bio 110 Notes

1/16/24

• Biomolecules
  • Fred Griffith
    • Looked at R and S cells/strains
      • Living S cells are deadly
      • But dead S cells transformed R cells into deadly S cells
  • Oswald Avery
    • Cell Extract determines phenotype
      • Crushed up S cells cells and extracted the heritable material (S factor) and put it into the R cells and they became S cells
      • Measured nitrogen and phosphorus in the white stringy stuff (s factor
• (Based off Avery’s experiment)
• Five Amino Acids
  • Threonine glutamate alanine cysteine histidine
• Nucleic Acids
  • 15N x 14g/mol N = 210g N

= 1.69

• • 4P x 31 g/mol P = 124 g P
  • When he separated the cytoplasm and the cell wall, the chromosomal membrane was loosely connected to the cell wall

Hershey and Chase:

• Bacteriophage Infecting E. coli
  • Phage made of Protein and DNA
  • Takes 5 minutes for phage to inject its DNA material
  • Measuring the radioactivity outside of the cell
  • Concluded that DNA is the heritable material
• Watson and Crick DNA model
  • Double helix
    • Strands have to be antiparallel
    • 5’ = phosphorus
    • 3’ = hydroxyl (HO)
    • Pyrimidines have 1 ring (cystine, thymine)
    • Purines have two rings (guanine, adenine)
    • Three rings make up one rung

Lab Notes 1/16/24

• Quantifying Doubling & Generation Time
• Exponential Phase: X=2n(exponent)X0(base)
• look at the slides log10/log2 = 3.32
• question 3 =log base 2 (2 exponent x=5)=232 and 60 minutes
• Stable isotopes depends on the number of neutrons

Quantifying DNA Amount

• Collect biomolecules sample
• Add sample to test tube of CsCl (#1)
• Spin test tube in a centrifuge (#2)

1/18/14

• Types of DNA
  • Conservative- ALL old and all new
  • Mosaic- ALL strands half new
  • Semi-conservative- half old and half new
• Meselson and Stahl experiments
  • Low concentration (low density)
  • High concentration of salt (high density)

1/24/25

• Tetrad~4 in each chromosome (pairs of homologous chromosomes)
• Pairs of homologous pairs separate in meiosis 1
• Chromatid recombination ~ allows for genetic diversity
• Chromosome pairing starts in Prophase 1
• Practice what the meiosis and mitosis look like in each of their stages
• Meiosis creates the sperm and cell and mitosis doubles the cells.
• One diploid — two diploid mitosis
• One diploid — two haploid meiosis
• Haploid — haploid mitosis
• Alternation of generations
  • Gametophyte - haploid (gametes) *Mitosis is used to make gametes*
  • Sporophyte - diploid (spores)

-What distinguishes male and Female?

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- Sex determination in mammals

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-how can parthenogenesis?

-Apomixis (mitosis)

-Automixis (self fertilization) (splits chromosomes in half)

Cells are Assembled Molecules:

*gel electrophoresis

• Yeast RNA separated by Size
  • tRNA (brings nucleic acids to the ribosomes) towards the bottom and rRNA (ribosomal RNA) towards the top
• Layer Chromatology (TLC)
• Column Chromatology
• Radioactivity of the amino acid is used to tell where the rRNA is and the tRNA (low radioactivity means that is where the rRNA is and high radioactivity is where the tRNA is)
• Because the leucine(amino acid) is co-eluting with the tRNA, we know that they are connected.

tRNA:

• Single stranded but folds in on itself
• Antiparallel base pairings
• Amino acids bind to the 3’ opposite of the 5’ and 3’ is the anticodon which interacts with mRNA = interacting with the ribosomes to create proteins

*Messleson and Stahl found that DNA separates in a semi-conservative way

• Methylated bases = different chemical structures and physical properties

- they are epigenetic changes

- chromatography

- inactive genes are hypermethylated and active genes are hypomethylated.

