AP Biology - Classification

Hierarchy

Domain, Kingdom, Phylum, Class, Order, Family, Genus, and Species

Modern classification system is based on

Morphology, Anatomy, Cytology, Chemistry, Chromosome #, and Molecular Differences**

Three Domains of Life

Bacteria, Archaea, Eukarya

Based on their cell type, ability to make food, and the number of cells in their body.

Evidence to indicate that all eukaryotes have a common ancestor

Membrane-bound organelles, linear chromosomes, and genes that contain introns

LUCA

foundation for all life

single-celled with lipid bilayer cell membrane

genetic code based on DNA

aquatic

able to process energy from light through cell membrane

would duplicate all of cell contents before dividing

Morphology

similar structures (ex. chambers of the heart, shape of a beak, homologous structures, vestigial structures, etc.)

Covergent evolution produces...

Analogous structures

Fossil Record

Evidence for classification

Absolute Dating of Fossils

uses known half life decay rate of elements to determine age of rocks where fossils are found.

Transitional Fossils

a fossil which exhibits traits common to both ancestral and derived groups; can show how a species might adapt to survive their new conditions

Evidence for Classification: Biochemical Evidence

providence evidence of evolution in terms of modifications in various biological molecules, such as enzymes (DNA/RNA, Photosynthesis, Cellular Respiration, Cytochrome c, etc.)

Evidence for Classification: Embryological Development

provides evidence for evolution as embryo formation in widely-divergent groups of organisms tends to be conserved; structures that are absent in the adults of some groups often appear in their embryonic forms

Cladogram

shows the relations between different species

Comparing DNA Sequences

allows us to decipher relatedness

offers advantages over protein sequencing

introns in DNA are less likely to be influenced by natural selection, proteins tend to express themselves as either useful or not useful

Mitochondrial DNA (mtDNA)

there is no change in mtDNA from mother to

offspring. (mtDNA can be traced back over

generations)

random mutations will alter the sequence and allow us to trace this "genetic drift" over time.

mDNA mutates at a faster rate so the mutations are more frequent and it's easier to see divergence over time

Molecular Clock

concept that evolutionary changes may occur at a predictable rate

Phylogenetic Trees

shows evolutionary history of a group of organisms

branches of tree show patterns of divergence from common ancestor

Points to keep in mind when reading a tree

1. Evolution produces a pattern of relationship among lineages that is tree-like, not ladder-like

2. Just because we tend to read phylogenetic trees from left to right, there is no correlation with the level of "advancement"

3. For any speciation event on a phylogeny, the choice of which lineage goes to the right and which goes to the left is arbitrary

4. The points described above cause the most problems regarding human evolution.

Root

The initial ancestor common to all organisms within the diagram

Node

Each node corresponds to a hypothetical common ancestor that specified to give rise to two (or more) daughter taxa

Outgroup

The least closely related species to the rest in the diagram

Clades

A common ancestor and all of its descendants

Ingroup

includes the species you are studying

3 Phylogenetic Pitfalls to avoid

1. Branch points show patterns of descent, not phenotypic similarities

2. The sequence of branching does not indicate the actual ages of the species

3. Brances that are side by side did not give rise to one another

Problems to Drawing Phylogenetic Trees

All 24 phyla of animal life sprang onto the scene in a short period (the bottom of a tree is messy)

As data grows, even computers struggle

to sort out the phylogenetic trees.

Mutation rates are not steady from branch to branch in phylogenetic trees

Studies of bacteria genomes have revealed genes that appear to have passed from one group to another rather than descending from a common ancestor

Cladistics

Trees that use molecular evidence and shared characteristics to show relatedness

groups organisms by common descent

Clade

a group of species that includes an ancestral species and all its descendants

can be nestled in larger clades, but not all groupings of organisms qualify as clades

Monophyletic

It consists of the ancestor species and all its descendants

Paraphyletic

an ancestral species and some, but not all, of the descendants

Polyphletic

various species with different ancestors

Shared Ancestral Character

a character that originated in an ancestor of the taxon

Shared Derived Character

An evolutionary novelty unique to a particular clade

If branches are different lengths...

the length can reflect the number of genetic changes that have occurred in that lineage

