Biology

8-25-16
Taxonomic Hierarchy:
Domain- Kingdom- Phylum- Class- Order- Family- Genus- Species
Evolution (because: genetic variation, inheritance of variation, nat selection)

Lesson 2: Atoms, Molecules, and Water

Covalent Bonds
Strongest bonds in cell
Based on sharing of electrons
Polar- has opposite charges, occurs when sharing of electrons is unequal
Nonpolar- equal sharing of electrons

Ionic Bonds
Based on attractive forces between ions (charged atoms)

Hydrogen Bonds
Form between slightly positive and slightly negative charges of polar covalent molecules
o Ex) water
o Ex) DNA nucleotides to form double helix
Weaker bonds
o Easily broken
Water
75% earths surface
Polar Molecule
o Formed by polar covalent
Good solvent
o Dissolves polar/hydrophilic substances
Proteins
Salts
Sugars
Other polar molecules
Oxygen
CO2
o Does not dissolve nonpolar/hydrophobic substances
Ex) Oil
Water stabilizes temperature
o Environmental temperatures
o Internal temperature of organisms
o High Specific Heat
Evaporative cooling
o High heat of vaporization
o Ex) sweating
Surface Tension
 o Cohesion
Water molecules stick together
o Adhesion
Water molecules stick to other surfaces
o Capillary Action
Combination of adhesion and cohesion to allow water to travel up stems of
plants
pH
Acids (0-6)
o Higher H+ concentration
o Donate H+ to a solution
Neutral (7)
Basic (8-14)
o Lower H+ concentration
o Donate OH- to a solution
pH and life
o Homeostasis
buffers donate or accept hydrogen protons and moderate the concentration
ex) blood plasma has buffering (bicarbonate and carbonic acid)

9-1-16
Lesson 4: Cell Structure and Function
Modern Cell Theory
All living organisms are made up of one or more cells
The smallest living organisms are single cells (and theyre the functional units of multicellular
organisms)
All cells arise from pre-existing cells

Cell Types all share some characteristics

Molecular components
o Biological molecules
Structural components
o Cytoplasm, cell membrane, ribosomes
Metabolism
o Extracts energy and nutrients from the environment
o Use energy and nutrients to build, repair, and replace cell parts

Microscopy
Light microscope
Transmission electron microscope
o More power to magnify
o Looking at interior structures
Scanning electron microscope
o Surface features , 3Dish
Cell Size
Prokaryotic are smaller than Eukaryotic
Why
o Surface area to volume ratio
Bigger size=reduction of SA/V ratio which makes it difficult to acquire materials
from environment to sustain
o Exchange with the external environment
o Diffusion within the cell
2 types
Prokaryotic (before the nucleus)
o ALL: Cell membrane, cytoplasm, ribosomes, DNA in nucleoid region
o SOME: flagellum, wall, pili, capsule
o 3 shapes
Spherical
Rod
Spiral
Eukaryotic (true nucleus)
o Plasma membrane=outer boundary
o Cytoskeleton
Microfilaments
Intermediate filaments
microtubules
o Endomembrane System
Membranes and organelles
Nucleus + Nuclear Envelope
o Nucleolus
Assembles ribosomes
o Chromatin
DNA + protein
o Nuclear Envelope
Double membrane with pores
Lysosomes
o Breakdown of macromolecules and organelles
Vesicles
o Move materials to and from golgi
o Storage and transport
o Can fuse with other membranes
ER
o Rough ER- modification and packaging of proteins
o Smooth ER- lipid synthesis; degrades toxins
Golgi Apparatus
o Modification, packaging, labelling
Interacts with Plasma membrane
Other organelles:
 Ribosomes
o Protein synthesis
Vacuole
o Storage
Peroxisomes
o Breakdown of fatty acids
o Detoxifies poisons
o Degrades hydrogen peroxide
o Mitochondria- synthesis of ATP
Has own DNA
Can divide on own
o Extracellular matrix
Holds cells together + communication
Made of network of substances secreted by cells
Plant Cells
o Central vacuole
o Cellulose cell wall
o Chloroplasts
Double membrane bound structure
Can divide on own
o Endosymbiosis
Origin of chloroplast and mitochondria
Intercellular Junctions
o Plasmodesma - channel between the cell walls of 2 adjacent plant cells
o Tight Junctions- join adjacent animal cells
o Desmosomes- join 2 animal cells together
o Gap junctions- act as channels between animal cells

9-6-16
Lesson 5: Cell Membrane and Transport
Membrane Functions
Isolates cell contents
Regulates exchange
o Selectively permeable
Communicates with other cells
Recognition
o Self vs non-self
Receptors
o Attachment sites for specific substances
Membrane Components
Phospholipids- arranged in a bilayer
o Isolate cell contents
o Saturated and unsaturated fatty acids (tails)
Cholesterol
 o Animal cells
o Acts as anti-freeze
Proteins- integral (pass all the way through bilayer)and peripheral (only on 1 surface)
o Transport
o Receptor-signals
o Recognition-self recognition
o Connection/attachment
o Enzymes
Carbohydrates
o Bound to lipids (glycolipids)
o Bound to proteins (glycoproteins)
Fluid Mosaic
Describes plasma membrane
Viruses may exploit receptors
Membrane Transport
Selectively permeable
Passive
o Simple diffusion
Through a permeable membrane
Follows concentration gradient of a substance
Moves substance from high concentration to low concentration to reach
equilibrium
Major driving force: concentration gradient
Steeper the gradient, faster the movement
Also impacted by temperature
o Facilitated diffusion/transport
Passive-down the concentration gradient
Large molecules, charged molecules, ions
Channel proteins
Carrier proteins
o Osmosis
Diffusion of water
Water moves from high concentration of water to low concentration of water
(less solutes to high solutes)
Tonicity= amount of solute in solution
o Measure by osmolarity
o Blood cells in 3 environments
Osmotic pressure changes shape of red blood cells in hypertonic, hypotonic,
isotonic solutions
o Plant Cells in 3 environments
Turgor pressure within a plant cell depends on tonicity of solution that its
bathed in
o 3 terms relate to extracellular environment
 Hypertonic= more solute outside cell (water moves outside cell/down
concentration gradient)
Isotonic= equal
Hypotonic= less solutes outside cell (water moves into cell)
o Important in regulating cell volume
Electrochemical gradient
o Arise from the combined effects of concentration gradients and electrical gradients
Energy required
o Active Transport
Pumps
Ex) sodium potassium pumps
Energy required in form of ATP
o Endocytosis
Phagocytosis= cell eating
Surrounds particles and pinches off to form an intracellular vacuole
Pinocytosis= cell drinking
Cell membrane surrounds a small volume of fluid with solute in it and
pinches off, forming a vesicle
Receptor-mediated
Uptake of a substance by the cell is targeted to a single type of
substance that binds at the receptor on the external cell membrane
o Exocytosis
Vesicle migrated to the plasma membrane, binds and releases its contents to
the outside of the cell
Ex) insulin is released by this

9-13-16 POST QUIZ 1

Lesson 6: Energy and Metabolism
Characteristics of Living Things
Acquire and use energy from their environment
Energy= ability to do work

What types of work do cells do?