2/1/24

DNA, RNA, Protein

• RNA polymerase ~ what cases this to transcribe DNA
  • Prevention of this is methylation
• Lactose structure
  • Glucose linkage (can be formed or broken)
  • Beta Galactosidase breaks the glucose linkage between galactose and glucose to free lactose

*Bacteria cells have only one chromosome\

Possible Induction Mechanism

• Jacob and Genome
  • Permease and beta galactosidase
  • When lactose is absent, they do not work
  • When lactose is present, they get cut off

- Genetic map of lactose digestion

- all four genetic elements in a single locust

- ex. lacI (initiator), lacO (operator), LacBeta, lacP (permease)

- lactose blocks the inhibitor when it is present and the opposite occurs when lactose is not present.

*Operons in bacteria are a series of elements/ a cluster of genes that are transcribed together to give a single messenger RNA (mRNA) molecule, which therefore encodes multiple proteins

• David Pribnow

- T7 virus, extracted DNA and then added RNA polymerase which will bind to an operator and then he adds DNase. Then he gets the RNA that the polymerase was on. Then he extracts the DNA

2/6/24

• Promoter is a sequence on a strand of DNA that helps transcribe the DNA.
• Transcription factors (bind at TATA box)
• The TATA box is what allows the transcription factors to bind to the promoter.
• DNA>>>transcription>>>RNA (mRNA, rRNA, tRNA)>>>translation>>>protein

Proteins from Amino Acids:

• Need all RNA, ATP/GTP, and amino acids in order to create proteins
• 64 probabilities for a codon when you have 3 available nucleic acids.
• UUU is phenylalanine

-DNA that have alignments in the mRNA are exons, and DNA that does’t are introns

- every three codons create an amino acid

- protein is usually modified after it is transcribed by mRNA

- all cells need energy to do work.

-energy is stored in bonds of amino acids

- ATP>>ADP energy is released

- (catabolism - breaking something down, anabolism - building something down)

- Redox reactions: IQ #3

- NADH transports electrons from one place to another

- biomolecules present in breastmilk: lipids, carbohydrates, and proteins

- casein protein has 225 amino acids and 224 peptide bonds

- 12 carbons, disaccharide in milk sugar

- peptide bond is a type of covalent bond

-*Glycolysis* - sugar splitting

- ends with 2 pyruvates

- harvesting energy the whole time during the process when the sugar is splitting

- citrate is potential energy (no need to go through glycolysis)

- citrate slows down the production of PFK

• AMP is a signal that the cell needs energy
• Low levels of ATP stimulates glycolysis
• Low ATP creates high activity and High ATP creates low activity
• Energy from covalent bonds stored in NADH, ATP, and acetyl-CoA
• 3 carbon pyruvate to lactate

2/8/24 Underlined words are important vocab

• Energy stored in ATP, NADH, FADH2, and acetyl COa
• Fatty acids stored in carboxylic acid group
• When dogs eat the fatty acids (synthetic)
  • When they ate the odd numbered acids, the dogs peed them out with a circle of carbons and one carbon. When the even numbered acids are eaten they are peed out with two carbons.
  • So two carbons have to be removed at a time (beta oxidation, only possible when oxygen is present)
• *OXYGEN IS THE FINAL ELECTRON HOLDER.
• When asked where the energy is stored, look for two carbon molecules and reduced electron carriers.
• know: deamination (needed when there is less energy present like ADP), hydrolysis, and oxidation
• Sugar >>>Glycolysis + pyruvate processing = NADH, Acetyl CoA (electron sponge), ATP needed for cellular respiration
• Fatty acids >> Beta oxidation = acetyl CoA (electron sponge), NADH (electron sponge), FADH2
• Proteins >>> deamination = acetyl CoA (electron sponge), NADH (electron sponge)
  • These energy holders turn into NADH, FADH2, and GTP
• Fig. 10.19 the cycle happens twice
• High energy nutrients gets oxidized
• * glycolysis happens in the cytosol
• beta oxidation, deamination, and citric acid cycle (aka Krebs Cycle) happens in the mitochondrial matrix
• Inside the mitochondrial matrix, there are less H+ because the pH is more basic around a pH of 8. ( so outer membrane is higher in H+ and matrix is lower in H+) (1 pH unit is 10x amount of H+)
• Electron transport chain end (complex 4 and has cytochrome C, good at bonding CO AKA carbon monoxide which is a poison) needs oxygen in order to produce water.
• When the H+ goes out of the matrix and then falls back into the matrix produces potential energy. Comes through the ATP synthase

