AS.020.151 Lecture 1: All lecture notes from Exam 1
12 Jun 2018
School
Department
Course
Chapter 1
Timeline of Life
Prokaryotes*(3.8*by*ago)- nucleic*acids,*synthesis*of*proteins,*membrane*
enclosed*proteins*and*molecules,*reproduce,*ocean
•
Photosynthesizers- led*to*more*oxygen*and*ozone*layer
•
Eukaryotes- nucleus*first*formed,*organelles*other*than*chloroplast*formed,*
single-celled
•
Multicellular*organisms- eukaryotic*cells*didn’t*separate,*groups*of*cells*
started*working*together
•
Organisms*on*land*(800*my*ago)- UV*radiation*too*intense*before*ozone*
layer*formed*from*more*photosynthetic*organisms
•
Land*plants
•
Land*animals- plants*as*food
•
Dinosaurs*
•
Mammals
•
Extinction*of*dinosaurs*(65*my*ago)
•
Scientific Method
Observations
1.
Questions
2.
Hypothesis
3.
Predictions
4.
Testing
5.
Chapter 15
Evolutionary Theory
Charles*Darwin
First*to*back*theory*of*evolution*with*scientific*observation
○
Species*change*over*time,*divergent*species*share*common*ancestor,*
mechanism*that*produces*change*is*natural*selection
○
•
Alfred*Russel*Wallace
Helped*develop*theory*of*natural*selection,*similar*to*Darwin's*theory,*
developed*around*the*same*time
○
•
Both*knew*principal*cause*of*natural*selection*is*the*environment
•
Natural Selection
Adaptation*refers*to*both*the*processes*of*evolution*and*the*characteristics*
themselves
•
Gene$pool- sum*of*all*copies*of*alleles*at*all*loci*in*a*population
•
Migration*of*individuals*between*populations*results*in*gene*flow,*which*
can*change*allele*frequencies
•
Genetic$drift- changes*in*allele*frequencies*from*one*population*to*the*next*
due*to*random*sampling;*small*sample*forms*new*population,*leading*to*
genetic*drift
•
Population$bottleneck-large*reduction*in*size*of*a*population*with*
reduction*in*genetic*variation
•
Hardy-Weinberg
Five*Assumptions*of*Hardy*Weinberg*Equilibrium
Mating*is*random
○
Population*size*is*very*large
○
No*migration*between*populations
○
No*mutation
○
Natural*selection*doesn’t*affect*alleles*under*consideration
○
•
No*population*will*meet*requirements
•
Useful*for*predicting*approximate*frequencies
•
Types of Natural Selection
Chapter 16
Phylogenetic Trees
Taxon- any*group*of*species*that*we*designate*or*name
•
Clade- a*taxon*that*has*all*of*the*descendants*of*a*common*ancestor
•
Ancestral$traits- shared*traits*inherited*from*a*common*ancestor
•
Homologous$trait- feature*shared*by*two*or*more*species*descending*from*
a*common*ancestor
•
Derived$trait- trait*that*differs*from*its*ancestral*form
•
Synapomorphies- derived*traits*shared*among*a*group*and*viewed*as*the*
evidence*of*the*common*ancestry*of*the*group
•
Homoplastic$trait- similar*traits*generated*by*convergent*evolution*and*
evolutionary*reversals*(bat*and*bird*wings)
•
Biological Classification
Binomial$nomenclature- Linnaeus*two*name*system
First*name*is*the*genus,*second*name*is*the*species
○
•
Monophyletic-one*taxon*contains*an*ancestor*and*all*descendants*of*that*
ancestor
•
Polyphyletic- group*that*doesn’t*include*its*common*ancestor
•
Paraphyletic- group*that*doesn’t*include*all*descendants*of*a*common*
ancestor
•
Chapter 17
Speciation
Caused*by*disruption*of*gene*flow,*gene*flow*required*to*maintain*a*species
•
Biological$species$concept-Ernst*Mayr,*species*are*groups*that*can*
interbreed*and*are*reproductively*isolated*from*other*groups
•
Allopatric$speciation-when*populations*are*separated*by*a*physical*
barrier*(geographic*speciation),*dominant*mode
Also*when*members*cross*barrier*to*form*new*population- founder$
effect
○
Founder*effect*group*has*incomplete*representation*of*the*gene*pool
○
•
Sympatric$speciation-does*not*require*physical*isolation
May*be*by*multiplication*of*chromosome,*resulting*polyploid*
organisms*cannot*interbreed*with*the*parent*species
○
More*common*among*plants
○
•
Reproductive Isolation
Prezygotic$barriers
