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CLEMSON / Biology / BIOL 3350 / What does retrovirus mean?

What does retrovirus mean?

What does retrovirus mean?


School: Clemson University
Department: Biology
Course: Evolutionary Biology
Professor: Michael sears
Term: Fall 2016
Tags: Evolutionary Biology
Cost: 25
Name: BIOL 3350, Week 1 & 2 Notes
Description: These notes cover the lecture material from the first two weeks of class.
Uploaded: 01/08/2016
8 Pages 152 Views 5 Unlocks

Mackenzie Gibson Sr. (Rating: )

Almost no time left on the clock and my grade on the line. Where else would I go? Kennedy has the best notes period!

Biol 3350  

What does retrovirus mean?

Chp. 1 

∙ Evolution, what is it?

o Genetic changes over time between generations

∙ Why study evolution?

o Underlies every discipline in biology

o Drug resistance

o Medical disorders – consequences of past evolution (ex: baseball  rotator cup issues because ancestors on all fours)

∙ Why is evolutionary thinking important?

o HIV: a case study

 Need evolutionary understanding to answer

∙ What is HIV?

o Retrovirus

o Spreads through contact with bodily fluids

o Different parts of planet have different levels of infection o Different people affected in different parts of the world

How do mutations give rise to new variations?

∙ How does it spread?

o Multiple different ways in different places

o Lifecycle

 Proteins on outside of virus bind to CD4 on cells

 Fuse with membrane and then empty out genetic materials  Converts RNA to DNA and integrates into host DNA

 Uses transcription and translation to make more of itself o Cell has to have certain receptors to get HIV

 Attacks T cells especially

o First contract AIDS, initial spike in replication then drops off  (acute phase)

o Chronic phase

o At some point causes immune response and then stresses out  immune system/attacks new T cells

∙ AZT We also discuss several other topics like What refers to the sum of the atomic weights of atoms in a molecule?

o Stops reverse transcriptase

What is the source of hiv?

o Cannot turn RNA into DNA (game over for retrovirus)

o Longer patient on AZT, less effective it became

 Virus not responding or body breaking it down

 Concentration to have benefit had to increase over time  (AZT basically ineffective over time)

 Longer on therapy = resistance

∙ Why does it fail?

o Reverse transcriptase makes mistakes

o Change it so it doesn’t find AZT or puts in then pulls it out o Makes virus immune to drug

∙ Mutations give rise to new variations

∙ Natural selection  

∙ Other therapies

o Lots of ways to attack antivirus Don't forget about the age old question of What are some emotional behavioral disorders?

o BUT, just pick one then few months later virus comes back o Lots of mutations in AIDS population SO

 Multi-drug treatment (cocktail)

∙ Decrease odds that virus will have enough mutations

to overcome all drugs


∙ Better chance to live longer if stick to the drugs Don't forget about the age old question of How do charophytes reproduce?

∙ Are humans evolving as a result of HIV pandemic?

o Maybe?

 Delta 32 – resistant to AIDS virus

 See least AIDS where most ppl have delta 32

 Potential to have impact but too early to tell

∙ Where did HIV come from?

o Every virus traced back to original ancestor (phylogeny) o Create family tree If you want to learn more check out Why is psychology more than just common sense?

o HIV similar to SIV – trace back to original organisms

∙ Why are untreated HIV infections usually fatal?

o Have to have enough copies in blood to pass it along

o High replication makes it lethal but transmits well

Chp. 2 – The pattern of evolution We also discuss several other topics like When did industrialization start in france?

∙ Two opposing views

o Special creation

 Species are immutable and variation among individuals is  limited

 All species created separately and genealogically unrelated to each other

 Young Earth (6000 yrs)

o Evolution

 Diversity due to descent with modification

 All life forms related

 Old Earth

∙ Microevolutionary change – variation across generations o Ex: beak sizes in Darwin’s finches

∙ Macroevolutionary change – variation across generations leads to  speciation over time

∙ Evidence to see which one is more supported We also discuss several other topics like What do connective tissues cover?

