bio

Bio94 Lecture 8

World’s newest monkey species was found in a lab, not on expedition Through fecal matter

Farmed salmon vs wild salmon Phylogenies can find difference between farmed salmon and wild salmon Biological questions Evolution; testable hypotheses

Bioinformatics- using lots of math and computers to answer biological questions Forensics- use intensive DNA analysis Identifying pathogens Medically, phylogenies important Cancer cell goes through evolutionary process Covid phylogeny Closest relative is bat

Ends of tree are called tips Start is Root Lines are Branch Split apart is node Outgroup is longest and different form all Synapomorphies Vertebrate, bones, tetrapods, aminotes, feather, warms blood, mammals Monophyletic- pull of branch Branches can rotate Paraphyletic If something was left off/something missing Polyphyletic Many groups that do same thing but separately Convergent evolution Monophyletic

Paraphyletic [study] ABC paraphyletic- leaves D EFG paraphyletic- leaves H Polyphyletic [study] From two distinct branches Such as DE

Polyphyletic and paraphyletic is not good Monophyletic question

Branch lengths can be: Arbitrary, just for showing relationships Next is based on genetic differences; more mutations= longer branch Molecular clock Estimate mitochondria and how far they are in terms of time Date of appearance; extinction (branch that goes nowhere)

Homology vs homoplasmy (convergent evolution) Something that looks same but from different ancestor

Have different fins Horizontal; vertical tails Polyphyletic group if in same group Relationship to hippo-like ancestor supported by Fossils Anatomy Development and embryology paleontology/sedimentology dna/genetics

Whales are mammals Warm-blooded Hair Mammary glands (milk production) Bear living young Developmental evidence of vestigial hindlimbs in baby dolphins Distinct fossils link whales to hippos Astragalus: ankle bone Shared by hippos and fossil whales Whales are artiodactyl mammals What can we learn from fossil? Ages, appearance, extinction, transitions Biases Habitat matters (in mud fossils more likely to be preserved) Tissue (soft tissue not best for preservation) Taxonomic bias (more hard part=more likely to fossilize) Temporal (time)- older fossil is more likely to be eroded and washed out of sediments Abundance- fossil record imperfect (rare animals less likely to be captured) Whales were put with hippos because of DNA sequencing Questions below

Precambrian(memorize order)

Origin of life
Origin of photosynthesis (and O2 production)
Origin of eukaryotes
Origin of multicellular animals

Bio94 Lecture 9 (check what we need on our own)

Convergent evolution/homoplasmy

Oldest to newest: large amount of oxygen (cyanobacteria), oldest fossils of eukaryotes appear, cambrian explosion, colonization of land

Order is cenozoic, mesozoic, and paleozoic Adaptive radiations Sudden appearance of lots of species inr relatively short period of time Example- silverswords Conditions for this to happen New habitat with few competitors Many niches (habitat being used) New traits (flowers and wings) Monophyletic tree Lots of unresolved nodes Know different species but cant tell who branched off from who

Cambrian explosion: the ultimate adaptive radiation First adaptive radiation Multicellular organs Appendages and mouth Exoskeleton New habitat can be exploited with different body forms Swimming Hox genes and animal diversification Hox genes are transcription factors that turn other genes on during development for anterior-posterior patterns Heads and tails (1 blue and 9-13 purple) Genes duplicate and diversify over time

Fecal transfer Bacteria good for destroying pollutants, climate change, important in gut Cancer treatment for fecal species Bacteria are very diverse Almost as big as head of a fly Vary in size, shape, motility Bacteria vs viruses Viruses have nucleic acid and protein shell (capsid) Membrane

Some viruses have DNA HPV, herpes (DNA viruses) RNA viruses (crops, ebola, rabies) (cold, west nile, dengue, zika, dengue) Reverse transcribing (RT) viruses (HIV, hepatitis B)

Viruses distributed partly by nucleic acid (DNA, RNA, reverse transcribing) Microbes Bacteria have peptidoglycan and cell walls Archaea have special RNA polymerase and methionine start codon (same as humans) We also have methionine start codon (eukarya) Archaea are known to be extremophiles How to know if bacteria causes a disease Koch’s psotulates

Microbe present in diseased animal
Culture the microbe
Infect an animal with the cultured bacteria
Reculture the bacteria

Problem is not all bacteria like to be in culture

Human microbe (also known as microbiome)

Immune, circulatory, digestion, behavior Metagenomics- pull sample of DNA and send to be sequenced Humans have >1000 microbes on body

