bio153 final

Horizontal Gene Transfer

It's possible for genetic material to get transferred between two different species

Taxonomy

study organisms, name them, and put them into similar groups

Phylogeny

deduce evolutionary relationship between organisms put similar groups

Predator and prey

Change in population sizes of predator and prey are known to synchronize

Epidemic

significant rise in occurrence of a disease, above the rate which is normally expected in a local population

Pandemic

Global epidemic, usually on more than one continent

Three groups of mammals

• Monotreme (lays eggs)

• Marsupial

• Placental

Most basic requirements for survival

1. Life needs energy

2. Life uses carbon to build their body

Organic molecules

Compounds which are made of carbons and hydrogens, connected by covalent bonds

Phototroph

use light as energy source

Autotroph

use CO2 as carbon source

Chemotroph

use chemicals (such as organic molecules) as energy source

Heterotroph

use organic molecules as carbon source

Chemoheterotrophs

consume organic carbon made by photoautotrophs

Prokaryote

cells without nucleus and other membrane-bound organelles

Eukaryote

cells with nucleus + organelles

Unicellular organism

• Body of the organism consist of a single cell

• Most prokaryotes (bacteria and archaea)

• Some eukaryotes

• Still live as a population

Multicellular organism

• Body of the organism are composed of multiple cells

• Most non-microscopic eukaryotes

• Compartmentalization of bodily function into tissues

• muscles, nerves, bones

• leaves, branches, roots

Viruses

• acellular forms of 'life'

• have DNA or RNA genome packaged by proteins

• Must infect host organism for reproduction

Binomial Nomenclature

An organism's scientific name is expressed in two parts, genus and species

Genus name

given to a group of closely related organisms

Species name

unique name given to a single kind of organism

Rules for Binomial Nomenclature

• The species name include both names of the binomial

• Both Genus and Species names are italicized

• First letter of Genus name in upper-case

DKPCOFGS

Domain

Kingdom

Phylum

Class

Order

Family

Genus

Species

International Code of Zoological Nomenclature (ICZN)

naming 'animals'

International Code of Nomenclature for algae, fungi, and plants (ICN or ICNafp)

naming organisms traditionally treated as algae, fungi, or plants

International Code of Nomenclature of Prokaryotes (ICNP)

naming Bacteria and Archaea

International Committee on Taxonomy of Viruses (ICTV)

naming Viruses

Cladistics

an approach for systematics saying that organisms should be classified using ancestral relationship as the primary criteria

Phylogenetic tree

Branched, tree-like representation of the relationships of organisms

Branch point

a common ancestor diverges into different species at the branch point

Dichotomy

a branch point where the common ancestor diverges into exactly two lineages

Root of the tree

the branch which represent the common ancestor of all taxa in the tree

Sister taxa

group of organisms that share an immediate common ancestor that is not shared by any other group

Basal taxon

lineage that diverges from all other members of the tree early in the history of the group

Properties of a phylogenetic tree

Property 1: a phylogenetic tree only shows how each organisms are connected to one another

• Therefore, the basic phylogenetic tree can be drawn in different shapes without changing the meaning

Property 2: The tree shows patterns of descent. This may not always correspond to how similar organisms look or behave.

• Cetaceans (Whales/dolphins) and seals look similar, as they are both marine mammals

• However, Cetaceans and seals do not share an immediate common ancestor

Property 3: The tree does not infer that a taxon evolved from a neighboring taxon

• The common ancestor of Chimpanzees and Humans is a different species from them

• This common ancestor does not exist today

Cladograms

A basic phylogenetic tree only shows how each organisms are connected to one another unless otherwise noted

Phylograms

phylogenetic tree which additional information are represented, typically by the lengths of each branch

Dichotomy (tree)

a branch point where the common ancestor diverges into exactly two lineages

Polytomy

a speciation event showing a common ancestor diverging into more than two species at once

Morphological traits

• shapes of the body

• Overall bodily shape such as 'having four legs'

• Tissues, such as bones and branches

• Individual cells, especially for unicellular organisms

• Organelles such as the nucleus and chloroplast (photosynthesis)

Biochemical traits

Presence and absence of metabolic pathways, etc.

