetics

Introduction to Genetics

1. Mendel's experimental approach

2. Background

3. Gregor Mendel (1822-1884)

• Discovered basic rules of inheritance in Eukaryotes

• Published: 1865

• Rediscovered: 1900

• Foundation of genetics

1. Experimental organism = Garden pea

Advantages

1. Inexpensive, easy to grow

2. Many varieties

3. Short generation (gen) time, many offspring

4. Clearly identifiable traits

5. Easy to control pollination

The movement of pollen grains from stamen (male) to carpel (female)

Self-fertilization VS. Cross-fertilization

3. Characters

1. Specific inherited property

2. Trait: Variant

EX: Seed texture

Round VS. Wrinkled

1. 7 contrasting pairs

1. Phenotypes

• Observable trait

• Expression of genes

4. Applied quantitative methods

1. Experimental approach

• Planned experiments

• Recorded data

1. Analysis of results

Scientific method

5. Developed true reading lines

B. Tested blending inheritance hypothesis

1. Idea at Mendel’s time

2. Gametes contain fluid from body

-> Blend to form offspring

b. Problems:

- Pops don't become uniform

- traits “skip” gen

2. Mendel crosses true-breeding plants with contrasting traits

P= Parental Gen

F1= first gen

F2= second gen

Predication: If blending is accurate, then F1 phenotype should be intermediate between P phenotypes

The results of Mendel’s garden pea hybridizations

-> Conclusion: Blending hypothesis rejected

C. Particulate inheritance hypothesis

Characters passed from gen to gen by discrete particles (now know these are genes)

Mendel's model

• Genes are discrete units of info

• Each parent contributes one allele to offspring

• Dominant (dom) alleles masks recessive (rec) alleles

• 2 laws of inheritance

1. Modern genetics

2. Background

3. Gene

- Basic unit of heredity

- Codes for a protein

- At a specific locus

1. Alleles

- Alternative versions of genes

Vary slightly in seq

- Dominant (dom): Expressed

- Recessive (rec): Masked

1. Genotypes (set of alleles)

For each character, individual inherits 2 alleles (one from each parent)

Identical alleles at locus	different alleles at locus

B. Mendel's Law of Inheritance

1. Law of segregation

The 2 alleles for a character segregate during gamete formation and end up in different gametes

If individual had identical alleles for particular character, then allele present in all gametes	If different alleles present, then ½ of gametes get one allele and other ½ of gametes get other allele

2. Law of independent Assortment

2 or more genes assort independently during gamete formation

Crossing Over

+

Independent Assortment

=

LOTS of genetic variation

Basis of Mendel's law are in meiosis

1. Genetic crosses

Mate 2 individuals and observe offspring

Basic steps when doing a cross:

- Determine parent genotypes

- Determine possible gametes for each parent

- Determine possible gametes in the offspring

- calculate the frequency (freq) of each possible genotype

1. Punnet square

Predicts allele composition of offspring from cross of individuals of known genotype

EX: Parent 1 genotype = Bb

EX: Parent 2 genotype = Bb

• Possible gametes for each parent

• Possible genotypes is the offspring

• Freq of each possible genotype

DETERMINE % OF EACH POSSIBILITY

1. Monohybrid cross

2. Cross between parents with different alleles at a single locus

3. Key points

F2

C. Dihybrid cross

1. Follows 2 characters

How mendel derived law of independent assortment (2nd law)

P: True breeding

F1: Dihybrid and dom phenotype

Gametes

F2: 9:3:3:1

Only if alleles are on different pairs of homologs

Imagine you are performing a cross involving seed color in garden pea plants. What F1 offspring would you expect if you cross true-breeding parents with yellow (Y) seeds and green (y) seeds? Yellow seed color is dominant over green.

Step 1: Determine parent genotypes

Step 2 Determine parent gametes

Step 3: possible offspring (F1) genotype

Step 4: Freq of each possible F1 Genotype?

Yy= 100%

What is the phenotype of offspring?

Yellow seeds

1. Probability in genetics

Solve genetics problems without a punnet square

Prob of an event = expected freq

Certain not to occur -> Prob = 0 = 0%

Certain to occur -> Prob = 100 = 100%

1. Multiplication rule for independent events

Occurrence of one event does not affect prob that other event will occur

P(this) and P(that)

Multiply separate probabilities

EX of multiplication rule: What is the possibility that two heterozygous parents will have a child that is homozygous recessive?

Parent Genotype? Bb and Bb

Parent Gametes? ½ B and ½ b ½ B and ½ b

Offspring genotype? bb

P(bb) = P(b from mom) and P(b from dad) 25%

1. Addition rule for mutually exclusive events

13: Chromosomes

I. chromosome theory of inheritance

1. Background

   • 1880’s - 1902

     • Chromosomes discovered

     • Process of mitosis observed

     • Mendel’s work rediscovered

     • Process of meiosis observed

All of above is in CTI:

• Genes are on chromosomes at specific loci

• behavior of chromosomes during mitosis explains how traits are passed

B. Thomas Morgan

Early 1900’s

1. Experimental organism

   • Drosophila melanogaster (fruit fly)

   • Advantages

     • Inexpensive, easy to maintain

     • 100’s of offspring every 2 weeks

     • Many identifiable traits

     • Easy to control matings

     • Total of 4 pairs of chromosomes

       • 3 pairs are autosomes

       • 1 pair of sex chromosomes

2. Traits

   • Wild type

     • Phenotype most common in natural pops

   • Mutant phenotypes

     • Alternatives to wild type

   • Symbolizing allele

     • Gene given symbol for 1st mutant observed

     • Ex. eye color in fruit flies

       • Red (wild type)

         • w+

       • White (mutant) (unusual)

         • w

The w’s are the alleles for eye color gene

Usually have red eyes (wild type)

Morgan found white-eyes male (mutant)

Experient:

• Red-eye female x white-eye male

3. Morgan’s experiment (in LG)

All white eyes = male. Why??? Eye color gene located on X chromosome

II. Sex chromosomes

1. Introduction

   • Autosomes (fig. 10.3)