Mechanical
o Movement
o Cell division
Transport
o Active
o Pump
Chemical Work
o Reproduction

Potential Energy (stored) vs Kinetic Energy (motion)

Where do we get our energy from? Food
 Chemical energy in molecules of food=potential energy

2 Laws describe basic properties of energy

1. Law of conservation
Is neither created nor destroyed
2. Amount of useful energy decreases with every conversion
Entropy- a measure of disorder
In living systems-energy is replenished by sun
Some of it becomes heat energy

Chemical Reaction
Process that forms and breaks chemical bonds that holds atoms together
Reactants-> products
Metabolism
o Sum total of all chemical reaction in an organism

2 types of metabolic pathways

Anabolic (small molecules built into larger ones)
o Energy is required
Catabolic (large molecules broken down into small ones)
o Energy is released
Both are required for maintaining cells energy balance

Free Energy (gibbs free energy)

G=H-TS
o G= Energy available to do work
o H= enthalpy, energy in a molecules chemical bonds
o T= absolute temperature (C + 273)
o S= entropy, unavailable energy
o Delta G= change in free energy
Delta G= Delta H- T Delta S

Exergonic Reactions
Energy is released
Spontaneous

Endergonic Reactions
Energy must be supplied
Not spontaneous

Activation Energy
Initial energy input needed to get a reaction started
o Destabilizes bonds in the reactants
Rate of an exergonic reaction depends on amount of activation energy
 To increase reaction rate:
o Increase energy of molecules (add heat)
o Lower the activation energy with a catalyst
Enzymes
Many proteins/some RNA molecules act as enzymes
Its shape stabilizes transient association between substrates
Orients and/or stresses bonds in substrates
Not changed or consumed in reaction
Different cell types contain different enzymes
o Enzymes specify cell structure/function
May be soluble or associated with membranes
Induced Fit Model= enzyme-substrate interaction
Factors that influence Enzyme Function:
o Concentration of substrate
o Concentration of enzyme
o Any chemical or physical condition that affects the enzymes structure may change rate
Temperature
pH
Regulatory Molecules (ex. Inhibitors)
Cofactors and coenzymes
Feedback Inhibition
Where the end product of the pathway inhibits an upstream process
o An important regulatory mechanism in cells
o If sufficient end product is available, process doesnt need to occur again/itll stop the
pathway

(9-15-16)
Lesson 7: Energy from Organic Molecules Part 1
ATP- the energy currency of the cell
Structure of ATP shoes basic components of 2-ring adenine, 5-carbon ribose, and 3 phosphate
groups
Phosphate bonds are unstable
Hydrolysis releases energy
Not suitable for long term energy storage
ATP Cycle
o Synthesis: energy input from exergonic reactions
o Hydrolysis: releases energy for endergonic reactions
Energy for cellular work
Fats, carbs, and proteins can be metabolized
Focus on glucose metabolism
Complete glucose metabolism
C6H12O6 + 6O2 6CO2 + 6H2O + chemical and heat energy
Glycolysis
2 parts
o Glucose Activation
o Energy Harvest
Net Products
o 2 ATP
o 2 NADH
o 2 Pyruvate
Oxygen is present= cellular respiration
Oxygen is absent= anaerobic pathways

Anaerobic metabolism
Fermentation
o Alcohol
o Lactic acid
Animal cells especially muscles
bacteria
Anaerobic cellular respiration
o Final electron acceptor- inorganic molecule
Purpose: regenerate NAD+

Ethanol Fermentation
Pyruvic acid-> CO2 + Acetaldehyde
Acetaldehyde-> Ethanol
NADH / \NAD+

9-20-16
Lesson 8: Energy from Organic Molecules Part 2
Energy from organic molecules
Anaerobic pathways (oxygen is absent)
o Ethanol fermentation or lactic acid
o Anaerobic cell respiration
Cellular respiration (oxygen is present)
o Pyruvate oxidation
o Citric acid cycle
o Oxidative phosphorylation
Mitochondria
2 membranes
Intermembrane space
Cristae
Matrix
Electron carrier FADH2
Picks up hydrogen and electrons from reaction
 Higher energy state
FAD= lower energy state

SUMMARY: 3 parts to cellular respiration

Pyruvate oxidation
o Products per glucose:
2 NADH
2 CO2
2 Acetyl CoA
Citric Acid Cycle
o Products per glucose:
6 NADH
2 FADH2
2 ATP
4 CO2
Oxidative Phosphorylation
o Products per glucose
28 ATP (varies depending on type of cell/tissue, etc)

Pyruvate Oxidation and Citric Acid Cycle

Pyruvate converted into acetyl-CoA before entering Citric acid cycle
Occurs in mitochondrial matrix
1 glucose powers 2 cycles

Electron Transport Chain and ATP Synthase

ETC is a set of molecules that supports a series of oxidation-reduction reactions
ATP synthase is a complex, molecular machine that uses an H+ gradient to regenerate ATP from
ADP
Located on inner mitochondrial membrane

Oxidative Phosphorylation
1. Electrons released
2. Oxygen accepts electrons, water is formed
3. H + ions are pumped through membrane creating a gradient
4. H+ flows through ATP Synthase; atp is synthesized (chemiosmosis)

Some poisons block Electron Transport

Cyanide poisoning
o Blocks electron transport
o Doesnt generate ATP-> cell death-> organism death

Versatility of aerobic cellular respiration (chart on Slide 10)

Glycolysis: carbs, some amino acids, glycerol
Pyruvate oxidation: fatty acids, some amino acids
 Citric Acid Cycle: some amino acids

Possible timeline for evolution of metabolism

1. Ability to store energy in ATP
2. Evolution of glycolysis
o Break down molecules, make ATP
3. Anaerobic photosynthesis (using H2S-hydrogen sulfide)
4. Use of H20 in photosynthesis
5. Evolution of nitrogen fixation
6. Evolution of aerobic respiration
o Harvest more ATP per food molecule
o

9-22-16
What to know for test:
Cell respiration
Where do reactions take place
Products and reactants of each stage
Energy yield
What does oxygen do?
Waste products
Terminology

Lesson 9: Photosynthesis
Interdependence of cellular respiration and photosynthesis
Photosynthesis
o Reactants: 6CO2 + 6H2O+ light energy
o Products: C6H12O6 + 6O2
Cellular Respiration
o Reactants: C6H12O6 + 6O2
o Products: 6CO2 + 6H2O+ ATP + heat energy
Photoautotrophs
Carry out photosynthesis (ex. Plants, algae, certain bacteria)

Photosynthesis
Photo=light, radiant energy
Synthesis= combination of separate substances to make a whole
Simplest equation: 6CO2 + 6H2O+ light energy -> C6H12O6 + 6O2
Primarily in leaves
o Chloroplast
2 membranes that surround the chloroplast
Outer membrane
Thylakoid membrane (inside innermost)
 Can be stacked up: Grana or granum
Stroma = liquid that surrounds granum
2 Parts
o Light dependent reactions
Light energy -> chemical energy (ATP and NADPH)
Requires light energy and water
o Calvin cycle
Synthesis of carbs
Requires ATP, NADPH, CO2
Electromagnetic Spectrum
Exists in different wavelengths
Visible light is one type of energy emitted from the sun (ROYGBIV)
Pigments absorb light energy mostly within the visible spectrum
Chart (slide 8)
o Chlorophyll a- primary photosynthetic pigment
o Chlorophyll b- accessory pigment
o Carotenoids- accessory pigments
Absorb various colors in orange, yellow range
Present in leaf tissue
Not visible because of so much chloropyll
As leaves dye, chlorophyll content diminishes and other pigments are visible
(why leaves turn red, orange, yellow)
Photosystems
Cluster of pigment molecules
Pigments absorb photons of light
Embedded in thylakoid membrane
Reaction center in Chlorophyll A
o When it get enough energy, it can lose an electron
o That electron needs to be picked up
Photosystem I and Photosystem II

