bio201 evolution and biodiversity mt1

morphological homology

the structural similarity in organisms due to shared ancestry that can be observed in their physical forms and features.

genetic homology

the similarity in genetic sequences or molecular structures between different species that indicates common ancestry.

convergent evolution

the process where unrelated or distantly related organisms evolve similar traits due to similar environmental pressures, resulting in analogous structures.

ribosomal RNA

an organism’s evolutionary history is documented in its genome—DNA coding for rRNA changes slowly. Comparing DNA sequences in these genes is used to investigate relationships between taxa that diverged hundreds of millions of years ago. The components of the ribosome are an excellent resource for studying the evolution of all organisms because all cellular organisms have ribosomes. The genes that encode the components of the ribosome originated in a common ancestor and may be directly compared. They are not under strong evolutionary pressure, so they change slowly. Mutations that change function may reduce fitness as ribosomes are essential for translation.

Mitochondrial RNA

an organism’s evolutionary history is documented in its genome—mtRNA evolves rapidly and is used to investigate recent evolutionary events. the mutation rate is higher in mitochondria because the mitochondrial genome is hyper-mutable compared with nuclear DNA, and this is thought to be due to damage caused by the high levels of reactive oxygen species (ROS) to which it is exposed [6,7], as well as the fact that mtDNA is replicated more frequently.

orthologous genes

genes in different species that evolved from a single ancestral gene—homology results from speciation (one species becoming two or more species)

ex: genes coding for cytochrome c in humans and dogs are orthologous

paralogous genes

homologous genes that arose via gene duplication within a genome/species—homology results from gene duplication

ex: olfactory receptor genes have undergone many duplications in vertebrates. humans have 380 and mice have 1200 functional copies of these paralogous genes.

molecular clocks help track evolutionary time

the number of nucleotide substitutions in orthologous genes is proportional to the time that has elapsed since the genes branched from their common ancestor.

for paralogous genes, the number of substitutions is proportional to the time since the ancestral gene was duplicated.

we can calibrate the molecular clock of a gene that has a reliable rate of evolution by graphing the number of genetic differences against the dates of evolutionary branch points that are known from the fossil record.

kingdoms

monera (prokaryotes), protista, plantae, fungi, animalia

domains (higher than kingdoms)

bacteria, archaea, eukarya

gene pool

all possible allele combinations present in a population of a species

a population has a gene pool; an individu

genetic equilibrium

the situation in which allele frequencies remain constant. it states that allele frequencies (genetic variation) in a population will remain constant from generation to generation if there are no factors causing those frequencies to change.

Hardy-Weinberg equilibrium

populations that are not evolving are said to be in hardy-weinberg equilibrium. at this equilibrium, allele frequencies don’t change. the sum of allele frequencies is equal to 1.

conditions required for hard-weinberg equilibrium:

• very large population

• no gene flow into or out of the population

• no mutations

• random mating

• no natural selection

departure from these conditions result in a change in allele frequencies in the population.

in reality, populations in nature never meet the conditions of hardy-weinberg equilibrium—all biological populations evolve.

the model is useful for predicting approximate genotype frequencies of a population.

specific patterns of deviation from hardy-weinberg equilibrium help identify mechanisms of microevolutionary change.

microevolution

sources of microevolutionary change:

• mutation

• migration (gene flow)

• nonrandom mating (sexual reproduction)

• natural selection

• small sample size (genetic drift)

evolution is a change in the genetic composition/allele frequencies within a population’s gene pool over successive generations.

gene flow ((sources of microevolutionary change/genetic variability))

genetic exchange due to the migration of fertile individuals or gametes between populations.

movement of individuals, and/or the genetic material they carry, from one population to another.

ex: pollen being blown to a new destination or people moving to new countries.

nonrandom mating ((sources of microevolutionary change/genetic variability))

inbreeding is a common cate of nonrandom mating.

inbreeding does not change genetic variation, but increases the allele frequency of homozygous genotypes.

inbreeding depression: inbred individuals have lower fitness than non-inbred individuals. (fitness: relative ability of a genotype to contribute to future generations)

hybrid vigor leads to higher relative fitness for hybrids by increasing heterozygous allele frequency.

assortive mating is a type of nonrandom mating where mates are selected based on phenotypes as an aspect of natural selection.