Purple is gram positive Pink is gram negative Antibiotics target peptidoglycans In gram-negative, peptidoglycan protected by cell wall layers In gram negative, some of these bacteria can be treated with ribosome inhibitors

Bio94 Lecture 10 What is a bacterial culture? Fresh broth and add bacteria Agar plate

Antibiotic needs to present for mutant to thrive Bacteria need genetic variation to evolve Transformation Cell dies Releases DNA Another cell takes the DNA Add DNA to its chromosome

Transduction Need a virus Bacteriophage/phage (virus) Virus w/ bacterial DNA instead of viral DNA When it goes to new host cell, it injects bacterial DNA New Add DNA to chromosome

Genetic variation through gene transfer Conjugation Plasmid- circle of DNA independent of rest of chromosome Two cells meet in conjugation and connect via conjugation tube Transfer copy of plasmid

How antibiotic resistant genes are transferred Option 2 Tube and small strand of DNA (former plasmid+ some other genes attached to it) Transfer and recombination

Part of DNA replicated and transfer

Metabolism: it’s all about moving electrons Potential energy: high or low Electron transport is like water balloon failing step by step instead of directly down In mitochondria, energy used to move H+ ions Oxygen accepting electrons Hydrogen ions form another gradient; as hydrogen ions fall through atp synthase to make ATP

Bacteria’s source of electrons and where electron lands varies greatly by species We pull our electrons from glucose Some bacteria pull from glucose and put it on nitrate (NO3-) Some use iron as electron acceptor Other donors are H2, H2S, NH3, CH4 Other acceptors SO4-, NO3-, Fe3+, CO2

Metabolic diversity

Autotroph: self synthesized from CO2, CH4, or other simple molecules Heterotrophs; get molecules from other molecules

Humans get it from organic (sugar) Photoautotrophs includes plants Chemoorganoheterotrophs, includes humans Cyanobacteria is photoautotroph

Chemoorganoautotroph

Chemolithoautotroph- sulfide inorganic; o

Chemoorganoheterotroph (ferment; breaks down organics)(anaerobe- non-O2 e- acceptor) Donor important over acceptor

Chemolithoautotroph Bacteria play a central role in global nitrogen cycles 78% nitrogen Amino acids, nucleic acids both have nitrogens in their structure nitrogen>form other organisms can use Nitrogen fixation Archaea and bacteria Plants also depend on this

Fixation is essential
Plants are essential
Bacteria make most of it possible Too much nitrogen can be bad for environment Fertilizer has NH3 Bacteria in soil make NO3- NO3- gets washed down stream (algae use NO3-) Dead algae die and decompose> low O2

Happens in Mississippi drainage Low oxygen zones caused Bio94 Lecture 11

Answer: B

Answer: A Clarification Aerobic- O2 is the final electron acceptor Anaerobic- O2 is NOT the e- acceptor Fermentation Anaerobic/aerobic- have an electron transport chain Fermentation- no ETC Glucose goes through glycolysis> makes pyruvate>>mitochondria which brings in O2; NADH, NAD+ ATP also made

No O2 Pyruvate>lactate NADH>NAD+ Regen NAD+ Glucose goes through glycolysis to make pyruvate which creates acetaldehyde>ethanol

Protists Find all over place

Protists don’t include some eukaryotic groups Can cause medical issues such as malaria Mosquito has plasmodium which is injected and into liver Go to bloodstream and move into red blood cells Inside RBC they eat hemoglobin and kills blood cell and releases male and female gametes Mosquito take in gametes Fertilization and infect mosquito

Giardia- days to weeks of diarrhea (filter water when camping) flagella Amoebic dysentery (bloody diarrhea) Techomonas vaginalis (sexually transmitted disease) Harmful algal bloom dinoflagellate Socal diatom produces domoic acid Brain gets smaller Protists are tasty Seaweed Red and brown algae Earth’s future depend on protists Play key role in global carbon cycles Phytoplankton floats in water Include diatoms, dinoflagellates Take CO2 out of air and fix the onto carbon compounds Some have CaCO3 shells Sink when they die Accumulate CaCO3 (carbon sink)

Secondary consumer eats primary consumer

Mitochondria evolved from bacterial symbiont Take in O2, pump out ATp Own DNA Endosymbiont theory Host cell (probably archaea) Host engulfs bacteria but does not eat endoSymbiosis- association between two organisms Host membrane and original membrane Secondary endosymbiosis with another membrane Support for hypothesis: mitochondrial size; independent fission; bacteria- style ribosomes, Mitochondrial DNA