     • Non sex chromosomes

     • Homomorphic (same shape)

   • Sex chromosomes

     • One pair

     • Heteromorphic (diff. shape) (x is longer, y is shorter)

     • During meiosis

       • Synapse (come together)

       • Crossing over can occur (Prophase 1)

     • Major sex determining genes and other types of genes

     • Sex-linked gene

       • On a sex chromosome

3. Sex determination in humans

In LG

*all cells have sex chromosomes

B. X-linked genes

1. Males

   • Only one X

   • X-linked alleles

     • Not homozygous or heterozygous

   • Hemizygous

     • Every allele on X is expressed

     • Regardless if dom or rec

2. Females

   • 2 copies of X

   • During embryonic development

     • One X in each cell inactivated by DNA methylation (CH₃)

     • Random process

   • Barr body

     • The inactive X chromosome

     • Stains darkly, condensed

     • Along inside of nuclear envelope

   • If female is heterozygous (X^AX^a) *Alleles in superscripts

     • Some cells, X^A inactivated

     • Other cells, X^a inactivated

       • Ex. in LG

III. Linkage (In LG)

1. Unlinked genes

   • Located on diff chromosomes

   • Assort independently

B. Linked genes

1. On same chromosome

2. Ex. Humans

   • ~20,000 genes on 23 homologous pairs

     • Many genes on each chromosome

Linkage

• Tendency for group of genes on same chromosome to be inherited together

• Violates law of independent assortment (Mendel’s law)

14: DNA

1. DNA is the genetic material

Chromosomes have 2 things

DNA: 4 nucleotide

Proteins: 20 amino acids

So where do GENES come from??????

A. Griffith (1928)

1.) Streptococcus pneumoniae

Two strains

a. Smooth (S) strain

• Colonies: Smooth, shiny (cell lumps)

• Capsule: → Protects from immune cells

• Virulent: Mice DIE

b. Rough (R) strain

• Colonies: Rough

• Capsule: Immune cell engulf and destroy R cells

• Avirulent: Mice LIVE!

B. Avery, MacLeod, and McCarty (1944)

1. Lysed cells (broken apart) ↓

2. Separated into

a. Polysaccharides

b. Lipids

c. Proteins

d. Nucleic Acids

1. Tested each for transforming ability

2. Only DNA could transform

Everyone else said there could be protein contamination or only for prok. not euk.

C. Hershey/Chase (1952)

1. T2 bacteriophage (phage) (eats bacterium)

a. Virus

b. Infects bacteria and then replicates

c. DNA core with protein coat

1. Purpose

Is protein or DNA the hereditary material??

↓ ↓

Sulfur (S) Phosphorus (P)

II. DNA Structure

A. Nucleotide structure

1) Each contains

• Phosphate group

• Sugar deoxyribose

  

• Nitrogenous base

2.) Bases

1. Purine

- 2 Rings

- Adenine and Guanine

1. Pyrimidine

- 1 Ring

- Cytosine and Thymine

B. Determining DNA structure

1.) Edwin Chargaff (1949)

• Amounts of each base in many organisms

• 2 Rules

a. Total purines = Total pyrimidines

A + G = C + T

b. Amount of A = Amount of T (1:1)

Amount of C = Amount of G (1:1)

2.) Rosalind Franklin (1951–1953)

X-Ray diffraction → key features of DNA 3d structure

• Helical

• Bases on inside

• Width is constant

III. DNA Replication

C. Elongation

1. Template read 3’ to 5’

2. Subunits are nucleoside triphosphate

(sugar + base) + 3 phosphate groups

1. Elongation is 5’ to 3’

2. DNA polymerases: Catalyze phosphodiester bond formation

a. Complementary

b. Can only add to 3’ end of existing strand

15: Gene Expression

I. Relationship between genes and proteins

Review

Genes

• On chromosomes

• DNA

• Info for making polypeptides NOT protein, but eventually yes

A. Central Dogma – Crick, 1958 (Watson/Crick)

• Unidirectional flow of genetic information

DNA → transcription → RNA → translation → Polypeptide

2.) Single stranded (ss)

3.) Types

1. mRNA (messenger)

  Encodes entire polypeptide (Instruction sheet for aa)

1. rRNA (ribosomal)

  Structural part of ribosome

1. tRNA (transfer)

  Brings aa’s to ribosome during translation

CC DNA and RNA

C. Genetic Code

mRNA = “language”

Codons = “words”

1.) Codon

• mRNA sequence

• Triplet (3 bases) A, C, G, or U (NOT “T”)

• Codes for 1 aa

• 64 different combinations

4 × 4 × 4 = 64 possible

5.) Reading frame

Correct grouping of codons

(the red dog ate the bug)

→ the red oga tet heb ug

6.) Universal

– Prok, euk, and viruses → Not on tree of life

II. Transcription: DNA to RNA

• Synthesizes RNA that is complementary to DNA

• 3 Stages

A. Initiation

DNA

• Only template transcribed (read 3’ to 5’)

• Transcription unit: DNA sequence that is transcribed

Promoter

• Specific DNA seq at 3’ end (upstream) occurs downstream

Starts

RNA polymerase

• Does not need a primer

• Binds to promoter, unwinds helix (DNA), begins transcription

B. Elongation – RNA Polymerase

• Reads DNA template 3’ to 5’

• Synthesizes 5’ to 3’

• Adds nucleoside triphosphate

• Energy from hydrolysis of 2 Pi

Lots of energy in phosphate bonds

When broken, they release energy

C. Termination

1. Specific DNA sequences signal RNA polymerase to stop

2. RNA transcript released from template

III. Translation: RNA to Polypeptide

b) function

• 3’ end binds to specific amino acid (determined by anticodon)

• Different tRNAs

• Different anticodons bind different amino acids

• Bring specific amino acids to the ribosome

2.) Ribosomes

Compromised of…

• Protein

• rRNA

Location: Cytoplasm

• Surface of RER

Function

• Bind to mRNA

• rRNA is a ribozyme (NOT ribosome)