• positive assortive mating: selection for the same phenotype

• negative assortive mating: selection for the opposite phenotype (less common)—leads to decrease in homozygous genotypes

small sample size (genetic drift)

consequences of small population size: genetic drift

consider taking a small sample of individuals from a larger population. if only two individuals were picked they almost certainly won’t reflect the allele frequency in the larger population

genetic drift decreases the genetic variation within a population and increases the genetic variation between populations.

two reasons of genetic drift:

1. bottleneck effect

2. founder’s effect

bottleneck effect

the change in allele frequency in a population due to a change following a sharp reduction in the population size.

consequences: low genetic diversity and depressed reproduction.

founder’s effect

when a small portion of a population migrates/seperated to another area, starting a new population

natural selection

natural selection is the only one of the five agents of microevolution that consistently works to adapt organisms to their environment.

genetic drift is random.

mutation has a negative or no effect.

gene flow doesn’t necessarily bring in genes that are better suited for the environment.

nonrandom mating doesn’t have anything to do with matching individuals to environment.

three modes of natural selection:

1. stabilizing selection

2. disruptive selection

3. directional selection

1. stabilizing selection

intermediate forms are favored over extreme forms

2. directional selection

when natural selection moves a character towards one of its extremes

3. disruptive selection

when natural selection moves a character to both its extremes

species

(for sexual organisms) one or more populations whose members are:

• capable of interbreeding

• able to produce fertile offspring

• reproductively isolated from other such groups

asexual species: species that can reproduce asexually. in asexual species, microevolution over time directly leads to macroevolution

macroevolution—causes of speciation

• allopatric speciation (geographical isolation)

• sympatric speciation (reproductive isolation)

polyploidy

polyploidy (extra set of chromosomes) is a major factor in sympatric speciation in plants.

different mechanisms for producing polyploids:

1. autopolypoidy: multiple sets from one parent

2. hybridization + allopolyploidy: closely related species produce a hybrid that must double its chromosome number to reproduce successfully; a new, viable hybrid species is thus formed.

sympatric speciation

the basis of macroevolution in sexual species is microevolution coupled with reproductive isolation (ways of preventing gene flow between species)

reproductive isolation can occur in ways:

• pre-zygotic barriers: prevent fertilization (zygote formation) between gametes from two species

• post-zygotic barriers: reproductive isolation after fertilization has occurred.

pre-zygotic barriers (sympatric speciation)

• habitat isolation (or ecological isolation): by differences in habitat occupied at the time of mating.

• temporal isolation: by differences in timing of mating

• behavioral isolation: differences in behavior that cause reproductive isolation

• mechanical isolation: differences in physical structure make mating impossible

• gametic isolation: mating occurs, but the sperm and egg cannot fuse, bc of two mechanisms; biochemical barrier (receptor recognition between egg & sperm) and chemical incompability (sperm cannot survive in female reproductive tract)

post-zygotic isolation (sympatric speciation)

• hybrid inviability: the most common type of post-zygotic barrier. zygote formed from mating of two species does not develop normally, the embryo is aborted.

• hybrid sterility: a zygote of a hybrid proceeds through normal development but is reproductively sterile (katır)

• hybrid breakdown: a zygote of a hybrid proceeds through normal development, but F2 generation is sterile.

homologous structures

they have the same origin—different form/function.

the similarity is due to having derived from the same common ancestor.

vestigial structures

remnants of structures that were functional in ancestral species.

virus

• not an organism

• no cell structure

• no alive outside host

• can not replicate in the absence of cell

• have genetic material

they are infectious particles

structure: nucleic acid enclosed in a capsid (protein coat) and sometimes a lipid-rich envelope (derived from host cell membrane)

capsids are built from protein subunits called capsomeres.

genetic material can be DNA or RNA, linear or circular, single or double stranded.

virus classification: nucleic acid—>symmetry of capsid—>naked or enveloped—> type of nucleic acid

almost all RNA viruses carry RNA dependent RNA polymerase (RdRp enzyme), this allows replication of the viral genome in the host cell.

each type of virus can infect only a limited range of host cells called its host range.

viruses identify their host cells by a “lock-and-key” fit between proteins on the outside of the virus and specific receptor molecules on the surface of the host cell.

• viruses of eukaryotes are tissue specific.

• viruses of prokaryotes are referred to as bacteriophages

viral replication steps

1. entry:

   1. naked nucleic acid

   2. fusion of envelop with host membrane

   3. phagocytosis of the capsid

2. disassembly

   1. release of capsid

   2. release of envelope and capsid

3. synthesis

   1. RNA genome—viral RNA dependent RNA polymerase

   2. RNA genome—viral reverse transcriptase

   3. DNA genome—host DNA polymerase

4. reassembly

   1. in nucleus

   2. in cytoplasm

5. exit

   1. lysis of host cell membrane

   2. exocytosis

virus reproductive cycles

• adsorption: recognition of viral coat/envelope by host cell membrane/cell wall receptor proteins

• penetration: entry of whole virus or just virus genome into host cell

• uncoating: removal of protein coat and envelope

• synthesis: copy of viral genome and synthesis of viral proteins

• assembly: assembly of viral particles

• release: removal of viruses from the host cell

reproduction of bacteriophages

lytic cycle—culminates in the death of the host cell

• similar to general reproductive cycle of viruses

• phages that reproduce only by the lytic cycle are called virulent phages

lysogenic cycle—does not destroy the host cell

• viral DNA (prophage) is incorporated into host cell’s chromosome and replicated when the bacterium reproduces

• occasionally a prophage will exit the host chromosome and initiate the lytic cycle to produce new viruses

• phages that reproduce using both types of cycles are called temperate phages

how to combat viruses?