Light Dependent Reactions

PS II
o Excited electron is donated to ETC
o Electron passed down ETC to PSI
o H+ pumped
o ATP synthase makes ATP
o Water is split- electron replaced
Gives us Oxygen waste product
Some for cellular resp, some released to environment
PSI
o Excited electron is donated to acceptor
o NADPH is generated
Organisms take CO2 out of air

The Calvin Cycle

Occurs in stroma
G3P- first product
6 turns for 1 glucose
3 stages
1. Carbon Fixation: The enzyme, RuBisCO incorporates carbon dioxide into an organic
molecule, Rubisco= enzyme, RUBP= substrate
It takes CO2 out of air and fixes it onto organic molecule
Rubisco= one of the most abundant proteins on earth

2. Reduction: the organic molecule

Energy from ATP and electrons from NADPH rearrange stuff and make G3P
3. Regeneration of RUBP: RUBP, the molecule that starts the cycle, is regenerated so that
the cycle can continue
Takes more ATP to do so

Photosynthetic Adaptations
When hot and dry, plants need to close to prevent losing water
Ex. Cacti have evolved variations in reactions outside the calvin cycle

Carbon Cycle
Reactions of photosynthesis and cellular respiration share reciprocal reactants and products

Biofuels
Corn
Sugarcane
Vegetable oil
Plant residues
Algae-store energy in oils

9-29-16 Post Test 2

Lesson 10: DNA Structure and Replication

What are genes?

Genes-discrete units of heritable information
Chromosomes- threadlike structures in cells that contain
o DNA
o Protein
Are genes made of DNA or Protein?
Frederick Griffith (1928)
Research on bacterial pneumonia
S strain- smooth-virulent (causes the disease)
R strain- rough- nonvirulent (dont cause disease)
Transformation: transfer of one or more genes from one organism to another
Mouse experiment
o Rough: survive
o Smooth: die
o Heat killed smooth: survive
o Rough & heat killed smooth: die

Avery, McCarty, MacLeod (1944)

Determined DNA was transforming molecule

Hershey and Chase (1952)

More experiments confirming DNA was the hereditary molecule
Bacteriophage- virus that infects bacteria
Experiment
o Radio-labelled bacteriophages (radioactive sulfur labels protein, radioactive phosphorus
labels DNA)
*Slide 10: DNA interactive &
Genes are made of DNA
DNA from the Beginning
How does DNA encode genetic information?
How is DNA replicated?
What is the structure of DNA?

DNA Nucleotides
Sugar (deoxyribose)
Phosphate group
Nitrogen containing base
o Pyrimidines:
Cytosine
Thymine
o Purines:
Guanine
Adenine
Erwin Chargaff
A=T
G=C

Watson and Crick model of DNA structure

Double, stranded helix
o Sugar-phosphate backbone: covalent bonds
o A-T, C-G, Bases hydrogen bond to their complement
 o Stands are anti-parallel
o Uniform diameter

DNA Replication *chart on slide 18

All cells come from pre-existing cells
DNA must be accurately copied
Semiconservative Replication
o Part of the parent DNA molecule is conserved in each new DNA molecule
o 2 strands: 1 old, 1 new

Replication fork is formed by the opening of the origin of replication

o Use old parent DNA as template
o Daughter will be complementary
Helicase separates the DNA strand
RNA primer is synthesized and elongated by the enzyme, DNA polymerase (only synthesizes in
5->3 direction)
On leading strand, DNA is made continuously whereas on lagging strand, DNA is made in short
stretches (Okazaki fragments)
DNA fragments are joined by DNA ligase

Telomeres and Telomerase

Telomeres- end of eukaryotic chromosomes; non-coding repetitive sequences
The ends of linear chromosomes are maintained by the action of the Telomerase enzyme
Telomerase active in most cells of embryos and during childhood development. Activity is low in
adult somatic cells
Cancer cells show activation of telomerase
Elizabeth Blackburn- discovered telomerase; 2009 Nobel prize

DNA Proofreading and Repair

Proofreading by DNA polymerase corrects errors during replication
In event of mismatch: its removed and replaced with correctly paired base
Nucleotide excision repair thymine dimers. When exposed to UV, thymines lying adjacent to
each other can form thymine dimers. In normal cells: theyre excised and replaced

10-4-16
Lesson 11: Gene Expression 1

Important concepts
What is a gene?
o A segment of DNA that contains hereditary info
How is info stored in DNA?
o Its stored in the sequence of nucleotides
Whats the relationship between genes, chromosomes, and DNA?
 o Chromosomes are made of DNA (and protein)
o Genes are segments of a DNA molecule
o Each chromosome has 1 DNA molecule and hundreds of genes
Gene expression
o Converting genetic info into functional molecules such as RNA and proteins

Human Genome Project

Sequence all 3.3 billion base pairs in human DNA
Identifying and mapping all the genes of the human genome
International effort: 1993-2003
Explains how genetic info is stored (medical applications, mutations/defects/disease, etc)

How are genes and proteins related?

Genes determine specific characteristics of an organism
Proteins are a cells molecule workers
Beadle and Tatum Experiments (1941):
o Hypothesis: genes might encode enzymes
o Exposed spores to mutagen
o Mutants grow in different types of media
o Amino acid mutants grown in media with specific amino acids added
o one gene one enzyme
Results showed:
A mutation in a single gene affected a single enzyme in a single biochemical
pathway
Nobel prize: 1958

Modification of the hypothesis in the 1950s

Not all proteins are enzymes
Some proteins consist of more than 1 polypeptide
one gene-one polypeptide
More modifications

2 Steps from gene to protein

Transcription
o DNA RNA
Translation
o RNA protein
The Central Dogma

RNA Structure
Single stranded
Ribose sugar
Uracil instead of Thymine
Types of RNA
Messenger RNA (mRNA)- carries the code from DNA (in nucleus) to ribosome
Ribosomal RNA (rRNA)- makes up ribosome
Transfer RNA (tRNA)- delivers correct amino acid to ribosome (adapters)

Transcription
DNARNA
3 steps
o Initiation
RNA polymerase is guided to promoter by transcription factors
Promoter- part of gene that is not transcribed; Attachment site for RNA
polymerase and other proteins
Is upstream of other stuff
Formation of Transcription bubble= transition to elongation
o Elongation
RNA polymerase tracks along DNA template, synthesizes mRNA in the 5 to 3
direction and unwinds then rewinds the DNA as it is read
Complementary base pairing between DNA template strand and mRNA. Uracil
nucleotides substitute for thymine nucleotides
mRNA is complementary to template strand and is nearly the same as the non-
template strand except U subs for T
o Termination
RNA polymerase reaches the termination sequence in the DNA template strand