2/13/24

• Proteins push H+ out of the mitochondrial matrix and then the ATP synthase pull H+ back into the matrix.
• High concentration gradient is a form of potential energy which brings the H+ ions into the channel into the matrix. (the H+ ions move the rod pulling the ADP and ATP together)
• Homeostasis of cellular respiration
  • Activators are lower in energy molecules (low energy inhibits more energy to be created)
  • Inhibitors are lower in energy molecules

- Redox Reactions

- Photosynthesis (oxidation of CO2, 1st part, and reduction of

-light absorbing pigments

- similar to complex four which manipulates electrons.

-Antenna Pigment Complex

- visible light strikes antenna complex

- absorbed energy sent to center

- light is the energy that moves the H+ ions in and out of the thylakoid space.

- cytochromes take the energy from the electrons and pump H+ ions from the stroma into the Thylakoid space (needs ATP synthase)

- inside thylakoids the pH is acidic when light is present and neutral when in the dark

- outside (stroma) is more basic in the light

- Why is water important in photosynthesis?

- water is being oxidized (Losing electrons) in photosynthesis and turned into Oxygen to fill in the holes in the photosystems.

- homeostasis of electron flow - bright light makes phosphates attach to thylakoid space and unstack the thylakoids.

- CO2 have oscillated

- * Rubisco is the most abundant enzyme on the planet. *

- involved in carbon fixation

- Carbon fixation cycle (the calvin cycle) = 9 ATP (needed more for photosynthesis) also (you're only using NADPH for non-cyclic flow, ATP is used for both cyclic and non-cyclic) and 6 NADPH

- 6 carbons start at Glucose->then two pyruvate (each has three) -> 2 acetyl CoA (2 carbon) -> krebs cycle and then come out as CO2.

-Acetyl CoA is where the fatty acids and amino acids go into the process

- amino acids only give off NADH and FADH2 whereas fatty acids only give off NADH in electron movement of cellular respiration.

- Carbon fixation cycle has to happen as many times as there are carbons in the product it is trying to make.

- endosymbiosis - other symbiotic lineages came to be because they engulfed another cell.

2/20/24

- E. fishelsoni has thousands of circular chromosomes around the cell in order to transcribe RNA into protein near the two daughter cells at the ends of the cell

- cell volume constrained because the cells demand affects the surface area

- as a cell gets bigger its volume grows faster than its demand.

- proteins are negatively charged but when hit with an electric charge, they are going to move towards the positive charge.

- proteins are mobile.

- some proteins in the membrane are not mobile

- cytoplasmic proteins can more around too

-100 molecules ~ 200 nM (nana moles) = 200 nm (nana meters)

-E. Coli is 2 um (length)

- human cell 10 um (length)

- evaporation through the leaves helps move nutrients through the plant because they don’t have a heart to pump it through.

- need a big enough surface area to contain the volume?

- If the demand (volume) is greater than the supply (surface area), the cell can’t live for very long.

- the bigger the volume the slower the cell takes to transport.

How can proteins turn off and on?

• Proteins are polymers made out of monomers which are made up of amino acids (there are 20 amino acids)
• R groups are hydrophobic
• Letters of amino acids is the sequence of a protein
• Tertiary structure is the shape of a protein (the twisting and overlapping)
• Phosphates are negative so when you put them onto the OH groups then the negatives will push other charges away and change the shape.