• immune response: via B-lymphocyte and T-lymphocyte cells

• vaccines: harmless variants or derivatives of pathogens that stimulate the immune system to mount defenses against the actual pathogen.

• drugs: most antiviral drugs interfere with viral nucleic acid synthesis

prions

prions are normal constituents of cells. they are are misfolded, infectious proteins that cause fatal neurodegenerative diseases in mammals. prions contain no genetic material (neither DNA nor RNA). Instead, they propagate purely by acting as a conformational template, binding to normal cellular proteins of the same sequence and inducing them to adopt the same aberrant, pathogenic fold.

the prion protein PrPc can undergo a conformational change to PrP-sc.

Prion diseases usually transmitted via contact with nerve tissues (brain or spinal cord)

prokaryotes

all prokaryotes were once in the kingdom monera, which is now divided into two kingdoms: eubacteria and archeabacteria

• lack a true nuclei

• lack the extensizce compartmentalization by internal membranes (organelles)

• small circular DNA

• extrachromosomal DNA = plasmids

• contain cell wall

plasmids

• most consist of a few genes

• prokaryotes mostly survive without their plasmids bc all essential functions are programmed by the chromosome

• they supply the cell with genes for resistance to antibiotics

• they replicate independently of the main chromosome

• they can be transferred between partners when prokaryotes conjugate

types of bacterial plasmids

1. fertility — (F) plasmids: conjugation

2. resistance — (R) plasmids: containing antibiotic or drug resistant gene(s)

3. col-plasmids: contain genes that code for colicins proteins that can kill other bacteria

4. degradative plasmids: enable digestion of unusual substances

5. virulence plasmids: turn the bacterium into a pathogen

glycocalyx

capsule or slime layer surrounding the outside of bacterial cell, made of polysaccharides, polypeptides or both

capsule: organized and firmly attached to the cell wall

slime layer: unorganized and loosely attached to the cell wall

functions of glycocalyx:

• antiphagocytic

• aid attachment of bacteria to different surfaces

• protect against drying when exposed to dry conditions

• trap nutrients

• help colonization with each other

flagella

• outside the cell wall

• made of filaments of flagellin protein

• attached to a protein hook

• anchored to the wall and membrane by the basal body

the motor is driven by a proton gradient

chemotaxis

in heterogeneous environment, prokaryotes are capable of movement toward or away from a stimulus = chemotaxis

• positive chemotaxis: moving toward

• negative chemotaxis: moving away

pili & fimbriae

• think proteins extended from plasma membrane

pili is in gram-negative bacteria, fimbriae is in both

• adhere bacteria to surfaces

• F-pilus (sex pilus): used in conjugation—exchange in genetic information

• flotation

cell wall

prevents the cell from bursting in a hypotonic environments.

however, prokaryotes plasmolyze (shrink away from their wall) and may die in a hypertonic medium.

contain a unique material called peptidoglycan.

peptidoglycan: a polymer of disaccharide (NAG & NAM)

gram-staining

gram-positive cell walls:

• teichoic acids:

  • lipoteichoic acid links cell wall to plasma membrane

  • wall teichoic acid links to peptidoglycan

• provide antigenic variation to aviod host defences

gram-negative outer membrane:

• lipopolysaccharides, lipoproteins, phospholipids

  • toxic

  • helps protect the pathogens against the defenses of their hosts

  • more resistant to antibiotics because outer membrane impedes entry of the drugs.

  • o-polysaccharide antigenic site (recognized by host immune system)

  • lipid A is an endotoxin

• forms the periplasm between the outer membrane and the plasma membrane

• protection from phagocytes, antibiotics

• porins (proteins) form channels throufh membrane

damage to cell walls

lysozyme (enzyme) digest disaccharide in peptidoglycan.

penicillin (antibiotic) inhibits peptide bridges in peptidoglycan

protoplast is a wall-less cell of plant, bacteria or fungi

bacterial spores

endospores: resistant cells formed by bacteria

how bacteria evade antibiotics

antibiotics attack the bacterial cell wall

some bacteria release themselves from their cell wall and these bacteria mat be attacked by the immune system by some survive and re-infect once the antibiotic has gone.

bacterial toxins

• endotoxin (ex: salmonella)

  • components of gram(-) bacterial cell wall

  • effect the host when bacteria die, and components are disintegrated

  • cause muscle pain and fever

• exotoxin (ex: cholera, botulism)

  • it is secreted out by bacteria

  • cause disease even in the absence of bacteria

  • inactivated upon sterilization

  • very small amounts can be a potent toxin

gene transfer in bacteria

• transformation: alteration of a bacterial cell’s genotype by the uptake of naked, foreing DNA from surrounding environment

• transduction: virus carry bacterial genes from one host cell to another as a result of aberrations in the viral reproductive cycle

• conjugation: direct transfer of genetic material from one bacterial cell to another