Prokaryotic transcription and translation occur simultaneously

Multiple polymerases can transcribe a single bacterial gene while numerous ribosomes
concurrently translate the mRNA transcripts into polypeptides. In this way, a specific protein can
rapidly reach a high concentration in the bacterial cell
Eukaryotic transcription occurs in nucleus

mRNA Processing
Eukaryotic mRNA contains introns that are removed
Exons are spliced back together
A 5 cap and 3 tail are also added

Alternative Splicing
Single primary transcript may be spliced into different mRNAs by the inclusion of different sets
of exons
Can produce different proteins from single gene
o 20,000 genes in human genome can encode > 80,000 different mRNAs

What is a gene?
Located at a particular place on a chromosome
A segment of DNA that can be transcribed (RNA)
 Transcription of protein coding genes produces mRNA that can be translated into a protein

(10-6-16)
Lesson 12:

(10-11-16)
Lesson 13: Control of Gene Expression

Gene Expression over time

Prokaryotes regulate gene expression in response to environmental changes
Eukaryotes regulate gene expression for development and to maintain homeostasis

Transcription Regulation is the Most Common Type

True of both eukaryotes and prokaryotes, but is particularly common in prokaryotes
Slide 4-7

Examples of Transcriptional Regulation in Prokaryotes

The lac operon produces the proteins for lactose metabolism
Lac operon is both positively controlled and negatively controlled
o Lac repressor protein inhibits transcription when lactose is absent (negative control)
o Cap activator protein promotes transcription when glucose is absent (positive control)

Environmental Conditions Required for Lac Transcription

Presence of glucose prevents activator from attaching

Regulation occurs at all stages in eukaryotes

Transcriptional Regulation
o Transcription factors (regulatory proteins)
o Chromatin Structure-Epigenetic regulation
Post Transcriptional Regulation
o mRNA alternative splicing
o mRNA transport
o Inhibition of Translation
Post Translational regulation
o Protein activity
o Protein stability

Transcriptional Regulation in Eukaryotes

Regulatory proteins/transcription factors
o Some require activation
Epigenetic
o Changes in a chromosome without change DNA sequence
 Chromatin structure
Chromosome inactivation
Barr body inactive X chromosome

Post- Transcriptional regulation in Eukaryotes

Alternative splicing
o 2 or more genes from the same primary mRNA transcript
Inhibition of transport
Inhibition of translation
o Reduced availability of molecules needed for translation
o Molecules block translation of mRNA

Post Translational regulation in Eukaryotes

Protein activity
o Addition or removal of phosphate groups
Protein Stability
o Proteins are degraded

Human Gene Expression

1. Each human cell contains the same set of genes (about 21000)
2. Human body -> about 200 different cell types
3. A fraction of the genes are expressed in each cell
4. Differential gene expression results in specialized cells
5. Differential gene expression occurs over time during development
6. Differential gene expression occurs to maintain homeostasis

(10-18-16)
Lesson 14: Reproduction at the Cellular Level: Cell Cycle and Mitosis

Mitotic Cell Division (Eukaryotes)

Somatic cells
Daughter cells identical to parent cells
Growth, repair, replacement
Asexual reproduction
Used for growth and development

Eukaryotic Chromosomes
Each species has a characteristic number of chromosomes
Chromosome number is not correlated to species complexity
Diploid- 2 sets of chromosomes (2n)
Haploid- one set of chromosomes (n)

Karyotype
 Number and appearance of the chromosomes in a eukaryotic somatic cell nucleus
Animal somatic cells- 2n
Gametes- n
Autosomes- same in males and females
Sex chromosomes- differ in males and females
Humans
o 22 pair of autosomes
o 1 pair of sex chromosomes

Replicated Chromosome
1. Sister chromatid
o Held together by cohesion proteins
2. Centromere
o Constricted region; site where spindle fibers attach
3. Short arm
4. Long arm

Homologous Pair
Chromosomes are the same size
Centromeres located in same location
Have the same genes in the same locations (may be different versions
of the genes)

Genes and Gene Loci

Locus= position of gene on a chromosome (loci= plural)

DNA Packaging ------------------------------------------------------------------------------

Eukaryotic Cell Cycle

Interphase= G1, S, G2
o G1- cell growth and protein synthesis
o S- DNA replication of the centrosome
o G2- further growth and protein synthesis final prep for division
M Phase= Mitosis and Cytokinesis
o Mitosis- nuclear division in which duplicated chromosomes are segregated and
distributed to daughter nuclei
o Cytokinesis- cytoplasm is divided, and 2 daughter cells are formed
G0 phase
Cells that arent actively preparing to divide enter alternate phase called G0
Sometimes, its temporary until it moves into G1
Some cases, it remains in G0 permanently

Mitosis- division of the nucleus

Prophase
 o Chromosomes condense and become visible
o Spindle fibers emerge from centrosomes
o Nuclear envelope breaks down
o Nucleolus disappears
Prometaphase
o Chromosomes continue to condense
o Kinetochores appear at the centromeres
o Mitotic spindle microtubules attach to kinetochores
o Centrosomes move toward opposite poles
Metaphase
o Mitotic spindle is fully developed
o Centrosomes are at opposite poles of the cell
o Chromosomes are lined up
o Each sister chromatid is attached to spindle fiber originating from opposite poles
Anaphase
o Cohesion proteins binding the sister chromatids together break down
o Sister chromatids (now called chromosomes) are pulled toward opposite poles
o Non-kinetochore spindle fibers lengthen, elongating the cell
Telophase
o Chromosomes arrive at opposite poles and begin to decondense
o Nuclear envelope material surrounds each set of chromosomes
o The mitotic spindle breaks down

Cytokinesis= division of cytoplasm

Plant cell- has cell wall around it
o Accumulation of vesicles (that contain cell material) at the cell plate
o The vesicles form new cell wall
Animal cell
o Microtubules pinch the cell in half at the cleavage furrow
o Kind of like draw string

Summary of Mitotic Cell Division

2 daughter cells
Exact copies of parent cell
o 2n 2n
o nn (some algae and plants, the body cell is a haploid)
growth, repair, replacement, asexual reproduction

(10-20-16)

Lesson 15: Cell Cycle and Mitosis II

Control of the Cell Cycle

2 irreversible points
 o Replication of genetic material
o Separation of sister chromatids
3 checkpoints
o Stops process if errors are detected
o Allows cell to respond
Protein regulators drive the cycle
o Examples
Cyclins (several different ones)= protein
Cyclin dependent kinases: cdks= enzymes
Cell Cycle Checkpoints
G1= restriction point
o Is the cell large enough?
o Are enough nutrients available?
o Is DNA okay?
o In humans and other animals, growth factors must be detected
G2 (after synthesis)
o Is replication complete?
o Is DNA okay?
o To make sure the daughter cells will have DNA in good shape
M (occurs at Metaphase)
o Are all chromosomes aligned?
o Spindle fibers properly attached?