Genetic traits

• Presence and absence of related genes

• Differences in those genes

Taxonomy using Morphological traits

• In general, organisms which share similar traits are likely to be evolutionary related to one another, especially when that trait is a complicated one like bone structure

• It is less likely for complicated traits to evolve independently in unrelated organisms and end-up looking near-identical by chance

• Skull morphology is used a lot for classification due to its complexity

Australian mole and North American mole

• look very similar

• Evolved under selective pressure for their ground-burrowing lifestyle

• Australian mole is marsupial

• North American mole is placental

• These species are not closely related at all

Convergent evolution

Unrelated lineages of organisms can develop similar-looking traits independently

Homology

similar traits in organisms shared through common ancestry got passed to all members of its lineages

• 'Feeding milk' is a homologous trait for all mammals

Analogy

similar-looking trait in organisms which occurred not by shared ancestry

• Mole-like traits developed independently in Australian and Placental moles lineages, and ended up looking alike

Shared ancestral character

trait held by the common ancestor which got passed on to all* descendants

Shared derived character

a unique character found in a lineage which developed after the common ancestor

Types of Homologous genes

Orthologous genes, Paralogous genes

Orthologous genes

A common ancestor diverges into two species

• Both species inherits the same genes from their ancestor (homologous genes with shared ancestry)

• Since they are in a different lineage, the homologous genes can now begin to evolve (mutate) differently

Paralogous genes

A gene makes a copy of itself within the same species

• The two copies of genes (in the same species) can begin to evolve differently

• You can not deduce evolutionary relationship between species if you are only observing paralogous genes within the same organism

Clades

Groups of organisms which are classified together

Monophyletic group

A clade where all members are descendants of their most recent common ancestor

Paraphyletic group

A clade where all members are descendants of their most recent common ancestor but there are more descendants of that ancestor which were not included

Polyphyletic group

A clade which includes members belonging to a different evolutionary lineage

Maximum parsimony

When there are multiple ways to describe a phenomena, the simplest explanation is most likely the correct one

Coccus

Ball

Coccus: single cell, alone

Diplococcus: two cells

Streptococcus: many cells in a chain

Staphylococcus: many cells in a cluster

Bacillus

Rod

Bacillus: single cell, alone

Streptobacillus: many cells in a chain

Morphological features of bacterial cell

Plasma membrane and the bacterial cell wall

Capsule/slime layer

Flagella and pilus

Endospores

Plasma membrane

lipid bilayer made of phospholipid, a hydrophilic 'head' and a hydrophobic 'tail', the heads face water while tails 'hide' from water, facing each other

Peptidoglycan

• made of two types of sugars in attached in a long, unbranched chain (backbone)

• One of the sugars have a short peptide attached (3 - 5 amino acids)

• attach to each other to form a mesh structure

Plasma membrane + Peptidoglycan

• Plasma membrane is a permeability barrier, but 'soft' and is not mechanically strong

• Peptidoglycan protects cell from osmotic pressure, mechanically strong

Gram positive cell wall

• Thick layer of peptidoglycan

• Relatively simpler structure

Gram negative cell wall

• Thin layer of peptidoglycan

• A second lipid bilayer surrounds the peptidoglycan layer (outer membrane)

Gram positive cells appear…

purple

Gram negative cells appear…

pink

Gram negative bacteria

Proteobacteria (such as E. coli)

Chlamydias

Spirochetes

Cyanobacteria (the photo-autotrophs)

Gram positive bacteria

Such as S. aureus and B. subtilis

Chlamydias:

don't have a peptidoglycan cell wall, still stain pink in Gram stain

Capsule and slime layer

A layer outside the bacterial cell wall

Made of sugars and/or peptides (species dependent)

Can be rigid (capsule), or more soft and flexible (slime layer)

Resists de-hydration, resists immune system of host organism, adherence to surfaces

Sub-cellular structures

Thylakoid membranes

• Multiple folds of lipid bilayer inside cyanobacteria

• Conversion of light energy to chemical energy (ATP)

Carboxysomes

• Polygonal structures made of protein shell, found inside cyanobacteria

• Fixation of CO 2 into organic molecules

Flagella

Long, whip-like structure attached to the bacterial cell wall

Rotation of flagella makes the cell move

Chemotaxis

bacteria has systems to move 'towards good things' and 'away from bad things'

Fimbriae

Shorter and more numerous

Attachment to surfaces and to other cells

Pilus

A longer tubular structure

Connects two bacterial cells to facilitate exchange of genetic materials (this is a form of horizontal gene transfer)

Endospores

Ultimate survival mechanism deployed by some Gram positive bacteria such as Bacillus subtilis

Vegetative cells (normally growing cells) form endospores to survive unfavorable environmental condition

Vegetative cells die in the unfavorable condition while the endospores persist

Endospores grow back to vegetative cells once environmental condition restore

The PROTECT experiment by the European Space Agency (ESA)

Bacillus subtilis spores were loaded on a spacecraft and delivered to the International Space Station on February 7, 2008

Bacillus spores were exposed to outer space for 1.5 years before they were brought back to earth

Only a fraction of the Bacillus endospores survived 1.5 years of exposure to outer space, and were able to grow back into vegetative cells