- Cellulose and starch contain glucose

- starch is easily digested by animals

- the cell wall contains cellulose

- glycogen have 1-6 bonds (alpha bonds so we can break them down)

2/22/23

• Covalent modulation is when the modulator forms a covalent bond with the protein by bonding a phosphate group
• Allosteric modulation bonds with a molecule loosely with the protein
• Epinephrine triggers liver to make glucose

***Kinase is an enzyme that adds phosphates

• Epinephrine binds in the extracellular pocket of the protein
• G proteins use GTP
  • The alpha subunit of the G protein picks up GTP and falls away and the phosphate is removed
  • This process happens because epinephrine changes the shape of an enzyme and it binds to the receptor on the membrane which then activates the G protein.
  • Alpha can’t regenerate itself without the presence of the beta and gamma subunits of the G protein
  • For every 1 cAMP it can make 2 PKA (Protein Kinase A)
    • PKA modulates Phos. Kinase
  • Glycogen synthase being turned off and Phosphorylase kinase is being turned on
  • Phosphorylase kinase that phosphorylates glycogen phosphorylase to produce glucose 1-P

2/27/24

• When one epinephrine binds to one epinephrine receptor, it creates millions of glucose
• Signal transduction Hallmarks:

- Specificity

- Amplification

- Change in shape and function

- Resting everything

- RNA world Theory

- RNA had to form from inorganic sources

- RNA self-replicates through ribosomes

- RNA catalyzes protein synthesis

- Miller’s Primitive Earth Experiment

- proves that amino acids and fatty acids were produced abiotically and that there were more in the “soup” than Miller had originally discovered.

- Unicellular Tetrahymena

- ribozyme from Tetrahymena that is made of RNA

- Ribozyme + RNA primer (5 base) + gel electrophoresis

- nucleotides can be lost or added depending on how many bases are left on the primer.

- fastest self-splicing ribozymes had the same bases they had before they were introduced to mutations.

- negatively charged particles are able to catalyze better

• Phylogenetic trees
  • Ones that we do
    • The branch length does not matter, where the branches connect matters

Mendel's Pea Plants

• A small change in nucleotide in one gene can make two entirely different phenotypes
• A mutation can change the gene
• Horizontal gene transfer
  • Transformation ~ cell becomes permeable and can take other cells DNA chromosomes
  • Transduction ~ Viruses replicate within a cell continuously while the cell is replicating its own genome and then the nucleotides of the viruses and the cells can explode out together and get picked up by another cell.
  • Conjugation ~ a cell can make a pilus and share its chromosomes with another cell
• Genome Duplication
  • When it causes all the nucleotides in two duplicate genomes
  • Maybe happened with the ancestor of the vertebrae which is why they have twice the normal amount of genomes compared to invertebrate
• Rapid Genome Changes
  • Picture - red lines are paralogs and black lines are chromosomes
• Four Mechanisms of Evolution
  • Mutations occur during replication errors
    • Point mutations
    • Deletions
    • inversions/insertions
    • Whole genome duplication
  • Darwin’s original tree of life
    • LUCA stands for (last universal common ancestor)
    • Parsimony ~ the simplest sequence is probably the original one
    • Genetic distance of 0 means that the sequences are the same
    • Ribosomal DNA -^
      • Because they make all the same proteins
    • Prokaryotes don’t have membrane bound organelles like eukaryotes
    • How did a true nucleus originate?
      • First two domains of life (bacteria and archaea) come from the same common species and then converge back together to form eukaryotes
    • Nuclear organization/nuclear packing
    • IQ #4 DNA are more like pearls on a string and not just a string
      • Each bead is called a nucleosome with DNA wrapped around it and wrapped twice around the protein core
      • 4 different histones that are duplicated in the nucleosome
      • And can be modified by allosteric or covalent bonding
    • IQ#11 2 each of 4 different kinds, histones don’t bind to specific areas but there needs to be around 240 nucleotides between each one. 200 base pairs in each nucleosome
      • By coiling the DNA around the histones, the nucleus can fit the whole chromatin strand inside of it.
      • The chromatin can’t be coiled together unless they are covalently modulated by methylation but only the loosely packed nucleosomes can be transcribed.
    • IQ#10 Eubacteria are missing because their genes don’t code for histones, so it looks like eukaryotic cells picked up genes from the archaea.
      • Coiled chromatin occurs in Prophase and then unravels through covalent modulation to be transcribed.
  • How did Eukaryotic cells evolved from Prokaryotic ancestors?