Uncontrolled Cell Division: Cancer

Mutations in genes that control the cell cycle
Mutations in somatic cells:
o Spontaneous mutations
o Environmental influences
o Viruses
Some mutations involved in development of cancer may be inherited

Proto-oncogenes
Specify normal cell functions
o Positive control of the cell cycle
o Cell cycle proteins
Proto-oncogene mutation oncogene
Oncogene
o Can cause cancer

Simplified example of proto-oncogene and oncogene

Normal G1 to S control
o Growth factor + receptor cyclin synthesis + cdk progression to S phase/DNA
replication
o Growth factors are external signals
 Mutated Cyclin gene
o Growth factor + receptorcyclin synthesis always on + cdkuncontrolled DNA
replication
o Not required due to mutation

Tumor suppressor Genes

Proteins that prevent uncontrolled cell growth
Negative control of cell cycle
Example: p53
o guardian angel of the genome
o Helps repair damaged DNA
o If DNA is irreparable- causes apoptosis
Example: Rb
o Regulates DNA replication
Normal and Mutated p53
The role of p53 is to monitor DNA. If damage is detected, p53 triggers repair mechanisms. If
repairs are unsuccessful, p53 signals apoptosis
A cell with an abnormal p53 protein cannot repair damaged DNA and cannot signal apoptosis.
Cells with abnormal p53 can become cancerous

Cancer requires multiple mutations

6 or more mutations in tumor suppressor genes and proto-oncogenes
Metastasis

HeLa Cells
Cultured human cells
o Widely used in research
Part of a biopsy of a cervical cancer tumor
Patient- Henrietta lacks
o Cells used without consent
Have been dividing continuously since 1951
Example of how cancer cells evade the controls of regular cells

Prokaryotic Cell Division

Binary fission= splitting in two
o Begins at origin of replication, and continues in both directions at once
o Cell begins to elongate. FtsZ proteins migrate toward the midpoint of the cell
o The duplicated chromosomes separate and continue to move away from each other
toward opposite ends of the cell. FtsZ proteins form a ring around the periphery of the
midpoint between the chromosomes
o The FtsZ ring directs the formation of a septum that divides the cell. Plasma membrane
and cell wall materials accumulate
o After septum is complete, the cell pinches in 2, forming 2 daughter cells. FtsZ is
dispersed throughout the cytoplasm of the new cells
2 categories of genes involves in most cancer
Proto-oncogenes
o Normal function proteins needed to push the cell through cell cycle
o Mutation oncogenes
Always on
Push the cell through cell cycle when conditions not met
Tumor suppressor genes
o Normal function- protein stops cell cycle
o Mutation-loss of function
No ability to stop cell cycle if conditions not met

(10-25-16)
Lesson 16: Meiosis and Sexual Reproduction
Genetic Variation
Sexual Reproduction
o Combines genetically unique egg and sperm
o Results in genetically unique offspring
Mutations
o Ultimate source of genetic variation
o Passed to offspring unless lethal
o Source of new alleles
Alleles
Alleles
o Alternate forms of gene
Diploid organisms One member of each pair came from the
o Alleles are carried on homologous chromosomes mother, one came from the father

Sexual Reproduction
Alternating meiosis and fertilization
o Meiosis in diploid germ line cells produces haploid gametes
o Fertilization produces diploid zygote

Features of Meiosis
Includes 2 rounds of division (meiosis I and meiosis II) but only 1 round of DNA replication
Each meiotic cycle has prophase, metaphase, anaphase and telophase
Synapsis: association between homologous chromosomes
Crossing over: homologous exchange DNA segments
Synapsis and Crossing Over
Prophase I
Recombinant chromosomes= chromosomes that have mixture of maternal and paternal
sequences
Non-recombinant= either completely paternal or maternal
Genetic variation

Independent Assortment
Metaphase I
Genetic Variation
Number of possible combinations= 2n

Stages of Meiosis
Meiosis I- already replicated
Prophase I: you can see distinct chromosomes AND homologous chromosomes have paired up
Metaphase I: the pairs line up at the cell equator
Anaphase I: Homologous pair are separated
Telophase I & Cytokinesis: nucleus and cytoplasm are divided
RESULT: 2 haploid cells
Meiosis II
Prophase II: chromosomes condense again (replicate?)
Metaphase II: chromosomes line up
Anaphase II: separate sister chromatids
Telophase II & Cytokinesis: split again
RESULT: 4 Haploid cells

Anaphase I and Anaphase II

I: separated homologous pairs
o Spindle fibers are atttaching so entire pair is pulled apart
II: separating sister chromatids
o spindle is attaching to sister chromatids on either side

Meiosis/Mitosis Comparison
both preceded by 1 round of DNA replication
o however: meiosis includes 2 nuclear divisions
o 4 daughter cells resulting meiosis are haploid & gen distinct
o Daughter cells resulting mitosis are diploid & identical to parent

How do meiosis and sexual reproduction produce genetic variation

Shuffling of homologues
o Random assortment of maternal and paternal chromosomes in metaphase 1
o New combination of chromosomes
o 8 million combinations in humans
 Crossing over
Genetically unique egg and sperm unite in fertilization

Summary of meiotic cell divisions

4 daughter cells
Haploid nuclei
2nn
Production of gametes for sexual reproduction

___________________________________________________________
(10-27-16)
Lesson 17: Patterns of Inheritance I

Gregor Mendel
Garden pea
Discontinuous traits
Model experimental organism
Prior to Mendel- Blending theory of inheritance

Monohybrid Cross
True-breeding parents- reproduce exact copies of themselves
o Cross-fertilization
F1- first generation of offspring
o Hybrids
Self-fertilization
F2- second generation of offspring
Mendels process for performing crosses included examining flower color (they were only
different in flower color)

Mendel identified seven pea plant characteristics

Mendels conclusions
Plants did not show intermediate traits (no blending of traits)
o each trait is discrete and intact
For each pair, one trait was dominant, the other recessive
The pairs of alternative traits examined were segregated among the progeny of a particular
cross
Alternative traits were expressed in the F2 generation in the ration of dominant to recessive
(the Mendelian Ratio)

Phenotype vs Genotype
Phenotype- observable traits
o Ex: purple flowers vs white flowers
 Genotype- genetic makeup
o Homozygous (ex. yy or YY)
o Heterozygous (ex. Yy or yY)
Phenotypic Ratio
Genotypic Ratio

Law of Dominance
the dominant allele conceals the presence of recessive allele

Law of Segregation
2 alleles of a gene segregate from one another at meiosis and are rejoined at random during
fertilization

Punnett Square
This Punnett square shows the cross between plants with yellow seeds and green seeds
The cross between the true-breeding P plants produces F1 heterozygotes that can be self-
fertilized
The self-cross of the F1 generation can be analyzed with a Punnett square to predict the
genotypes of the F2 generation
Given an inheritance pattern of dominant-recessive, the genotypic and phenotypic ratios can
then be determined

Human Traits (chart on 17.10)

Some human traits are controlled by a single gene
Some of these exhibit dominant and recessive inheritance

Autosomal Recessive Inheritance Autosomal Dominant Inheritance

Dihybrid Cross
 True Breeding parents that differ in 2 traits
o Ex. A dihybrid cross in pea plants involves the genes for seed color and texture
The P cross produces F1 offspring that are all heterozygous for both characteristics
The resulting 9:3:3:1 F2 phenotypic ratio is obtained using a Punnett Square

Law of Independent Assortment

Alleles of one gene assort independently from alleles for other genes when genes are on
different pairs of homologous chromosomes

Test Cross
A test cross can be performed to determine whether an organism expressing a dominant trait is
a homozygote or a heterozygote
Cross individual with unknown genotype with homozygous recessive individual

Extensions to Mendel
Mendels model of inheritance assumes
o 1. Each trait is controlled by a single gene
o Each gene has only 2 alleles
o A clear dominant-recessive relationship between the alleles
Most genes do not meet these criteria!