  Catalyzes peptide bonds

C. Elongation

• Series of repeated cycles

• Each adds single amino acid to growing polypeptide chain

1.) Large Subunit (ribozyme)

• Catalyzes peptide bond formation

2.) Translocation

• Ribosome moves down one codon on mRNA in 5’ to 3’ direction

17: Gene Regulation

Types of Genes

1. Constitutive

• “Housekeeping”

• Constantly transcribed → RNA always being created

• Proteins always needed

• Example: enzymes for respiration

2. Regulated

• Transcribed only at certain times or in certain cells

I. Prokaryotic Gene Regulation

Transcriptional level

• Information in DNA → information in RNA

Operon

• Set of genes controlled as a unit

A. lac Operon

• Lactose metabolism in Escherichia coli

• E. coli live in the human large intestine

• Adjust to changes in chemical environment

• If host drinks milk, E. coli digests lactose

1. Components

a. Promoter

• DNA sequence

• Not transcribed

• RNA polymerase binds

b. Operator

• DNA sequence

• Not transcribed

• Binding site for repressor

• “On-off” switch

c. 3 Structural Genes (transcribed)

lacZ: β-galactosidase (β-gal)

Lactose → glucose + galactose

lacY: Permease

• Transmembrane carrier

• Transports lactose into cell

lacA: Transacetylase

• Next to each other

• Share single promoter

• All on or all off

Overview

Transcription

• Single continuous mRNA molecule

• Each gene has its own start/stop codon

Translation

• Produces 3 separate proteins

2. Proteins that regulate lac operon (Negative Regulation)

a. Repressor

• Coded for by lac repressor gene

-> Not part of lac operon

-> Pi = promoter

-> Constitutive

Binding site on operator:

When repressor fails to bind:

• Operon is ON (transcription occurs)

When repressor binds:

• Operon is OFF (no transcription)
  

b. Catabolite Activator Protein (CAP)

Two forms

• Unbound: inactive

• Bound to cAMP: active

Promoter

• Inefficient (low affinity for RNA polymerase)

• CAP-binding site present

cAMP levels

• High when glucose is scarce

• Low when glucose is abundant

Inactive CAP (no cAMP)

• Does not bind

• Promoter has low affinity for RNA polymerase

• Transcription reduced

Positive Regulation (Active CAP)

• CAP binds

• Bends DNA helix

• Increases promoter’s affinity for RNA polymerase

• Transcription enhanced

B. Chemical Environments

1. Lactose present & glucose absent

• Lactose enters cell
  → Allolactose (isomer)

• Allolactose binds to allosteric site on repressor
  → Repressor changes shape
  → Inactivated
  → Cannot bind

II. Eukaryotic Gene Regulation

Multicellular eukaryotes

• Many different types of cells

Differential gene expression

• Expression of different genes by cells with same genome
  → Cell specialization
  → Different tissue types

Gene Regulation in Eukaryotes

Occurs at multiple levels:

• Chromatin structure

• Transcription

• RNA processing

• Protein processing
  

  

A. Regulation of Chromatin Structure

1. Euchromatin

• Loosely packed
  → Transcription occurs

• Active genes

2. Heterochromatin

• Highly condensed
  → No transcription

• DNA methylation

• Example: Barr body

B. Regulation of Transcription Initiation

1. Promoter

• RNA polymerase binds & begins transcription
  

2. Control elements

• Non-coding DNA

• Binding sites for transcription factors (TFs)

3. Transcription factors (TFs)

• Proteins

• Increase or decrease RNA polymerase binding

C. RNA Processing

• Post-transcriptional regulation

Includes:

1. 5’ cap & 3’ poly-A tail

2. Splicing of pre-mRNA

D. Protein Processing

1. Post-translation regulation

2. Polypeptide → functional protein

3. Chemical modifications

• Glycosylation

• Phosphorylation

4. ER & Golgi

18: DNA Technology

DNA Technology

techniques for sequencing and manipulating DNA

1. Polymerase chain reaction (PCR)

2. Introduction

3. Purpose: produce many copies of DNA seq in short time

4. Based on: DNA replication

5. 3-step cycle repeated many times

Each cycle:

1. Denaturation

2. Annealing

3. Extension

4. Thermal cycler

• automatically controls and alternates temperatures

• programmed periods of time and number of cycles

5.

1. template DNA sample containing DNA seq to be amplified

2. primers

• synthetic sequence of single stranded DNA

• short (around 15-20 bases)

• dNTPs: A, C, G, T

1. Taq polymerase

B. Process of PCR

Step 1: Denaturation

• Temp > 90 degrees C

• Backbone

Sugar-phosphate

covalent bonds

-> strong and remain intact

- bases

H bonds

-> weak and break

-> double stranded dna separates into two single strands

Step 2: Annealing

1. temp

40 degrees - 65 degrees C

1. primers

1 for each single stranded DNA

-> Anneal (bind) at 3’ end of target strand

Step 3: Extension (Elongation)

1. Temp increases to around 72 degrees C

2. Taq DNA polymerase

Thermus Aquaticus

Bacterium in hot springs

Enzymes stable at high temperatures

Begins at primers

Synthesizes DNA 5’ to 3’

1. 30-40 cycles

C. Gel electrophoresis

1. Agarose gel (polysaccharide):

Molecular sieve

1. Nucleic acids separate on basis of size

2. Method

• Sample of PCR mixture loaded into gel

• Electric current

• DNA (-charge) migrates toward + electrode

• Smaller fragments move faster

1. Visualize bands, remove fragment from gel and use in other techniques

   

D. Uses of PCR

Amplify small amounts of DNA

• Fingerprints, blood at crime scene

• Single embryonic cell

• Extinct species

II. DNA sequencing

• Purpose: Determine nucleotide seq of DNA

• Based on: Semi-conservative replication (DNA lecture)

A. Dideoxy chain termination sequencing

1. Sequencing machine

2. Ingredients

3. dsDNA fragment -> Denatured by heat into single strands

1. Primer (DNA)

- Short stretch of nucleotides

- Designed to base pair with 3’ end of template

1. DNA polymerase

- Adds nucleotides to growing strand (5’ to 3’)

