biol midterm 4

construction of pedigrees

• m (square), f (circle)

• affected = filled

• unaffected = clear

probabilities with pedigrees

1. assign genotypes for affected and marriages with rare traits

2. assign passed on genotypes

3. calculate probabilities

incomplete dominance

mixed phenotypes for heterozygous individual

co-dominance

both phenotypes expressed in heterozygous individual

multiple alleles

more than two alleles possible for one trait

epistasis

one phenotype (gene) completely masks the other

polygenic

multiple genes affect trait

pleiotropy

one gene affects multiple traits/phenotypes

continuous traits

• decided by multiple genes

• each provide an additive component

• bell distribution

environmental effects

• provides some variability to any one genotype

• smooths out continuous trait’s curve

gradual change

• generation to generation

• random or directional

natural selection

• survival of the fittest

• selective pressures

• adapt to the environment

• random mutations

natural selection works if

• genetic diversity

• inherited traits

• more individuals are born than can survive

• favorable traits selection

natural selection evidence

• fossils show intermediates between ancestors and living

• comparative analysis show the relatedness of body structure

• related organisms have similar embryos

artificial selection

humans choose favorable traits

population

an interbreeding group of individuals

gene pool

• stock of all genes in a population

• all alleles of all genes

allele frequencies

1. sum up the frequencies of all alleles

(BB x 2) + Bb (bb x 2) + Bb

1. determine allele frequencies

total B alleles/total alleles (p) total b alleles/total alleles (q)

HWE

• p²+2pq+q²

• p² x total individuals

• 2pq x total individuals

• q² x total individuals

a population is at HWE when

• p and q do not change over time

• expected genotype frequencies match observed frequencies

• when no assumptions are broken

no selection

(HWE trait)

• all genotypes are equal

• violation leads to change in allele frequencies

no mutations

(HWE trait)

• no alleles are created or destroyed

• small or large changes to DNA for new alleles

• change allele frequencies

no migration

(HWE trait)

• no alleles enter or leave a population

• violation leads to gene flow

gene flow

movement of alleles between populations

large population size

(HWE trait)

• minimize chance effects

• violation leads to genetic drift

• can be caused by bottleneck event & founder effect

genetic drift

chance events that dramatically change allele frequencies

bottleneck event

sudden decrease of population size via catastrophe

founder effect

• small number of individuals become isolated from broader population

• bottleneck without catastrophe

random mating

(HWE trait)

• violation can lead to a certain phenotype becoming more prevalent

speciation

creation of new species

• through independently evolving

• accumulated mutations and differences prevent breeding

biological species concept

only members of a species can mate with each other

reproductive barriers

factors that prevent different species from reproducing

pre-zygotic

(reproductive barrier)

• gametes never have a chance of joining

post-zygotic

(reproductive barrier)

• gametes fuse, but offspring are less viable/fertile

habitat isolation

(pre-zygotic)

• species do not encounter

• physical barriers, ranges are too far, don’t overlap

temporal isolation

(pre-zygotic)

• species mate at different times

behavioral isolation

(pre-zygotic)

• species have different courtship rituals

• visual, auditory, chemical

mechanical isolation

(pre-zygotic)

• genitalia or pollinators are incompatible

gametic isolation

(pre-zygotic)

• mating takes place, fertilization can’t occur

chemical incapability

sperm may never reach the egg

biochemical incapability

sperm cannot fertilize the egg

reduced hybrid viability

(post-zygotic)

• offspring unhealthy and frail

• embryos not fully developed

reduced hybrid fertility

(post-zygotic)

• sterile

• chromosomes and genes incompatible

• incompatibilities in cytoplasm

biological species concept exceptions

• fossils

• asexual organisms

• some hybrids are able to form

morphological species concept

members are similar in body shape, size, and structural features

ecological species concept

members fill the same ecological niche

phylogenetic species concept

small group of individuals that share common ancestor

allopatric speciation

non-overlapping habitats

sympatric speciation

overlapping habitats

vicariance

(allopatric)

• nature splits up a habitat

dispersal

(allopatric)

• migration into a new habitat

sexual selection

(sympatric)

• mate preference in a population

habitat differentiation

(sympatric)

• same habitat but population divides into two new species

• have a specific task in the same area

polyploidy

large chromosomal rearrangements

• auto — accidental failure of mitosis

• allo — two different species mate; nature or lab

cloning

moving DNA from one location to another

steps of cloning

1. isolate gene of interest (PCR)

2. find suitable plasmid

3. insert gene w/ restriction enzymes

4. copy the plasmid

PCR

polymerase chain reaction

PCR steps

1. denature - heat to separate DNA strands

2. anneal - add primers to sequence of interest

3. elongate - extend DNA copy @ 72ºC

4. repeat 30-35 times

plasmid

• circular piece of DNA

• originally from bacteria

origin of replication

(plasmid)

• DNA replication

promoter

(plasmid)

• express our gene of interest

selectable marker

(plasmid)

• identify eukaryotic cells that have taken in a plasmid

antibiotic resistance gene

(plasmid)

• identify prokaryotic cells that have taken in a plasmid

restriction sites

(plasmid)

• insert gene of interest here

• its enzymes cut DNA

CRISPR

• delete/insert specific stretches of DNA

• gRNA guides complex to cut site

• Cas9 cuts

cancer

• mis-regulation of cell cycle

• mitosis gone wrong

• uncontrolled cell division

resisting cell death

(hallmark of cancer)

• evade apoptosis

sustained proliferative signaling

(hallmark of cancer)

• produce their own growth factors

evading growth suppressors

(hallmark of cancer)

• no longer respond to…

• grow uncontrollably

activating metastasis and invasion

(hallmark of cancer)

• lack of contact inhibition

• no anchorage-dependence

enabling replicative immortality

(hallmark of cancer)

• DNA replicates forever

inducing angiogenesis

(hallmark of cancer)

• generated their own blood vessels

mutated genes

• oncogenes and tumor suppressor

  • TS wouldn’t notice mitosis going wrong

• at least one _______ for cancer

mutated genes actions

• replicate DNA with errors

• rapid growth

• divide improperly

tumor

mass of rapidly dividing cells

virus structure

• RNA (single) or DNA (double) genome

• protein coat aka capsid

• membrane

SARS-CoV2 lifecycle

1. RECOGNITION

• spike binds to ACE2 receptor on respiratory tract cell

2. FUSION

• virus enters va endocytosis

3-6. UNPACKING

• virus contents in cell

7-9. REPLICATION

• of DNA and proteins w/ host machinery

10-12. REASSEMBLY

• w/ viral particles

13-14. RELEASE

• infect other cells and lysis

lysis

host cell is broken open

HIV lifecycle

1. recognize and enter host cell

2. virus unpacked into genome

3. reverse transcriptase converts RNA into DNA

4. integrates into the host genome

5. latency phase

6. replicate and reassemble

reverse transcription

making DNA out of RNA

reverse transcriptase

enzyme that makes DNA out of RNA

reverse transcription steps

1. RT makes DNA copy of RNA

• turns into hybrid

2. RNA template is removed by RT

• broken down

3. RT uses single DNA strand to make second copy