(11-1-16)
Lesson 18: Patterns of Inheritance II

Linked Genes
Located on same chromosome
Tend to be inherited together
Crossing over disrupts linkage
o More likely when genes are farther apart

Do the Mendelian Rules of Inheritance apply to all traits?

Assumptions
o Each trait is controlled by a single gene
o Only two possible alleles for each gene
o One allele is dominant to the other
o Most dont meet this

Incomplete Dominance
Heterozygote has intermediate phenotype
Homozygous Red + Homozygous White= Heterozygote Pink

Co-dominance
Human ABO blood typing: A & B alleles are co-dominant
 Punnett square above shows an AB/AB type cross

Multiple Alleles
3 alleles in human population (A & B are co-dominant, I
is recessive)
Each person has only 2 alleles
6 genotypes, 4 phenotypes
Inheritance of the ABO blood system in humans is shown
Note: the +/- trait for blood is a different gene called the
Rh factor

Polygenic Inheritance
Phenotype depends on combined effects of 2 or more genes
Phenotypes tend to be continuous
o You have range of phenotypes
Examples
o Human height
o Human eye color
o Human skin color

Environmental Influences
Genotype+ Environment Phenotype
Environment plays role in expression of genotype
o Ex: Siamese Cat- fur markings are expressed based on temperature

Thomas Morgan Experiments with Fruit Flies

First discovery of a gene on a particular chromosome
Discovered a white eyed male fruit fly
Mated the white eyed male with normal female- all F1 offspring had red eyes
Allowed F1s to mate: all white eyed F2 offspring were males
In Drosophila, the gene for eye color is located on the X chromosome. Red eye color is wild type
and is dominant to white eye color

Punnett Square of an X-linked trait

Crosses involving sex-linked traits often give rise to different phenotypes for the different sexes
of offspring, as is the case for tjis cross involving red and white ye color in Drosophila. In the
diagram, w is the white-eyed mutant allele and the W is the wild type, red-eye allele

Biological Sex Determination in Humans

22 pairs of autosomes
1 pair of sex chromosomes
Y chromosome highly condensed
o Recessive alleles on males X have no active counterpart on Y
 o SRY gene on Y initiates male phenotype
Many genes involved in normal development
o Hormones are a factor

X-linked Recessive Inheritance

Human Genetic Disorders

X-linked recessive
o Hemophilia
o Red-green colorblindness
o Duchene muscular dystrophy

Pedigree Analysis

Autosomal Recessive Pedigree Autosomal Dominant Pedigree

How do errors in chromosome number affect humans?

Nondisjunction
Aneuploidy
o Monosomy (n-1)
o Trisomy (n+1)
Genetic Disorders: Nondisjunction of Autosomes
Trisomy 21- Downs Syndrome
Effects of Nondisjunction of Sex Chromosomes
Nondisjunction in Father

Nondisjunction in Mother

Screening for Genetic Disorders

1- Identify Carriers
o Pedigree analysis
o DNA analysis
2- Embryo Screening
o In vitro fertilization
o Pre-implantation genetic diagnosis (PGD)
Screen embryo DNA for genetic disorders
3-Prenatal Testing
o Amniocentesis
o Chorionic villus sampling
4- Newborn Screening
o 29 disorders currently screened for in VA
o Mostly metabolic disorders
o Gene sequencing for newborns

(11-3-16)
Lesson 19: Biotechnology

What is Biotechnology?
Use of artificial methods to modify the genetic material of organisms, cells or biological
molecules to produce novel compounds or perform new functions
Brewing industrygenetic engineering
Recombinant DNA- combining genes or portions of genes from different organisms
Genetic engineering- modifying an organisms DNA

Transgenic Organism
Transgenic organism- bacteria or animals that express DNA that has been modified or derived
from other species
 Genetically modified Organism (GMO)- an organism that receives recombinant DNA (not
necessarily from another species)

DNA Recombination in Nature

Sexual reproduction
Bacteria-transformation
o Plasmids
Tiny circular DNA molecules
Genes that convey special properties
Viruses

Techniques
Gel electrophoresis
o Separate charged molecules on the basis of size
o DNA is negatively charged
Polymerase Chain Reaction (PCR)
o Amplify DNA of regions of interest
o Required materials
Taq polymerase
Primers
Nucleotides
Thermal cycler

Applications of Biotechnology: Cloning

3 types
o Molecular cloning
Tools
Steps
Cut DNA with gene of interest and plasmid (vector) with same
restriction enzyme. Plasmid has selection marker-ampicillin resistance
gene
Combine the 2 pieces of DNA (cut DNA and cut plasmid).
Complimentary sticky ends will anneal
Add DNA ligase to seal the pieces
Incubate bacteria with recombinant plasmid
Grow bacteria on a plate with antibiotic ampicillin. Only cells that have
taken up the recombinant plasmid will survive and grow. As bacteria
divide and reproduce the plasmid and gene of interest are copied
(cloned)
o Reproductive cloning
Somatic cell nuclear transfer
Low success rate
Purposes:
Reproduce animals with special properties
 Repopulate endangered animals
Clone your favorite pet
o Therapeutic cloning
Clone human embryos for use in research
Source of stem cells for medical treatments
Study human development

Applications of Biotechnology: Medical applications

Gene therapy
o Deliver functional gene to patient
o Only clinical trials available in the US at this point
Genetic screening
Production of human vaccines, antibiotics, hormones

Applications of Biotechnology: Agriculture

GMO crops- 10 USDA approved crop plants produced in US
o Resistance to herbicide
o Resistance to pests
o Resistance to disease
o Altered oil content
GMO Farm raised salmon
o Grow faster
No labeling is required

Applications of Biotechnology: Forensics

DNA fingerprinting
o STRs (short tandem repeats) Example: AGATAGATAGAT
o Alleles inherited from parents
o Different alleles- different number of repeats
o Amplify DNA samples
o Separate using gel electrophoresis
o 13 STRs used by law enforcement
Genomics
Study of entire genomes
o Mapping chromosomes
o Sequencing genomes

Proteomics
Study of the proteome
Proteome
o All the proteins produced by a cell type

11-10-16
Lesson 20: Evolution: Introduction to how populations evolve
Evolution is a central principle in biology
Explains the similarities among living things
Accounts for the great diversity of life
Accounts for many features of the physical world

Scientific Theory
A well substantiated explanation of some aspect of the natural world. Can incorporate:
o Facts: phenomenon that has been repeatedly observed
o Laws: descriptions (law of motion)
o Tested hypothesis

Evolution and Religion

Evolution deals with the natural world, religion deals with spiritual experiences
Evolution is not a belief system
Many world religions do not have any direct conflict with evolution
Accepting evolution does not require you to abandon your religious beliefs

How does understanding evolution benefit us?