Maximum Parsimony

simplest explanation is probably the right one

Obligate Intracellular Parasite

consist of a DNA or RNA core, packaged in a protein capsid

Prokaryotic Virus

Phage

10^31 known phages

Eukaryotic Viruses

More Diverse

DNA or RNA genome

Many have lipid envelopes surrounding protein capsid

viral specificty

viruses can only infect specific cells in specific organisms

Bacteriophage

a virus that infects bacteria

tail fibers attach to the host cell; the capsid contains nucleic acid

body stays on outside, injects DNA/RNA into host cell, Phage DNA directs assembly of new phages, phages lyse host cell and spread

Reverse transcription of retroviruses

an RNA containing virus converts viral RNA into double stranded DNA

Two ways viruses get into cells

virus injects only nucleic acid into host

whole virus enters cell

Virulent Phage Life Cycle (Lytic Cycle)

causes harm to the host

adsorption, entry, replication, assembly, and release

Lysogenic Cycle

Does NOT harm the host

uses a repressor protein that prevents viral replication so the host cell's normal cell cycle determines when viral replication occurs; not a full hostile takeover

Host DNA is not hydrolyzed during process

natural selection may explain the evolution

Problem with viral mutations

Each time a virus replicates there is potential for mutation.

any "typos" that occur can later the viral characteristics and may allow the virus to infect cells it previously could not or may aid the virus in avoiding detection by the immune system

non-lethal strains can become lethal

vaccines

aid in the immune response by allowing the immune system to react faster

Viroids

infectious entity affecting plants, smaller than a virus, and consisting only of short, circular RNA without a protein coat

do NOT code for proteins

Prions

infections proteins

misfolded version

no nucleic acid

don't use energy

don't die; replicate using existing proteins

highly heat resistent

affect nervous tissue of animals

Chronic Wasting Disease (CWD)

Cruetzfeldt-Jakob disease

Mad Cow Disease

Bacteria Staining

stained with two dyes, purple and pink to determine which antibiotics will work for each kind.

Gram-positive - purple dye

Gram-negative - pink dye

show what antibiotics will work

Pertinent parts of the cell

Nucleoid Region (circular genome)

Cell wall (maintains cell shape in hypotonic environments)

Cytoplasm

Cell membrane or plasma membrane

Glagella

Ribosomes

Plasmids (gene carrying, circular DNA structures that are not involved in reproduction)

Peptidoglycan

series of sugars cross lines with short polypeptides

Bacteria Motility

Flagella (a long, thin filament anchored to the plasma membrane; may be one or many anchored all over the bacteria)

Pili (shorter and thinner filaments that help bacteria stick together in clumps)

Modes of Nutrition

Photoautotrophic mode of nutrition is very ancient (according to fossil evidence)

Cyanobacteria generate oxygen as a waste product of their photosynthesis

Many early bacteria went extinct as the oxygen was created by cyanobacteria

Some anaerobic bacteria or non-oxygen using bacteria survive in areas where oxygen did not reach (descendants still alive in oxygen-free environments)

Nitrogen Metabolism

Nitrogen is essential for the production of amino acids and nucleic acids

Prokaryotes can metabolize nitrogen in a variety of ways

Nitrogen fixation

some prokaryotes convert atmospheric nitrogen to ammonia

Asexual reproduction, yet wide Genetic Variation in bateria species

mutation and genetic recombination

binary fission, conjugation, transformation, and transduction

Horizontal Gene Transfer

when bacteria exchanging genes are members of a different species

Conjugation

a "mating bridge" of cytoplasm forms between two bacterial cells, donor cell copies the DNA in its plasmid and transfers one copy to the recipient cell, cells separate

Transformation

uptake of DNA by bacteria from the external environment

ex. Griffith's experiment with mice

Transduction

bacteria exchange DNA through bacteriophage (viruses), virus replicates its genome in the 1st host and reassembles, host DNA may get mixed into the viral capsid instead of the viral genome and end up being transferred to the next host cell

ex. Avery-Chase Experiment

Antibiotics

medicines used to kill bacteria by inhibiting their growth or reproduction

Biotechnology

process of manipulating organisms or their components to make useful products

ex. fermentation (oldest form of biotech)

(Biotech also encompasses) Genetic Engineering

Direct manipulation of genes for useful and practical means

creating recombinant or transgenic organisms

ex. seeded vs. seedless, GMO, etc.

Why genetically modify livestock?

study the genetic control of physiological systems, build genetic disease models, improve animal production traits, produce new animal products

Ways that recombination occurs naturally in organisms

Prokaryote: transformation, transduction, and conjugation

Eukaryotes: crossing over, reduction to haploid cells in meiosis, random sorting during meiosis, and random fertilization of egg

Can we simply transfer DNA from a prokaryote into a eukaryote?