- Needs 3’ OH

1. Deoxyribonucleotides

- dNTP

1. 4 Dideoxyribonucleotides

3. Process: Synthesis

1. Begins at 3’ end of primer

2. If dNTPs added -> Elongation continues

3. Until a ddNTP inserted (at random)

-> Elongation stops

(b/c no free 3’ OH)

1. Set of labeled fragments

- Various lengths

- Color of label represents last nucleotide in fragment

5. Process: Separation of DNA fragments

1. Polyacrylamide gel

• Polymer (molecular sieve)

1. Shorter fragments move faster

• Seq not important

1. Fluorescent detector

- senses color of each tag

6. Result: Spectrogram

• Seq of entire DNA fragment

B. Uses of sequencing

1. Medicine

• Identify genes and determine risk of genetic disease

1. Forensics

• Identification

• Paternity testing

1. Evolutionary biology

- Determine evolutionary relationships

III. Applications of DNA technology

1. Species diversity

Bar-coding (UPC)

• Sequencing from standard part of genome

• Ex: Animals - Mitochondrial gene

• Barcodes compared

Ex: two samples of algae Same species!!!

Bio Lab (01:119:117)

• PCR

1. Gene therapy

1. Background

- Use of gene to treat or prevent disorders caused by a single defective gene

- Insert normal allele into somatic cells

- Risky

- Currently, mostly in clinical trials

- Recent FDA approval for: 1 type of blindness and 2 blood disorders

2. Methods

1. In vivo

• Modified so doesn't cause disease

• Delivers therapeutic gene

1. Ex vivo

🔴 EXAM 2 (lectures 10-18)

✅ 19: Human Genetics

I. Study of Human Genetic Variation

A. Introduction

1. Difficult to study

• Few offspring

• Long generation time

• Cannot do experimental mating

2. How to study

a. Large extended families

• Analyze previous matings

• Medical: genetic disorders

b. DNA sequencing

→ genetic basis of similarities & differences

B. Pedigree Analysis

• Family tree

• Inheritance patterns over several generations

• Predict inheritance of phenotypic traits controlled by genotype at a single locus

• Genetic counseling

Example: Widow’s Peak

• Autosomal dominant

• W ≠ w
  

1. F2 genotypes?

2. Genotypes of sisters’ parents?

3. Genotypes of others

II. Mendelian Inheritance Patterns

A. Autosomal Recessive Condition

(not on sex chromosomes)

1. Introduction

a. Recessive allele

• Codes for malfunctioning protein or no protein at all

b. Heterozygote (Aa)

• Dominant allele codes for enough protein → normal phenotype

• Carrier for recessive allele

c. Homozygous recessive (aa)

• Has condition

• Most born to parents who are carriers

d.

• Many human genetic conditions inherited as single-locus autosomal recessive traits

2. Human conditions due to autosomal recessive genes

a. Albinism

• Albino = lacking skin pigmentation

b. Cystic fibrosis

i. Normal allele

• Codes for transmembrane protein
  → transport of Cl⁻
  

ii. Recessive allele

• Protein defective or missing
  

iii. Homozygous recessive

• Thick, sticky mucus

• Builds up in many organs

c. Sickle-cell disease

i. Hemoglobin (Hgb)

• 4 polypeptide chains: 2 alpha & 2 beta

• Single amino acid substitution in beta chains
  → glutamic acid → valine
  

ii. Abnormal RBCs

• Destroyed → anemia

• Clump → block capillaries → tissue damage & pain
  

iii. Heterozygotes

• Normal allele → normal Hgb

• Abnormal allele → abnormal Hgb

• Resistance to malaria → evolutionary advantage

B. Autosomal Dominant Conditions

(much rarer)

1. Achondroplasia

• Form of dwarfism

• Allele is dominant

• Phenotype of heterozygous genotype = dwarf

• Genotype of individuals who are NOT dwarfs = dd

2. Lethal Alleles

a. If recessive:

• Heritable

• Homozygous recessive → death

b. If dominant:

• Death often before reproductive age

• Late-onset diseases
  → no symptoms until reproductive age
  

Example: Huntington Disease

• Death of brain cells

• Overall deterioration → death

• Adult onset (> age 40)

• Child with HD parent has 50% chance of inheriting

• Genetic test for allele

III. Non-Mendelian Inheritance Patterns

A. Changes to chromosome number (chr)

1. Introduction

a. Disomy

• Normal 2n state

• 2 copies of each chromosome (homologous pairs)

Mistakes can happen during meiosis

b. Nondisjunction

• Homologous chromosomes

• Sister chromatids

C. Aneuploidy

• Abnormal number of particular chromosome (+ or −)

Trisomy

• 3 copies of one chromosome

• 2 copies of all others
  → 2n + 1

Monosomy

• Missing one chromosome of a pair
  → 2n − 1

• Monosomics for all autosomes die in utero

1. Down syndrome

• Langdon Down

• Trisomy 21

• Nondisjunction in mother (↑ with age)

Characteristics:

• Short stature

• Physical & mental impairment

• Heart malformations, respiratory disease & leukemia

2. Aneuploidy of sex chromosomes

a. Turner syndrome (45, X0)

• Female

• Underdeveloped ovaries (sterile)

• No Barr bodies

b. Klinefelter syndrome (47, XXY)

• Male

• Underdeveloped testes (sterile)

• Have Barr bodies

c. XYY syndrome (47, XYY)

• Male

• Usually fertile

• Don’t transmit extra Y

B. Changes to chromosome structure

1. Caused by error in meiosis or damaging agents

2. Four types:

a. Deletion

• Removes a chromosomal segment

b. Duplication

• Repeats a segment

c. Inversion

• Reverses a segment within a chromosome

d. Translocation

• Moves a segment from one chromosome to a nonhomologous chromosome

3. Cri du chat

• Deletion on chromosome 5

Characteristics:

• Intellectually disabled

• Speech disabilities

• Small head

• Cry sounds like a distressed cat

IV. Genetic Testing

• Earlier diagnosis of genetic disorder
  → greater chance for preventing or alleviating effects

A. Fetal testing

• Before birth

1. Amniocentesis

• 14th–16th week

• ~20 mL fluid

• Contains live fetal cells

2. Chorionic Villus Sampling (CVS)

• 8th–10th week

a. Chorionic villus tissue

• Placenta

• Derived from fetus
  → fetal genotype

b. Tissue sample

• Many cells

• Rapidly dividing

B. Newborn screenings

Example: Phenylketonuria (PKU)

• Normal:

  • Phenylalanine metabolized to tyrosine
    

• PKU:

  • Autosomal recessive disorder
    

✅ 20: Intro to Evolution

Evolution

• Decent with modification

• Charles Darwin

1. Pre-Darwinian ideas

2. Life is constant

• Species (spp) are unchanging

1. Aristotle (384 - 322 BCE)

2. Judeo-Christian cultures

Natural theology

• Discover God's plan by studying nature

• Carolus Linnaeus (1707 - 1778)

Naming & classifying organisms

Early 1800’s: Idea of ‘no change’ starts to be questioned

1. George Cuvier (1769 - 1832)

2. Paleontologist

3. Rock layers in Paris

• Species appeared & disappeared

• Species in deeper layers different from modern species

1. Catastrophism

Each layer resulted from a catastrophe

-> Destroyed many species

-> New species migrated in

2. James Hutton

1. Geologist

2. Gradualism

Geologic change from gradual mechanisms

Ex: Valleys formed by rivers

3. Charles Lyell

1. Geologist

2. Refined gradualism -> uniformitarianism

• Processes today are same as in past & at same rate

• Earth is > 6,000 years old

C. Jean Baptiste de Lamarck

1. Studied fossils & observed lines of decent

2. Two principles

3. Use and disuse

• Body parts that are used -> change

= Acquired characteristics

• Parts not used -> deteriorate

• Ex: Giraffes

1. Inheritance of acquired characteristics

• Ex: Giraffe has short neck

-> Stretches & gets long neck

-> offspring have long neck

1. Darwin's work & ideas

2. Background

3. Voyage on HMS Beagle (1831 - 1836)

• Ships naturalist

• Observations

• Read

1. After voyage

• Naturalist, published trip accounts, wrote books

• Developed theory of natural selection, but did not publish it

1. 1858

• Alfred Russell Wallace

Theory of natural selection!

• CD & ARW presented Linnaean Society

1. 1859

• “On the Origin of Species by Natural Selection”

• Better support & earlier notes than ARW

B. Observations and connections

1. Variation

2. Overproduction

Not all survive to reproduce

C. Evolution by natural selection

1. Natural selection is mechanism

2. “Survival of the fittest”

• Fitness

Ability to survive and have viable offspring

• Better adapted organisms more likely to survive & reproduce

1. As result, population changes over time

= Evolution

• Favorable traits

-> Increase in frequency (freq) over generations

• Less favorable traits

-> become scarce or disappear

1. Populations evolve

Individuals do not evolve

Example of natural selection

1. Grasshopper lays eggs

2. Yellow and green grasshoppers hatch

3. Predator (bird) eats the grasshoppers that are easy to see (the yellow ones)

4. Green grasshopper are left to reproduce

5. Evidence for evolution

6. Artificial selection (= Selective breeding)

• Humans

• Desirable traits

• Species changes from wild ancestors

• Ex: Agriculture

• Ex: Dog lineage

1. Direct observation

Ex: Antibiotic resistance in bacteria

1. Homology

• similarities due to common ancestry

• Phylogenetics: study of evolutionary relationships

1. Homologous structures

Ex: Mammalian forelimbs

• Different appearance and function

• Same patterns of bones, muscles, and nerves

1. Embryonic development

Similarities in early development of different animals species because they share CA

1. Vestigial organs

2. Undersized and not functional

3. Evolved from CA in which structures were functional

4. Ex:

• Hind limbs bones in whales and pythons

• Wing bones in flightless birds

• Muscles to move the human ears

4. Molecular homology

1. Genetic code is universal

2. Homologous genes: Inherited from CA

Ex: Humans and bacteria share genes

D. Fossil record

1. Remains or traces in sedimentary rock of previously existing organisms

2. Record of ancient organisms

• Where and when they lived

• Used to infer lines of descent that gave rise to modern-day organisms

Evidence of Evolution

• Artificial selection

• Direct observation

• Homology

• Fossil record

Summary

1. Evolution

2. Natural selection

Requires heritable phenotypic variation population

1. Evolutionary mechanisms: Unity and diversity of species

2. Evolution links all fields in science

✅ 21: Population Genetics

Key Definitions

• Population: Group of individuals of the same species living in the same area at the same time that interbreed to produce viable offspring

• Evolution: Change in allele frequencies in populations over generations

• Microevolution: Small changes in allele frequencies over a few generations

• Population genetics: Study of genetic variability and evolutionary forces in populations

I. Variation in Individuals

A. Phenotypic Variation

• Observable differences among individuals

Types:

1. Either/or variation

   • Controlled by a single gene

   • Example: pea plants

2. Continuous variation

   • Controlled by multiple genes

   • Example: human height

B. Genetic Variation

1. Differences in DNA sequences

2. Sources:

• Mutation → new alleles

• Sexual reproduction → new allele combinations

Key Relationship

Genetic variation → Phenotypic variation → Natural selection

II. Detecting Evolution in Populations

A. Allele Frequencies

Alleles in individuals:

• Alternative forms of a gene

• Individuals can be:

  • Homozygous (AA, aa)

  • Heterozygous (Aa)

Law of Segregation

• Alleles separate into gametes

Alleles in populations:

• Gene pool: all alleles in a population

• Fixed allele: only one allele present

Allele frequency

• Proportion of an allele

• Must sum to 1.0

B. Genotype Frequencies

• Proportion of genotypes in population

Example:

