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