Lab:

• Gram-positive has no cell wall so easier for stain to be seen
• Gram negative have strong cell wall so stain is harder to see

3/26/24

Eukaryote and Serial Endosymbiosis:

• Prokaryote is engulfed in an ancestral eukaryote
• Then the eukaryote engulfs a photosynthetic prokaryote
  • Genes in each prokaryote (mitochondria and chloroplast) were retained (have circular chromosomes).
• Diploid chromosomes terminology
  • Loci ~ location on a chromosome (usually where the allele is)
  • Homologous chromosomes (diploid)
  • Dominant and recessive allele ~ heterozygous
  • Dominant and dominant or recessive and recessive ~ homozygous
• Flower Anatomy
  • Stigma (female parts)
  • Stamen (male parts like sperm)
  • 3:1 ratio of cross with true-breed yellow and true-breed green (more yellow)
  • Only homozygous recessive can get true-breed green
• P > F1>F2
• P = YY + yy
• F1 = Yy (Y or y)
• F2 = YY and Yy and yy (¼ green and ¾ yellow)
• F3 = (¼ green and ¾ yellow)
• Randomness Causes Deviation
  • ex) sperm = Yy + yy = egg (Y or y)
  • ex) sperm = Yy + YY = egg (Y or Y)
• Meiosis Contributes to Randomness
• Allele pairs separate independently during separation or formation of gametes
• Frequency = percentage and they should add up to one or 100%
• (p+q)^2 = 1 then p^2 + 2pq + q^2 = 1
• Null hypothesis = O=E
• A population might not be at equilibrium if it is evolving, but in reality, if a population is evolving, it is not at equilibrium.

Not In Equilibrium (opposite = in Equilibrium)

1. Nonrandom mating

2. Genetic flow

3. Natural selection

4. Small population size

5. Mutations

What determines Phenotype?

• Environment
• Genetics
  • *What determines phenotype is situational*

Tables in Lecture (3/28/24)

-Residual sum of squares is offspring height/phenotype - predicted height/phenotype = x´2(squared)

-Slope - y intercept = best fit (smallest number)

-if heterozygous is breaded continuously,they will continue to have the same alleles and they won’t become fixed

-if only four genotypes are present on a table it means that they are on one chromosome so they won’t travel with another and cross and mix alleles (recombinant chromatids/crossing over)

Hardy-Weinberg Equilibrium

~ allele frequencies are p and q

~ (expected) genotype frequencies p^2, 2pq, q^2

~ (observed) genotype frequencies AA Aa aa

~

Influenza virus is single stranded RNA and has 8 stranded chromosomes

Rhagoletis Ma…(maggot fly)

• Lay eggs in Hawthorn fruit and eggs hatch into maggots which eat the fruit.
• parasitoid wasps lay eggs in maggots and babies eat the maggots.
• Apples became a lot more viable food source but lesser quality then that of the hawthorn fruit
  • Apple maggots carry less wasps eggs
• Apple maggots mature earlier than Hawthorn maggots because apple ripen earlier than hawthorn fruits
• Apple and hawthorn maggots = sympatric because they are the same species in similar geography (genetic material is different but physicality is the same)
• Are they different species?

How do you define species?

• Morphology ~ how the species look
• Ecological species concept ~ do they have a role in the ecosystem? environment and habitat (even a little percentage of hybridization mean this is possible)
• Biological species concept ~ reproductive isolation (interbreeding naturally)
• Phylogenetic species concept ~ defined by their unique characteristics

Adaptive Radiations

• Start of a new species, usually occur because of a mass extinction
• A niche or role in the ecosystem of a certain organism becomes open
• Cambrian, Devnian, ect.
• Why are orchid subfamilies so diverse?
  • Living above ground with different environmental pressures
  • Different pollinators pollinating the orchids
• Flight is to complicated to occur because of natural selection (evolved three separate times)
• Synapomorphies ~ circles or dashes are the origin of a characteristic or trait (shared/derived trait)
• Homoplasy ~ when a character evolved multiple different times in different lineages
• Symplesiomorphy ~ shared, ancestral trait
• Conversion evolution ~ when independent evolution of similar traits in species of different periods of time (responsible for homoplasies).
• Node ~ when branches converge = common ancestor

Bio 4/9/24 notes

• Greater cell differentiation in last stages occurs for the elongation of digits in bats to allow for flight.
• BMP2 stimulates bone growth maybe a mutation in earlier bats genes that cause the bones to grow more
• Mutation = adaptation in populations
• Differences and similarities between prokaryotes and Eukaryotes (in slides)
  • Archaea with p-lipids with isoprenes?