∙ Evidence of microevolution

o Voluntary wheel running behavior of mice

 Evolve to have higher activity

o Examples of selective breeding

 Dogs – lots of variation

 Cattle – humans have created variation

 Corn

 Wild mustard

o Flowering time shows genetic differences

o Vestigial structures

 Kiwi wing – evolve flightlessness

 Snake – limbs, has genes to grow legs still

 Human pelvis (coccyx) – evidence of tail in ancestors  Goosebumps – remnant of thermoregulatory past when  had more hair

 In genome…

∙ Pseudogenes – genes we have that are inactive but  

active in other species

o Evolution in real time

 Stickleback – freshwater vs marine

∙ Why microevolution matters

o Need policies

o Pests/Invasives – develop resistance

o Conservation – conserving species, need to know about genetics  ∙ Evidence of Speciation

o What is a species?

 Hard to define

o Biological species concept – Ernst Mayr

 Species are populations or groups of populations in which  individuals are interbreeding or have potential to  

interbreed and produce fertile offspring

o Phage 6 – virus that infects pseudomonas bacteria

 Strain that can infect other bacteria

 Two strains no longer exchanging genetic info – two lines  that are considered different species

o Fruit flies

 Lived on different substrates

 When put together, flies tend to breed with those that eat  the same thing as they do

 Producing reproductive isolation

o Stickleback

 Body size differences (genetically based) depending on  location  

 Gill raker sizes depending on what they’re eating

o Ring species

 Spread north = more complex songs

 Meet and cannot interbreed in one part of the ring

∙ Why speciation matters

o Human disease  

o Zoonotics – flu jumps from animals to humans

o Conservation – what different things are

∙ Evidence of Macroevolution

o Fossils exist and most don’t look like things that are alive today o Can predict where in time you should find certain fossils o Things in fossil records resemble things alive today (in same area

things resemble each other and not found in distant places) o Transitional forms

 Blenny – terrestrial fish

∙ Has intermediate forms

∙ Common ancestor

 Dinosaurs and birds

∙ Archaeoptreryx transitional form from dinosaur to  


∙ Link between early dinosaurs and birds and finding  


 Turtles

∙ Early stages of life look like evolutionary past

∙ Why macroevolution matters

o Evolutionary medicine – look at past to understand disorders now ∙ Evidence of common ancestry: all life-forms are related o Homology – similarities (despite different functions) between  different species – inherited from common ancestor

o Homoplasy – due to convergent evolution but NOT common  ancestry

o Structural homology

 Bones

 Orchids

∙ Why is homology important?

o Helps construct evolutionary tree (phylogeny)

 Use parsimony

 Represents descent with modification

o Helps to make predictions in evolutionary systems

 Longer the line = older lineage/older trait

 Norrell and Novacek

∙ 18/19 cases highly correlated

∙ Molecular homologies

o Repeats lead to misalignment in crossing over  

o Can end up with diseased genotypes

o Nearest ancestors have same mutations and same problems but  go further back and ancestors don’t share same defects o Processed pseudogenes – nonfunctional in DNA

 Cuts out intron and inserted at another locus after reverse  transcription

 Accumulate mutations

 Older = further back in lineage

 More recent = found in less species

o Genetic code itself is a universal molecular homology

 Works the same across almost all organisms

 Suggests common origin

∙ Why common ancestry matters

o Kriston McGary

 Mutations lead to some phenotype

∙ The age of the earth

o Geological time scale

o Uniformitarianism – idea that processes we observed now  occurred at same rate in past as they do now

 Earth must be really old

o Use radiometric dating to date age of earth

 Radioactive isotopes break down at certain rate

 Use rate to age things

 Decomposition rates aren’t sensitive to climate, temp.