Medicine
o Antibiotic resistance
o Evolution of infectious diseases
Conservation
o Defining species of conservation concern
o Understanding why species go extinct and how extinction might be prevented
o Understanding problems of small populations
Agriculture
o Artificial selection- evolution driven by human selection
o Pesticide resistance
o Genetically modified organisms

Theory of Evolution
= change in populations of organisms over time
Unifying theme in biology
All life has evolved and diversified from a common ancestor

What is a population?
Group of individuals of the same species living in a given geographical area
o Individual organisms cannot evolve

Influences on evolutionary thought

James Hutton and Charles Lyle-
Uniformitarianism
o The earth developed gradually through natural processes over long periods of time
o These processes are still at work
 o The earth is old
There has been enough time for evolution to occur
Questions remained about the mechanism for evolution

Inheritance of acquired characteristics

Jean Baptiste Lamarck (1801)
First proposed mechanism for environment
Modifications in an individual could be passed to offspring
o Modifications caused by environment
o Modifications due to use or disuse

Charles Darwin and Alfred Russell Wallace

Independently conceived of Natural Selection as a mechanism for evolution
Charles Darwin
o Travels to South America, Australia, southern tip of Africa
Alfred Russell Wallace
o Travels to Brazil, Malay, Archipelago

The Wallace Line

Separation of Asian bird and mammal species with autralia or mixed origins
Wallacea- group of islands in this region; many endemic species

Charles Darwin and the Voyage of the Beagle (1831)

5 year voyage
Survey coast of South America
Darwin served as naturalist

Observaitons made by both Darwin and Wallace

Fossils
Unique organisms
Variation between mainland and island species
Variation on different islands

Influence on both Darwin and Wallace

Essay on the Principle of Population
Thomas Malthus
o Increase in human supply led to increase in human population growth
o Shortages occur and poor people suffer

How does Natural Selection Work?

1. Offspring inherit traits from parents
2. Resources for survival and reproduction are limited, more offspring are produced than can
survive
3. Variation in offspring
 Offspring with traits that allow them to better complete for resources, survive and
reproduce more than other offspring
Descent with modification

Variation and Adaptation

Natural selection requires genetic variation
Source of new alleles= mutation
3 possible outcomes of mutation
o No effect on fitness
o Increases fitness
o Decreases fitness
Adaptation- heritable trait that aids in survival and reproduction in a given environment

Natural Selection
Fitness
o Survival and enhanced reproduction of individuals with favorable variations (for a
particular environment)
Natural selection works on phenotypes
Successful phenotypes have the best adaptations
Environment= abiotic + biotic
Video: phylogenetic Tree of Anole Lizards
o All feed on small prey like spiders and crickets, but divide up habitats by vertical space
Long tale slender species lives in grasses/buses- grass bush anole
Longer leg, stocky species- trump ground anole
Higher up tree-small with short leg- twig anole
Higher up, large green- big canopy anole
o Differences in traits are adaptations to various habitats
Compare roaming ability
Speed
o Ex. twig lizard short leg provide firm grasp instead of speed
Grasp leaves
o Ground lizard cant grasp
o Big canopy lizard- tiny hairs on toepad to bind with surface
Tiny islands- placed female and male on island with thin branches
Came back year later
o Check height off ground, diameter branch, whatnot
Came back year later
o Avg leg size was shortened

Modern Synthesis
Relationship between natural selection and genetics
Microevolution
o Change in a populations genetic structure
Macroevolution
 o Changes that give rise to new species or higher taxonomic groups

Population Genetics
Study of frequency, distribution, and inheritance of alleles in a population
Gene pool
o Sum of all genes in a population
Allele frequency
o Relative proportions of the different alleles in a population
Behind phenotypic change is genetic change

Evolution
Changes in allele frequencies in a gene pool over time
Example: ABO blood type in population of Jordan
o IA allele= 26.1%
o IB allele= 13.4%
o i allele= 60.5%
o TOTAL= 100%
o A change in these allele frequencies would be evolution in this population

Hardy-Weinberg Principle
Equilibrium population
o Idealized, evolution free population
Genetic equilibrium
o No change in allele frequencies

Genetic equilibrium is maintained if these conditions are met

No mutation
No gene flow
Large populations
Mating is random
No natural selection
o No populations exist where ALL of these conditions are met

Mechanisms of Evolution
Mutation
Gene flow
Small populations resulting in genetic drift
Non-random mating
Natural selection

11-15-16
Lesson 21: Mechanisms of Evolution & Evidence of Evolution
Mechanisms of Evolution
Mutation
o Germ cell mutations can be inherited
o Rare
o Beneficial-spread by selection
o Neutral- may persist
o Harmful- eliminated by selection
o Source of new alleles
o random
Gene flow
o Spreads advantageous alleles
o Helps maintain all the organisms over a large areas as one species
o Occurs by migration and dispersal
Individuals, seeds, pollen
Small populations resulting in genetic drift
o Chance events change allele frequencies in a small population
o Special cases of genetic drift
Population bottleneck
Event that reduces population
o Natural disaster
o Construction, over hunting, etc
Population that survives has difference in allele frequency from original
population
Founder effect
Magnification of genetic drift, migrates away from large parent
population carrying with it an unrepresentative set of alleles
Non-random mating
o Inbreeding
o Assortative mating
Preference for mates that are similar to ones self
Natural selection

Evidence of Evolution
Fossils
o Progression of form
o Transition fossils
o Not complete for all organisms
Anatomy
o Homologous structures: similar bone structure indicates common ancestor
o Vestigial structures: residual non-functional structures left from common ancestor
Embryology
o As vertebrate embryos develop they go through similar stages
o Some structures are not retained
o Ex) gill slits and tails in humans
 Biogeography
o Ex) Marsupial evolution
Probably evolved in North America
Expanded to south America and pacific rim
North American marsupials went extinct
Marsupials migrated to Australia and new Zealand via Antarctica
Separation of Australia and New Zealand led to independent evolution and
adaptive radiation of marsupials
Rejoining of N and S America, new migrations northward
American opossum evolved
Molecular evidence
o Universality of DNA
Common ancestor to all life
o Similarity in specific DNA sequences
o Near universality in genetic code
o Universality of glycolysis
Artificial selection
o Domestication of animals and plants

Evolution by natural selection occurs today

Multi-drug resistant TB
XDR TB
MRSA- methicillin resistant Staphylococcus aureus
Pesticide resistant insects
Guppies in Trinidad
Round up resistant Pigweed

11-17-16
Lesson 22: Sexual Selection/Speciation

Sexual Selection
Natural Selection that acts on traits that help an animal mate
2 processes
o Intra-sexual selection: competition for mates; usually between males
o Inter-sexual selection: mate selection based on a phenotypic characteristic; females
usually choose
Sexual dimorphism
o Morphological differences between males and females of the same species

What is a species?
Morphological species
o Based on morphology or form
Biological species concept
 o A group of actually or potentially interbreeding individuals that produce fertile offspring
Phylogenetic species
o Based on evolutionary relatedness

What are some cases where the biological species concept does not fit?
Asexual organisms
Situations where reproductive isolation is hard to observe
Fossil organisms

Reproductive isolation
Isolating mechanisms
o Traits that prevent interbreeding to produce viable fertile offspring
o Prezygotic
Temporal
Ecological (habitat)
Behavioral
Mechanical
Gametic
o Postzygotic
Hybrid inviability
Hybrid sterility

Temporal Isolation- 2 related frogs exhibit temporal reproductive isolation

Ecological Isolation- speciation can occur when 2 population occupy different habitats. The habitats
need not be far apart

Behavioral isolation- difference in courtship colors and behaviors

Mechanical Isolation- shape of the male reproductive organ varies among male damselfly species, and is
only compatible with the females of that species. Reproductive organs incompatibility keeps the species
reproductively isolated

Gametic Isolation- gametes are incompatible due to molecular markers one egg and sperm that are
species specific

Post-Zygotic
Hybrid inviability
o Cross fertilization occurs
o Hybrids dont develop or are weak and short-lived
Hybrid Sterility
o Cross fertilization occurs
o Hybrids are healthy and vigorous, but sterile
Speciation
The formation of 2 species from 1 original species

How do new species form?