Metabolic Diversity of Prokaryotes

• Source of electrons and source of protein (two components are necessary)
• Lithotrophs: use inorganics as electron donors (only prokaryotes)
  • Lithoautotrophs
  • Lithoheterotroph
• Phototrophs (only plants or prokaryotes)
  • Photoheterotrophs
  • Photoautotrophs
• Chemotrophs (mostly animals)
  • Chemoheterotrophs
  • Chemoautotrophs

Why are Prokaryotes important to Learn about?

• First living organism (origin of earth's molecular oxygen
• Major photosynthesis contributors
• Only organisms that can fix nitrogen into biologically useful forms
• Primary decomposers
• Some are pathogens

Protists

• Taxonomy
  • The three domain system
• Protists
  • Ingestive
  • Absorptive
  • Photosynthetic
• Green and red algae have two membranes around their chloroplasts (archaeplastida)
• Alveolata, Excavata, Rhizaria,Stramenopila have 4 membranes around chloroplasts
• Understand the reasons why it is important to know about Protists
• Costs and Benefits of Terrestriality (moving from aquatic environment to land)
  • More access to sunlight (too much could damage DNA)
  • Better access to gasses
  • More nutrients in the land
  • Would need stronger structure because they no longer need their buoyancy
  • Less water
• How did plants face stressors moving to land
  • Desiccation
    • Cuticle
    • Stomata
    • Sores
    • Gametangia to protect gametes
    • Retention of embryos on parent plant
      Flowers to protect gametophytes
  • Decreased availability of appropriate habitats (combined with difficulty dispersing spores/gametes without water)
    • spores/pollen/seeds carried by wind and animals
    • Heterospory (made pollen and seed production possible)
  • Exposure to UV Light
    • Flavonoids
  • Gravity –> vascular tissue
    • Vascular tissue
      • Xylem
      • Phloem
    • Leaves
    • Seeds
    • flowers/fruits
  • Alternation of Generations
    • Gametophyte = haploid
    • Gametes = haploid
    • Zygote = diploid
    • Sporophyte = diploid
    • Spores = haploid