∙ Why does age of earth matter?

o Earth has to be as old/older than oldest forms of life known ∙ KNOW

o 5 characteristics that distinguish evolution from special creation

Chp. 3 

∙ Evolution by natural selection

o Mice on beaches  

 Mismatch background then attacked more by predators  Could lead to evolution by shift in allelic frequencies

∙ Artificial Selection: Domestic Animals and Plants

o We are giving plant/animal high reproductive fitness

o Tomatoes

 Wild tomato has genes that limit its growth (fw2.2)

o In nature, could be selecting against variants

∙ Evolution by natural selection

o KNOW 4 postulates

 Necessary for evolution to occur by natural selection

o 1. Individuals in a population differ from one another

o 2. The differences are heritable

o 3. Some individuals are more successful at surviving and  reproducing than others

o 4. Successful individuals succeed because the variant traits they  have inherited and will pass to their offspring

∙ The Logic of the Theory of Natural Selection

o Five Facts

 1. Populations would increase exponentially

 2. Populations normally remain fairly stable

 3. Resources are limited so struggle amongst members of  population  

 4. Populations display variation

 5. Variation is heritable

∙ Darwin’s theory of evolution by natural selection

o Mice population (different colors)

 Variation is inherited

 More individuals are born than can be sustained by  


 Some variants survive and reproduce better than others  Survivors contain less dark alleles – population mean has  moved to lighter colored mice

∙ Important points

o Natural selection is a process that results in descent with  modification, or evolution

o Selection acts on individuals

o Populations evolve

o Evolution is a statistical phenomenon

o Natural selection has no intent, unlike artificial selection  Which works best in environment

∙ What is fitness?

o Individuals that survive had higher fitness

o Good fit in environment then survive well

o Not most physically fit organisms

∙ Evolution of Flower Color in an Experimental Snapdragon Population o Exhibit Darwin’s 4 postulates

o Evolved means allele frequency has changed, not necessarily  genes

o White flowers visited more than yellow

o Has evolution occurred?

 Frequency of white 2% higher

 Small gradual change

∙ Evolution of beak shape in Galápagos finches

o How do you get speciation from some founding population  Common ancestor

o Medium ground finch studied on Daphne Major

o Is the trait (beak depth) variable?

 Yes, variation in population in nature

o Is the variation heritable?

 Heritability – resemblance between parents and offspring  due to genetics

 Small parents = small beaked offspring

 Large parents = large beaked offspring

 BMP4 gene may drive differences in beak size

o Do individuals vary in success at surviving and reproducing? And  is this nonrandom?

 Crash in population with drought

 After drought, average size a little larger (bigger beak =  more access to food = better survival)

o Did the population evolve?

 Offspring have increased in beak size

 Evolution cannot predict future

 No ideal phenotype

∙ Natural selection acts on individuals but its consequences occur in  population

o Individual itself has not changed

o Evolution does not always proceed as quickly as possible to  produce best adapted organism

∙ Natural selection acts on phenotypes but evolution consists of changes in allele frequencies

o If beak size not heritable – offspring will be all different  phenotypes

o If beak size is heritable – offspring will look more like parents ∙ Selection isn’t forward looking

o Does not have access to future

o Evolution only uses info from past to produce future phenotype o Makes things good enough to get genes to next generation and  survive

∙ Can new traits evolve?

o Corn continued to evolve to more oil content

 Epistatic interactions can produce increases

 Could be accumulating mutations

o Carnivorous plants

∙ Natural selection does not lead to perfection

o Depending on environment, tradeoffs occur

o Preferred trait could be preyed on more

o Evolution often lagging behind

∙ Natural selection is nonrandom but not progressive

o Changing target every year

o Traits can only evolve to extent environment selects for it o Never use terms higher or lower life forms  

∙ Fitness is not circular

o Fit after environment set it up not fit to begin with

∙ Selection acts for good of individual, not good of species o Higher fitness – more genes represented in future generations o Male lions in new pride kills the babies (not good for species but  gets rid of others’ genes)

o Viruses try to make it to next generation

∙ Evolution of Evolutionary Bio

o “Nothing in biology makes sense except in the light of evolution” ∙ Three serious problems with the evolutionary theory

o Variation

 Didn’t know about genes

o Inheritance

 Mendel’s work explained mutation rates and how variation  is maintained

 Ways for traits to be inherited

 Skin color

∙ Blending inheritance

∙ Mutation could take off  

o Time

 Given rates of evolution, did not seem like earth had been  around long enough for variation we have

 No idea how old the world was

∙ The modern synthesis

o Fisher and Wright

o Can change postulates to include modern knowledge

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