1. Isolation of population
No gene flow
2. Genetic Divergence
No longer able to interbreed to produce vigorous fertile offspring
Allopatric Speciation
o different native land
o Geographic barrier separates groups
Sympatric Speciation
o same native land
o No geographic separation
o Polyploidy- due to errors in meiosis, an organism has more than 2 sets of organisms

Extinction
= the death of all members of a species
Background extinction
Environmental change
o Biotic or abiotic environment
o Competition among species
o Habitat destruction

11-29-16
Lesson 23: Systematics History of Life on Earth

Organizing Life on Earth

In the evolution of life on Earth, the 3 domains of life- Archaea, Bacteria, and Eukarya- branch
from a single point

Systematics and Classification

Systematics
o Reconstruction and study of evolutionary relationships
Phylogeny
o The evolutionary history of a group of organisms
Phylogenetic Tree
o Illustration of the evolutionary relationships
o Hypothesis of the evolutionary relationships

Phylogenetic Tree
Its rooted and shows how different organisms, in this case the species and subspecies of living
apes, evolved from a common ancestor
Phylogenies are Hypothesis Based on the best available Data
The data often comes from multiple sources
o Molecular-DNA and protein sequences
o Morphology
o Physiology
o Behavior

Branch points imply evolutionary change

The phylogenetic tree is rooted by an organism that lacked a vertebral column. At each branch
point, organisms with different characters are placed in different groups

Limitations to phylogenetic trees

Morphological similarity
o Not always indicative of close evolutionary relationships
o Homologous vs analogous structures
o Best to use morphological and genetic similarity
Show sequence of changes, but not timing

Homologous vs Analogous structures

Homologous= common ancestry
Analogous= insect wing vs bird wing- no common ancestry
o Convergent evolution: selection for similar features in similar environments

Cladistics
Cladistics- method of constructing phylogenetic trees base on grouping closely related
organisms into clades
Clade- a group of taxa with the same set of shared derived characteristics, including an ancestral
species ( characteristic that differs from ancestral species)
Lizards, rabbits, and humans all descend from a common ancestor in which the amniotic egg
evolved. Thus, lizards, rabbis, and humans all belong to the clade amniota. Vertebrata is a larger
clade that also includes fish and lamprey

Taxonomy and Classification

Classification
o The practice of placing species and groups of species into the taxonomic hierarchy
Taxonomy
o Science of naming and grouping species
Binomial system of nomenclature
o Genus+ species
o Always italicized or underlined

Hierarchical Classification System

 At each sublevel in the taxonomic classification system, organisms become more similar. Dogs
and wolves are the same species because they can breed and produce viable offspring, but they
are different enough to be classified as different subspecies

Early Life on Earth

Age of the earth
o 4.54 billion years
No physical record of the origin of first cells
Prebiotic conditions on earth
o No oxygen (Oparin and Haldane, 1920s)
o No ozone layer
o No living organisms
o Long periods of time (200-400my)

Prebiotic evolution
Chemical evolution
o Simple molecules accumulate on the prebiotic Earth complex molecules

Single cells- first life forms

RNA world
o RNA stored hereditary info
o Ribozymes catalyzed replication
o Ribozymes discovered in early 1980s
o RNA functions later replaced by DNA and proteins
Membranes
o Probably simpler than phospholipid bilayers

The earliest organisms

Primitive anaerobic bacteria
o Earliest fossils 3.5 billion years old
o Consumed organic molecules in their environment and depleted the supply
o Lived at high temperatures
Photosynthetic bacteria
o Initially used H2S as a hydrogen source
o Later remove hydrogen from water

The oxygen crisis

Significant amounts of O2 -2.3 bya
Stable O2 content- 1.5 bya
Deadly to some anaerobic bacteria
Changed the conditions that supported prebiotic evolution

Aerobic Metabolism
Use of oxygen fro metabolism would be advantageous
 More energy released

Stromatolites
Layered structures of sediments and biofilms containing photosynthetic cyanobacteria

Eukaryotic cells
First cells 1.7 bya
Endosymbiotic theory
o 1. Infoldings in the plasma membrane of an ancestral prokaryote gave rise to
endomembrane components, including a nucleus and endoplasmic reticulum
o 2. In a first endosymbiotic event, the ancestral eukaryote consumes aerobic bacteria
that evolved into mitochondria
o 3. In a second endosymbiotic event, the early eukaryote consumed photosynthetic
bacteria that evolved into chloroplasts

12-1-16

Lesson 24: History of Life on Earth

Earths Changing System Affected Evolution

Climate changes
Changes in the atmospheres composition
Continental drift
Changes to the earth as a result of life forms

Multi-celled organisms
Eukaryotes only
Differentiation of cell types and tissues allowed novel adaptations
Multi-cellularity evolved independently in algae (which gave rise to plants) and animals

Colonial Algae
Not truly multicellular
Some specialization

Multi-celled algae

Animal Diversity
Precambrian
o 610-544 mya first fossil animal bodies
The Cambrian explosion
o Adaptive radiation of animal forms
Invertebrates
o 530 mya (40 million year span)
 o The Burgess Shale

Life on Land
Ozone layer
o Protection from UV radiation
Obstacles to success on land
o Support
o Controlling water loss
o Gas exchange
o Reproduction
Advantages for plants
o More sunlight
o More nutrients
o No predators

Animal Movement onto Land

Arthropods
o Exoskeleton
Vertbrates
o Tikaalik roseae
Fishapod
Transitional species
o Advantages to land
Less competition
Fewe predators
New food sources
Many niches

Terrestrial animal evolution

Tetrapods
o Four limbed vertebrates
o Some groups have lost their limbs
o Some groups have returned to water
o Amphibians
Semi-aquatic
o Reptiles
Amniotic eggs
Scaly skin
Improved lungs
o Birds
Feathers
Flight skeleton
Endothermy
 o Mammals
Hair
mammary glands
endothermy

Key Points:
humans and chimpanzee- common ancestor 6 mya
Bipedalism- all hominins
Lucy- Australopithecus afarensis
Larger brains- Homo
Homo Erectus- larger brain and larger body size; dispersal
Many hominin species co-existed
Homo sapiens- only surviving species