Bacterial growth

Bacteria replicates by binary fission

Parent cell divides into two new cells

Bacterial population grows exponentially

Escherichia coli divides once every 20 minutes under optimum condition

One cell becomes 8 cells after 1 hour

One cell becomes 262,144 cells (0.26 million) after 6 hours

One cell becomes 68,719,476,736 cells (69 billion) after 12 hours

How antibiotic resistance spreads

More cell division means more DNA replication, More DNA replication means more chance for DNA to mutate, Reproducing to huge population increases the chance that some members of population, by chance, have the mutation to react to new challenges in environment

Requirements of life / growth:

Needs energy

Needs carbon source

Among many other elements like nitrogen

Photoautotrophs make organic molecules from:

sunlight, water and CO2

Chemoheterotrophs use organic molecules to:

extract energy and as a carbon source

Fermentation

Use pyruvate to regenerate NAD+

Pass electrons from NADH to pyruvate to regenerate NAD +

Pyruvate gets turned into fermentation products in the process

alcohols, acids, etc.

Fermentation happens anaerobically

Aerobic Respiration

TCA cycle extracts energy which is left inside pyruvate

aka Krebs cycle, Citric acid cycle

One pyruvate eventually becomes 3 CO 2

TCA cycle makes more NADH (and other electron carriers) + ATP

NADH gives electrons to Electron Transport Chain

Regenerates NAD+

Energy is produced as electrons pass through ETC, which is used to make ATP

At the end of ETC, electrons are put onto O2, the terminal electron acceptor

Aerobic respiration vs Fermentation

Aerobic respiration: up to 38 ATP

Fermentation: 2 ATP

Anaerobic Respiration

Respiration can be done using molecules other than O 2 as terminal electron acceptors

NO 3- (nitrate)

SO 42- (sulphate)

Non-O 2 electron acceptors are not as effective as O 2 to drive electrons through ETC

Anaerobic respiration does not produce as much energy as aerobic respiration

Still produces much more than fermentation

Obligate aerobes

Oxygen required for survival

Facultative anaerobes

Can use oxygen when available

Can survive by anaerobic respiration and/or fermentation if necessary

Obligate anaerobes

Can not survive when oxygen is present

Oxygen is extremely reactive and is poisonous for organisms who does not have protective measures

Yogurt fermentation

Must be done anaerobically

Lactobacillus bulgaricus and Streptococcus thermophilus are put into milk

Both Gram positive lactose-fermenting bacteria

Lactose fermented to lactic acid

Acidifies the product, thickening the solution

In addition, L. bulgaricus and S. thermophilus performs other other metabolic activities

All of this contributes to the taste and texture of yogurt

Acidification of yogurt (+ high incubation temperature) suppresses growth of other bacteria such as E. coli

Alcohol fermentation

Yeast (Saccharomyces cerevisiae), a unicellular eukaryote (Fungi)

Used for many food processes, including production of alcohol from various sources of starch

Type of starch contributes to the type of alcoholic beverage produced

Alcohol production begins to inhibit yeast growth after a while

Distillation is necessary to produce alcoholic beverage with a higher alcohol %

Cyanobacteria & producing glucose

Gram negative photoautotrophic bacteria

Only clade of bacteria capable of photoautotrophy

Use sunlight to produce organic molecules like glucose from CO 2

Carbon fixation

Chemical energy generated by sunlight gets stored in glucose

Filamentous bacteria

Cells in multicellular body specialize their function and depend on one another for survival

Some cells in cyanobacteria filament terminally differentiate to heterocysts: cells specialized for nitrogen fixation

Heterocysts can not survive on its own, Can not photosynthesize and depends on neighboring vegetative cells to provide glucose etc.

Heterocysts form barrier to block O2 entry, allowing nitrogen fixation inside their cell

Heterocysts provide fixed nitrogen to neighboring cells

Proteobacteria

Gram negative

Very diverse, variety of free-living and symbiotic microbes

Photoautotrophs, chemoheterotrophs, etc.

Ancestors of eukaryotic mitochondria via endosymbiosis

Cyanobacteria

Gram negative

Only bacterial photoautotroph which does oxygenic photosynthesis

Ancestors of eukaryotic chloroplasts via endosymbiosis

Gram-positive bacteria

Gram positive

Very diverse: variety of free-living and symbiotic microbes

Mainly chemoheterotroph

Staphylococcus aureus, Bacillus anthracis, Bacillus subtilis, Lactobacillus bulgaricus, etc.

Mycobacterium tuberculosis (although M. tuberculosis does not have a conventional Gram positive cell wall)

Chlamydias

'Gram negative'

Obligate parasites, survival inside host cells

No peptidoglycan cell wall