• f(AA) = 0.64

• f(Aa) = 0.32

• f(aa) = 0.04

Total = 1.0

C. Hardy-Weinberg Equilibrium

Definition

• Population is not evolving

Equations

p + q = 1

p^2 + 2pq + q^2 = 1

• p = f(A), q = f(a)

• p^2 = f(AA), 2pq = f(Aa), q^2 = f(aa)

Conditions (must ALL be met)

1. Very large population

2. Random mating

3. No mutation

4. No gene flow

5. No natural selection

→ If any condition is violated → evolution occurs

How to Solve HW Problems

1. Identify what is given

2. Use equations

3. Solve

Key Examples

• If p = 0.7, then q = 0.3

• If q² = 0.36, then q = 0.6, p = 0.4

• Allele frequencies stay the same across generations in HW

III. Factors Affecting Allele Frequencies (Evolution)

A. Genetic Drift

Definition:

• Random changes in allele frequencies (strong in small populations)

Effects:

• Reduces genetic variation

• Alleles lost by chance

Types:

1. Founder Effect

• Small group forms new population

• Different allele frequencies from original population

2. Bottleneck Effect

• Sudden reduction in population size

• Survivors not genetically representative

• Loss of variation

B. Nonrandom Mating

Random mating:

• Equal chance of mating

Nonrandom mating:

• No random mixing

Effects:

• Does NOT change allele frequencies

• Changes genotype frequencies

Example: Inbreeding

• Increases homozygous genotypes

• Decreases heterozygotes

C. Mutation

Role:

• Source of genetic variation

• Creates new alleles → changes gene pool

• Provides raw material for natural selection

Important Notes:

• Not all mutations are passed on:

  • If in somatic cells → not inherited

  • Often harmful

• Mutations are rare

  • Usually do NOT significantly change allele frequencies (especially in large populations)

D. Gene Flow (Migration)

Definition:

• Movement of alleles between populations

Effects:

• Alters allele frequencies in both populations

• Can increase or decrease variation

E. Natural Selection

Key Idea:

• Main mechanism of evolution

How it works:

• Acts on phenotypic variation

• Some individuals are better adapted

Results:

• Better-adapted organisms:

  • Survive

  • Reproduce more

→ Differential reproductive success

Over time:

• Favorable traits accumulate

• Population becomes better adapted

→ Adaptive evolution

FINAL SUMMARY (what to remember most)

• Evolution = change in allele frequencies

• Hardy-Weinberg = no evolution baseline

• If HW conditions break → evolution occurs

• 5 forces of evolution:

  1. Genetic drift

  2. Nonrandom mating

  3. Mutation

  4. Gene flow

  5. Natural selection (most important)

✅ 22: Speciation

I. Species

A. Introduction

1. Microevolution

• Changes in allele frequency over time in a population
  → Population is still the same species

2. Macroevolution

• Large-scale evolutionary changes
  → Leads to formation of new species

• Example: divergence into very different organisms (ex: cats vs dogs)

3. Speciation

• Formation of two species from one

• Increases biodiversity

Biodiversity facts:

• ~2 million species identified

• Estimated 10–100 million total

B. Species Concepts

1. Morphological Species Concept

• Based on physical structure (shape, form, anatomy)

• Works for:

  • Sexual organisms

  • Asexual organisms

  • Fossils

2. Ecological Species Concept

• Based on ecological niche

• Focuses on:

  • Interactions with environment

  • Resource use

• Works for:

  • Sexual organisms

  • Asexual organisms

3. Biological Species Concept (BSC)

Ernest Mayr

Definition:
A species is a group of populations whose members:

• Interbreed in nature

• Produce viable offspring

• Share a common gene pool

• Have gene flow between populations

Key idea:

• Reproductively isolated from other species

Limitations:

• Cannot be applied to:

  • Fossils

  • Asexual organisms

II. Reproductive Isolation

• Prevents:

  • Interbreeding

  • Production of viable offspring

• Stops gene flow between species

A. Prezygotic Barriers

(occur before fertilization)

1. Prevention of Mating Attempts

a. Habitat Isolation

• Same area, different habitats

• Example:

  • One species prefers sandy soil

  • Another prefers loamy soil

b. Temporal Isolation

• Breed at different times (day, season, year)

c. Behavioral Isolation

• Different courtship behaviors or signals

• Example: mating calls

Application example:

• Eastern vs Western meadowlarks
  → Different songs prevent mating
  → Behavioral isolation

2. Mating Attempted but Fertilization Prevented

a. Mechanical Isolation

• Reproductive structures don’t match

• “Lock-and-key” mechanism

Examples:

• Different genital structures

• Flowers & pollinators:

  • Wide flower → bees

  • Tube-shaped → hummingbirds

b. Gametic Isolation

• Egg and sperm incompatible

External fertilization:

• Egg receptors bind only same-species sperm

Internal fertilization:

• Sperm cannot survive in different species’ reproductive tract

B. Postzygotic Barriers

(occur after fertilization)

1. Reduced Hybrid Viability

• Embryo fails to develop properly
  → Dies early

2. Reduced Hybrid Fertility

• Hybrid survives but is sterile

Example:

• Horse (2n=64) × Donkey (2n=62) → Mule (63 chromosomes, sterile)

3. Hybrid Breakdown

• First generation is viable

• Later generations:

  • Weak

  • Sterile

III. Process of Speciation

• Formation of new species from one original species

Requires:

• Reproductive isolation

• Gene pool divergence

A. Allopatric Speciation (“Other homeland”)

• Most common

1. Separation

a. Geographic Barriers

• Mountains

• Rivers

• Lakes

→ Populations become isolated

b. Migration

• Small group colonizes new area

→ Founder effect

2. Divergence

• Gene pools evolve separately

• Even if populations meet again:

  • They cannot interbreed

B. Sympatric Speciation (“Same place”)

• Occurs without geographic isolation

• New species forms within same area

• Less common

Mechanisms of Sympatric Speciation

1. Polyploidy

• More than 2 sets of chromosomes

Process:

• Meiosis error → gametes are diploid (2n)

• Fertilization → tetraploid (4n)

Result:

• 4n organisms:

  • Can reproduce with each other

  • Cannot reproduce with original 2n population

Notes:

• Common in plants

• Rare in animals

2. Sexual Selection

• Differences in traits (appearance, behavior)
  → Can lead to reproductive isolation

3. Habitat Differentiation

• Subgroups use different resources or habitats
  → Reduces interaction → speciation

IV. Pace (Rate) of Speciation

A. Speciation Models

1. Punctuated Equilibrium

• Long periods of little/no change

• Short bursts of rapid evolution

• Triggered by environmental change

2. Gradualism

• Slow, steady accumulation of changes

• Continuous evolution over time

• Proposed by Darwin

B. Speciation Rates

• Range:

  • 4,000 years → 40 million years

• Average:

  • ~6.5 million years

Example: Euhadra (Japanese land snail)

• Single gene change → shell spirals differently

• Changes genital alignment
  → Cannot mate

= Mechanical isolation

Extra Concepts (from notes)

Tree of Life

• All organisms share a common ancestor

• Speciation creates branching pattern of life

Scientific Method

1. Observation

2. Question

3. Hypothesis

4. Prediction

5. Experiment

6. Analyze results

7. Conclusion:

   • Supported

   • Not supported → revise

8. Report results

✅ 23: Phylogenetics

Evolution

• Decent with modification

• Natural selection

• Populations (Individuals do not evolve) (change in allele frequencies)

1. Systematics

The study of diversity of organisms and evolutionary relationships

2 Parts

- Taxonomy = Describing, naming, and classifying

- Phylogeny = Evolutionary history

1. Taxonomy

1. Binomial nomenclature

a. Naming species (Developed by Carolus Linnaeus - unique 2 part name)

b. Genus + specific epithet (Ex: Homo sapiens)

Named 11,000 species of plants and animals -> Still used today

c. Rules (Ex: Tyto alba)

- Latin/latinized

- Genus name upper case, but specific epithet is not

- Both italicized or underlined

- Genus can be abbreviated (T. alba)

2. Hierarchical classification

a. Species = smallest unit of classification

b. Levels

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

Taxon (taxa pl.) - grouping of organisms at any one of these levels

Ex: Family genus & species

Mnemonic - learning technique that aids in encoding/retrieval of info

Dear King Phillip Come Out For Goodness Sake

c. From species to domain

-> Each level more inclusive

d. All species at a level share characteristics of that group

Ex: Spinus tristis

Domain Eukaryota

Kingdom Animalia

Phylum Chordata

Class Aves

Order

Family

Genus

Species

1. Phylogeny

- Study of evolutionary history and relationships among organisms

- Based on shared ancestry, not phylotypic similarity

II. Basics of phylogenetics

1. Phylogenetic tree

2. Branching diagram

• Patterns of descent from a common ancestor (CA)

1. Many hypothesis

B. How to read a tree

1. Most recent common ancestor

• Root

• Ancestor from which all taxa in tree have descended

1. Branch points = Nodes

2. Dichotomies: Divergencies of 2 lineages from a CA

3. Branches can rotate without changing relationships

3. Extant species

• Currently living

• At tips of branches

4. Basal Taxon

• 1st lineage to diverge from CA of group

5. Sister taxa

• Organisms that share an immediate CA

• Each other’s closest relatives

  

6. Polytomy

- Branch point with > 2 descendent groups

- Evolutionary relationships not clear

Summary

III. Constructing phylogenies

1. Character

2. Defined attribute of a species

3. States: Alternate forms of a character

1. Compare characteristics and states

-> The more closely 2 species are related, the more they share

Must result from common ancestry

1. Character states may be similar for two reasons

2. Homologous (inherited from a CA)

Connection -> Intro to evolution

• Look and function differently

• Underlying structure is the same

• Inherited from CA

Homologous structures

• Share common evolutionary relationships

1. Analogous

• Independently acquired

• Similar adaptations in organisms from different evolutionary lineages

• Similar environment

-> Similar selection pressure

-> Similar character

(Do not share a CA with that character)

-> Convergent evolution

Analogous structure

Aerodynamic principles

-> converged on structures for flight

5. Choosing characters

Ex: Anatomical/morphological features

Developmental and life history traits

Molecular data

a. Morphological data

b. Molecular data

- Compare DNA sequences

Genes are sequences of 100s of nucleotides

Ex: 12 nucleotides -> 12 characters

A, C, G, or T at each site -> States

If a gene in 2 organisms shares many nucleotides

then possibly homologous

Compare RNA sequences

Compare amino acid sequences of proteins

B. Cladistics

1. Widely used method of systematics

Uses homologies to classify organisms based on common ancestry

Claude - group which includes ancestral species and all its descendants

2. Three possible groups

GB 116

Lecture 1 = phylogenetics review and virology

✅ 25: Population Ecology

Ecology

Study of interactions between organisms and environment

1. Introduction to population ecology

2. Basic concepts

3. Population

• Definition

• Interact and breed

• Share common gene pool

• Same resources and environmental factors

Evolves as a natural selection acts on variation

1. Population ecology

• How biotic and abiotic factors affect populations

• How and why populations change over time

1. Features of populations

2. Size: # of individuals

3. Density: # of individuals per unit area or volume

B. Change in population size over time

N = # of individuals

t = time

B = # births

D = # deaths

1. Change in # of individuals

ChangeN/changet = B - D

Ex: 10 births and 40 deaths

ChangeN/changet = 10 - 40 = -30

Ex: 20 birds and 5 deaths

ChangeN/changet = 20 - 5 = 15

If N started at 15, population increased 100%

If N started at 150, population increased 10%

1. Per capita change

a. How much does the average individual contribute to the population

- b = per capita birth rate = B/N

- m = per capita death rate = D/N

Ex: A population of 100 has 15 births and 10 deaths per year

What are the birth and death rates?