No. Lack of introns in prokaryotes makes it impossible to make functional mRNA in eukaryotes directly

Have to be able to synthesize DNA that is all exons to express eukaryotic gene in prokaryotes

cDNA (Complimentary DNA)

use mature mRNA to pair complementary DNA bases with RNA "message"

reverse transcriptase is used to turn the mRNA in prokaryotes into double stranded DNA that can be inserted in the eukaryotic code

cDNA refers to the double-stranded DNA that was derived from prokaryotic mRNA

Genomic library and cDNA library

Genomic library holds the DNA sequences derived from genomic DNA

cDNA library represents the DNA sequences generated from mRNA

each is categorized by their suitable vector

Developing cDNA library

1. Initial extraction and purification of mRNA

2. Production of cDNA

3. Treating the ends of cDNA

4. Ligation of the cDNA to the vector

Genetic Engineering allows us to...

isolate specific genes and work with them.

Cloning allows us to...

make multiple copies of the gene of interest

Types of Artificial Cloning

1. Transgenic Gene cloning - copying segments of DNA

2. Reproductive cloning - copying whole animals

3. Therapeutic cloning - using stem cells to replace/repair tissue

Stem cells

an unspecialized cell that can reproduce itself indefinitely and differentiate into specialized cells of one or more types

stem cells isolated from early embryos (first 5 days) at the blastocyst stage are called embryonic stem (ES) cells

Steps of Genetic Engineering

1. Identify the gene you want to transfer

2. Insert gene of interest into a vector (DNA molecule capable of replicating inside host cell)

3. Introduce vector into host

4. select transformed cells with gene of interest

Restriction Enzyme

enzyme that cuts DNA at a specific of nucleotides

cut unevenly leaving overhangs of DNA

bring in another strand of DNA cut in the same way and recombine the two strands with a new gene sequence

allows us to separate and study individual pieces of DNA

Polymerase Chain Reaction (PCR)

used to analyze short segments of DNA or RNA even in very minute quantities.

allows us to produce thousands of copies of a segment in hours

can produce many copies of specific target segments of DNA

allows us to produce enough DNA to make it functional

Three-step cycle of heating, cooling, and replication

produces an exponentially growing pool of DNA molecules

1. Denaturation

2. Annealing-med temps

3. Extension

PCR Applications

Since DNA doesn't need to be in pure form and can be mixed in with other materials, PCR has widespread uses

1. diagnose genetic diseases

2. DNA fingerprinting

3. Cloning ancient DNA

4. Find bacteria and viruses

5. Paternity or Familial links

6. Study human evolution or gene flow

Gel electrophoresis

uses electrical charge to separate nucleic acids or proteins that differ in size, charge, or other properties

From negative to positive (or from positive to negative)

smaller pieces of DNA move faster (sieve) through the gel than the larger ones

Automated Sanger Sequencing Steps

1. PCR with fluorescent, chain-terminating ddNTPs

2. Size separation by capillary gel electrophoresis

3. Laser excitation & detection by sequencing machine

Single nucleotide polymorphisms (SNPs)

DNA sequence variations that occur when a single nucleotide in the genome sequence is altered

Occur 1 in 300 nucleotides

can occur in both coding (gene) and noncoding regions of the genome

result in RFLPs (different-sized fragments of DNA)

DNA Microarray

Test to detect mutations in genes to determine how the mutation contributes to a disease

can also be used to study the extent to which certain genes are turned on or off.

Steps of DNA Microarray

1. Obtain two samples (patient DNA and control sample)

2. Fragment DNA and attach dye (green to patient, red to control)

3. Combine samples and allow them to mix

4. Analyze the color pattern for each disc to determine if mutation is present/absent or level of gene expression

Plasmid Maps

used to determine the location of restriction enzyme sites on plasmid

perform restriction enzyme digest, run gel, measure fragments

How to construct a plasmid map

1. start at 12:00, pick one of the enzymes first fragment length and place on map

2. ask "is the smaller fragment of that cut found in the second digest?" (If yes, the second enzyme digest should occur within the initial fragment of the first enzyme)

3. use trial and error to figure out the combination so that the second enzyme cuts create the fragments found within the double digest combination

4. label where each restriction enzyme made its cuts