Secondary endosymbiosis- when one protist engulfs another protist Protist with chloroplast and nucleus and host protist Protist gets engulfed Lose the nucleus 4 membranes of chloroplast

Primary Endosymbiosis chloroplast Land plants, green algae, red algae Secondary endosymbiosis Protiss means another protist Brown algae, lost the symbiont

Protists have diverse feeding strategies Extending of pseudopodia False foot Cilia beat and have small water currents Alternation of generations Sperm (n) egg (n)> fertilize> zygote (2n)> go through mitosis> sporophyte (2n)> meiosis> produce spores (n)> mitosis> gametophyte gametophyte> sperm and egg

Preview plants Red algae (aquatic) to angiosperms (land)

Preview mosses Sporophytes and gametophytes Mosses are where it's wet

Preview: gymnosperms (pine trees) Sporophyte (2N0 Gametophyte Gamete Pollen contain sperm Fertilize and make seeds

Bio94 Lecture 12

Chemolitho

Peptidoglycan

A drug that destroys mitochondria Slime molds alternate between asexual and sexual reproduction Actin critical for pseudopodia

In this species of diatom, fully formed actin necessary for movement

When the toxin was washed off the culture, the cells began to move again Wildfire burn scars are a flood risk Plants and ecology are social justice issues Redlining- less plant life people of color hotter areas More biodiversity Repeating evolutionary themes for plants and animals In order for a population to survive, organisms must Heritable variation Reproductive advantage To transition from water to land, organisms must: Have structural reinforcement Kelp collapses easily out of water Be desiccation resistant Prevent drying out Have UV protection More at surface of water Protect gametes that swim We’ve been genetically modifying plants for at least 12,000 years Corns, bananas, Chemistry + botany + traditional medicine= new drugs Where did land plants come from? Plants come from aquatic ancestor Some type of green algae proof: Chlorophyll a, b B carotene Thylakoids Cell walls Sperm Peroxisome Store starch

Paraphyletic Omit all others Polyphyletic has convergent traits Green algae: chlorophyll, Nonvascular- terrestrial first, land Moss Vascular is up to down Seedless plants: vascular, Ferns: with spores that disperse Gymnosperms and angiosperms Have seeds Gymnosperms (naked seed)- pine trees Angiosperms (covered seed)- flowering plants that also have fruit flowers Barriers to living on land Water loss and UV damage Cuticle Stoma can open and close Gas exchange CO2 in and O2 out H2O movement Some plants have coating

Resisting gravity First vascular tissue Reinforcement Tracheids Small tubes 2 walls Questions Where are gametes made? D/C Gametophyte has gametangia: male (antheridium) and female (archegonium) Where are spores made? A Which step shown in the figure will be the most problematic on land? D Bio94 Lecture 12

A, D, E

D Mosses Cuticles, pores Gametophyte haploid (n) Female and have eggs inside Male and make sperm (flagella) Hold over from green algae Fertilized egg will grow sporophyte Gametophyte dominant Sporophyte grow up top (2n) Homosporous (look alike) bisexual, can’t tell by looking if produce male or female gametophyte

Gametophyte Male (produce sperm) and female (egg) Sperm needs water to swim to egg Egg fertilized and grows into a zygote which becomes a sporophyte Meiosis in sporophytes, haploid spores come out Ferns Can have both male and female Sperm flagellated Big sporophyte (diploid) Advantages Backup of genes More diversification liked duplication and diversification Diploid more successful on land Spores are haploid Homorspous

Male, female Sperm flagellated (need water to get to egg) fertilized> embryo Sporophyte grows out of gametophyte Vascular- vessel that allow water and nutrients to travel around Sporangia- makes spores

A, C, F Heterosporous Microspores and megaspores Gymnosperm Cones Spread through wind

Heterpsore Definite male and definite female Angiosperm Fruit

2 female nuclei + 1 sperm= 3n endosperm Endosperm divides and becomes nutrition for the seed Diverse flowers attract diverse pollinators Directed-pollination Moth favored wild type white while bee favored pink genetically altered flowers Seeds are very diverse Seed coating, nutritive tissue, embryo 3n endosperm Phylogenies are works in progress Dicot is paraphyletic Eudicots- true dicots (monophyletic) Dicots cotyledons Monocots are monophyletic medicines