N = 100

B = 15

D = 10

b = B/N = 15/100 = 0.15 births/year/individual

m = D/N = 10/100 = 0.1 deaths/year/individual

b. Use rates (b and m) to calculate expected change in population size

changeN/changet = B - D

= bN - mN

= N(b - m)

Ex: a population of 200 has a birth rate of 2.0 and a death rate of 0.15

N = 200 b = 0.2 m = 0.15

What is the expected change in population size per unit time?

200 (0.2 - 0.15) = 10 individuals added to population per unit time

b = bN = 0.2 x 200 = 40 births

D = mN = 0.15 x 200 = 30 deaths

1. Per capita growth rate (r)

r = b - m

changeN/changet = N(b - m)

= rN

If b < m then r < 0 -> population declining

If b > m then r > 0 -> population increasing

If b = m then r = 0 -> Zero population growth (ZPG)

(Births and deaths cancel out, occurring at same rate)

1. Instantaneous growth rate (r inst)

r at one specific point in time rather than a larger interval

dN/dt = rinstN

II. Population growth models

1. Exponential growth model

2. Describes population in which conditions are ideal

• Low population density

• Every individual has access to abundant resources and free to reproduce at physiological capacity

1. Population growing at (r max)

2. Intrinsic rate of increase

Max rate at which population could increase under ideal conditions

1. Microorganisms have highest r max

Ex: Bacteria reproducing by binary fission every 20 min

1 cell -> >1 billion in 10 hours

1. Large organisms tend to have low r max

2. J-shaped curve

3. Exponential growth model isn't as realistic in nature

Environmental resistance

As population density increases

• Less resources/individual

• Build up toxic wastes

Some populations may undergo exponential growth for short periods of time

But over long periods of time, growth rate may slow and go down to nearly zero

B. Logistic growth model

1. Accounts for environmental resistance

As population reaches limit of environment's ability to support it, population growth rate approached zero

1. Carrying capacity (K)

• Max population that can be sustained by a particular environment for an indefinite period

• Assumes no changes in environment

1. S-shaped curve (sigmoid)

• First part is exponential growth

• Levels out as K approaches

1. Equation

More realistic than experimental model

1. S-curves in nature usually not perfectly logistic

• Populations tend to fluctuate around K

• Environment is never completely constant -> K may change

III. Life history

• Patterns of survival, growth, and reproduction

• Trade-offs

1. Reproductive strategies

3 main variables

• Age at 1st reproduction

• How often organism reproduces

• # offspring per reproductive episode

1. Semelparous

• Short-lived (reproduce early)

• Reproduce once

• Very many offspring

Ex: Many insects, salmon

1. Iteroparous

• Long lived (reproduce later)

• Reproduce many times

• Fewer offspring

Ex: Most verts

B. Life history extremes

Connect differences in traits with growth models

1. r-selected species

2. Usually found in temporary or unpredictable environments

3. Tendency for:

• High growth rates (r)

• Small body size

• Early maturity

• Rapid production of many offspring

• Little or no parental care

• Short life span

2. K-selected species

1. Usually in relatively stable environment

Population size usually close to K

1. Tendency for:

• Long life span with slow development

• Large body size

• High competitive ability

• Defenses against predators

• Relatively old at 1st reproduction

• Few offspring

• Parental care

Life History

• Allocation of resources to survival, growth and reproduction

• Natural selection

✅ 26: Community Ecology

Community

• All populations of different species that live and interact in the same place at the same time

Community Ecology

• Study of interactions that determine distribution and abundance of individuals and populations

Resource

• Anything in environment that meets the need of a species

1. Community interactions

2. Competition -/-

Most important determinant

1. 2 or more individuals attempt to use same resources

2. Types

3. Intraspecific

4. Interspecific

3. Competitive exclusion

G.F Gause

Paramecium aurelia & P. caudatum

- Closely related to protists

- Cultured under constant conditions and food

Competitive exclusion principle

Conclusion: 2 species competing for the same limiting resources cannot coexist

4. Ecological niche

1. Eugene Odum

• Habitat = “address”

• Niche = “profession”

1. Role of species within community

• Use of resources

• Interactions

• All factors needed to survive, stay healthy, and reproduce

1. Fundamental niche

• Ideal circumstances

1. Realized niche

• Actual interactions and use of resources

Species with identical niches cannot coexist

-> Competitive exclusion

Species with similar niches can coexist

-> One species may exclude the other species from part of its fundamental niche into a realized niche

Resource partitioning

Species specialize their use of resources and thereby limit competition with others

B. Predation +/-

1. Predator eats prey

2. Results in evolutionary “arms race”

Each exerts strong selective pressure on other

-> Coevolution

Interdependent evolution of 2 interacting species

vii. Behavioral defences

• Fleeing

• Living in groups (Ex: herbs, school)

b. Plants

Herbivory +/-

Can’t escape predators

Adaptations to decrease chance of being eaten

• Mechanical (Ex: spines, thorns)

• Chemical (Ex: toxic to herbivores)

C. Symbiosis

• Intimate, long-term relationship between 2 or more species

• Usually involves one species living in or on the other

• 3 main forms of relationships

1. Parasitism (+/-)

- Parasite benefits and host can be harmed (rarely killed)

- Ex: heartworm in dog

1. Mutualism (+/+)

- Both partners benefit and each dependent on other

- Ex: Mycorrhizae

Fungi and roots of many plants

Roots provide organic molecules from photosynthesis

Fungi provide essential minerals from soil

1. Commensalism (+/0)

- one organism benefits and the other is neither harmed or helped

- Ex: Cattle egrets and african buffalo

II. Ecological Succession

• Continuous process of community development over time

• Changes in plant and animal species

1. Primary succession

Change in habitat not previously inhabited

Ex: New volcanic island

1. Bare rock: No organisms, no soil

2. 1st organisms

Lichen (Mutualism between algae and fungi) & mosses

Break down rock and begin to form soil

1. Larger pants:

First grasses,

Then shrubs and trees

B. secondary succession

Existing community cleared by disturbance that leaves soil intact

Ex: Forest fire

Abandoned ag field