- Fungi species: 4/16/24

• • Chytridiomycota
  • Zygomycota
  • Glomeromycota
  • Basidiomycota
  • Ascomycota
• Homoplasies are statistically unlikely to happen but are possible
• Bikonts ~ two flagellum
• Uniconts ~ one flagellum
• Opisthokonta ~ rear flagellum
  • Fungi
    • Can be single celled (like yeast) or multicellular hyphae and have weblike bodies called mycelia
    • Have cell walls made of chitin also what insect exoskeletons are made of (carbohydrate)
    • Hyphae form filamentous mycelium → single cell thick, many cells long (great for absorption)
      • Filaments can be separate from the cell wall or coenocytic
    • Sometimes “fruiting bodies” (sexual reproductive parts like the mushroom tops) are produced
      • glomeromycota
    • Use four sexual reproductive strategies and one asexual strategy
      • Swimming gametes and spores ~ Chytridiomycota
      • Zygosporangia ~ zygomycota
      • Basidia ~ Basidiomycota
      • Asci ~ Ascomycota
    • Nutritive modes
      • Mutualistic
      • parasitic/predatory
      • Commensal
      • Saprophytic
    • Generalized Fungal Life Cycle
      • Asexual reproduction is the most
      • Sexual reproduction less often but different from other organisms mitosis cycle
      • Ancestor and all its descendants are monophyletic
      • Ancestor with only come of its descendants is paraphyletic
    • Why should we care about fungi?
      • Decomposers
      • Components of mycorrhizae in ~ 90% of plants
      • Components of lichen
      • Cause many plant diseases
      • Cause animal diseases
      • Produce some antibiotics
  • Choanoflaguletes
    • Closest animal relative that isn't exactly an animal
    • Are sessile protists
  • Characteristic of animals
    • Multicellular
    • Eukaryotic
    • Lack cell walls but have an extracellular matrix
    • Heterotrophic ~ can not make their own food [some use absorptive feeding and most use ingestive feeding (ingesting food from their mouth)]
    • All are capable of movement
    • All (except sponges) have cells organized into different tissue layers
    • All (except sponges) have muscles and nerves
    • All (except sponges) have Hox genes that control development of various body parts
  • Characterizing Animals
    • Symmetry ~ asymmetrical (no symmetry), radial symmetry, bilateral symmetry
      • Have eyes and centralized nervous system that will engage with the environment before any other body parts (cephalization, head first)
    • Number of tissues ~ diploblastic vs. Triploblastic
      • Two tissue layers
      • Three tissue layers
    • Acoelomates vs. Pseudocoelomates vs. Coelomates
      • Coelom = fluid-filled cavity surrounded by mesoderm on one side (pseudocoelomates) or on both sides (coelomates)
    • Protostomes vs. Deuterostomes
      • Zygote → eight-cell stage → Blastula →
        • Cells twist relative to each other = spiral cleavage
        • Cells stacked upon each other = radial cleavage
    • Protostomes: Lophotrochozoa vs. Ecdysozoa
      • Lophophore
      • Ecdysis

Lab Notes:

• Richness is number of species
• Species diversity is the distribution of species

4/23/24

Phylogeny of Animals:

• Homoplasies ~
• Synapomorphies ~ similar to analogous structures
• Opithesticonts ~ fungi and mammals
• Deuterostomes ~
  • Echinodermata ~ skin that has spikes which are usually used for walking (starfish, urchins)
  • Chordates ~ have a notochord that supports the developing organisms and have a dorsal hollow nerve cord (like a spinal cord) and have gill slits (sea squirts, lancelets, Hagfish, sharks, sting rays, trout, tuna, Salmon, Bass, Lungfish, Amphibia: frogs, salamanders, Reptiles: lizards, turtles crocodiles, snake, birds (only birds have feathers), placentas, marsupials, monotremes
    • vertebrates ~ skeletal cord
    • Urochordates ~
    • Cephalochordates

* Gnath= jaw

Stome=mouth

Chondr=cartilage

• Everything below Gnathostomata chordates have jaws
• Sarcopterygii ~ are fish that use muscles in their fins to swim
• Tetrapods ~ have four limbs
  • “Limbs from fins” hypothesis evolved from step changes
• Amniotes ~ amniotic sac contains fluid that holds embryo, have allantois to collect waste, and Yolk sac
• ***Birds are within the reptilian (paraphyletic grouping) family
• Mammals have synapsid skull
  • Produce milk
  • Warm blood
  • Large 4 chamber heart
  • High metabolism rate
  • Hair
  • Red blood cells without nuclei
• Placental mammals → Primates → related to humans (grasping hands with flattened nails, large brains, color visions, parental cair
  • Prosimians - lemur, new world monkeys, gibbons, orangutans
  • Arthropods - gorillas (no tails)
  • Hominids - humans, Bonobo, Chimpanzee
• Common ancestor of humans and chimps was present 5-7 million years ago
• Homonins ~ (originated in Africa)
• early hominids
• Australopithecus
• Paranthropus ~ walk on all fours
• Homo ~ large brain, small teeth, walk on two legs

Mitochondrial human evolutionary tree

• Length of branch indicates the number if nucleotides
• Close relations are similarities in mitochondrial sequences

Lab: review for exam

• Humans are very similar considering nucleotide sequences
  • Different ethnicities still only have 0.1% genomic differences
  • Amount of melanin produced by skin cells is what creates the different shades of skin color and 34 genes are responsible for that
  • Race does not exist in a biological sense, it is a social construct