Mechanical$isolation- male*and*female*cannot*physically*reproduce
○
Temporal$isolation-differences*in*breeding*seasons
○
Behavioral$isolation- different*mating*behaviors
○
Habitat$isolation-in*different*habitats,*can't*interbreed
○
Gametic$isolation- sperm*and*egg*don't*bind*into*zygote
○
•
Postzygotic$barriers
Hybrid$zygote$abnormality- zygote*can't*mature*anymore
○
Hybrid$infertility- many*hybrids*are*infertile
○
Low$hybrid$viability- may*not*get*to*sexual*maturity
○
•
Reinforcement- more*effective*prezygotic*barrier*may*evolve*if*hybrid*
offspring*survive*poorly
•
Factors Influencing Speciation Rates
Ecological*specialization*(diets)- environment*around*you*shapes*organism,*
allopatric*in*most
•
Population*bottlenecks- few*genes*expressed*more*frequently,*causes*
speciation
•
Type*of*pollination*(animal*vs*wind)- depends*on*physical*structure*of*
female*parts,*can't*be*pollinated*with*other*types*of*reproductive*plants,*
reproductive*barrier,*species*remain*separate
•
Environmental*changes- cause*natural*selection
•
Sexual*selection
•
Chapter 2: Part 1
Atoms and Molecules
Electrostatic$attraction-protons*and*electrons*experience*this*force
•
PONCHOS- 98%*of*dry*weight*of*biological*molecules
Phosphorous
○
Oxygen
○
Nitrogen
○
Carbon
○
Hydrogen
○
Sulfur
○
•
Bonding
Strongest*to*weakest:
Covalent
○
Ionic
○
Hydrogen
○
Dipole-Dipole*interactions
○
Van*der*Waals-hydrophobic
○
•
Covalent$$bond- two*atoms*share*a*pair*of*electrons
Molecules*can*interact*through*non-covalent*interactions
•
Nonpolar*vs.*Polar*Covalent*Bonds
Nonpolar-electronegativity*difference*less*than*0.5
○
Polar-electronegativity*difference*of*0.5*or*greater
○
•
Polar*molecules*are*hydrophilic
•
Nonpolar*molecules*are*hydrophobic
•
Ionic$bond- two*atoms*trade*electrons
Anion-net*negative*charge
•
Cation-net*positive*charge
•
Formal$charges- when*total*number*of*electrons*differs*from*protons
•
Ionic*interactions*typically*between*two*ions*present*in*a*solvent*(water)
•
Interactions*Between*Nonpolar$Molecules
Van*der*Waals*
•
Hydrophobic*Interactions
•
Chapter 2: Part 2
Macromolecules
Proteins,*nucleic*acids,*carbohydrates,$lipids
•
Polymers*form*through*condensation*and*break*apart*through*hydrolysis
•
Carbohydrates
Stored*energy*(starch,*glycogen),*short*term
•
Structural*molecules*(cellulose)
•
Recognition*molecules*in*membrane
•
Monomers- monosaccharides
Covalently*linked*through*glycosidic*bonds
○
Two*common:*pentoses,*hexoses
○
All*monosachharides*have*hydroxyl$groups
○
•
•
Polymers- polysaccharides
Three*main*types
Starches- polymers*of*glucose,*storage*in*plants
§
Glycogen- highly*branched*polymer*of*glucose,*energy*storage*
in*mammals
§
Cellulose- most*abundant*C*compound,*structural
§
○
•
Lipids
Composed*mainly*of*hydrocarbons
•
Nonpolar,*insoluble
•
Major*functions
Store*energy,*long*term
○
Cell*membranes*(phospholipids)*
○
Thermal*insulation
○
•
Three*Classes
Triglycerides
○
Phospholipids
○
Sterols
○
•
Triglycerides
•
Fatty*Acid^,*carboxyl*group*is*polar
Amphipathic-hydrophilic*end*and*hydrophobic*tails
§
○
Include*fats*and*oils
○
Carboxyl*and*hydroxyl*groups
○
Three*fatty*acids*(carboxyl*groups),*glycerol
○
Phospholipids
Two*fatty*acid*chains,*phosphate*group*and*glycerol
○
•
Chapter 2: Part 3 (Acids)
Acidic$molecules
Capable*of*giving*up*one*or*more*H+*ions*(protons)
AH*<->*A-+*H+
§
Usually*breaking*of*very*polar*covalent*bonds*between*H*and*
electronegative*atom
§
○
•
Basic$molecules
Capable*of*forming*covalent*bonds*with*one*or*more*H+*ions*
(protons)
B*+*H+*<->*BH
§
Due*to*presence*of*lone*pair*electrons
§
○
•
Measurements*Related*to*H+*Ions
How*many*H+*ions*in*solution?*pH
○
How*willing*is*acid*to*give*up*H+?*pKa
○
•
pH
Measures*concentration*of*H+*in*solution
○
pH=-log(concH+)
○
•
Buffers
Buffered*solutions*resist*changes*in*pH*when*small*amounts*of*H+*or*
OH- ions*are*added*or*removed
○
•
pKa
Acids*can*be*protonated or*deprotonated
○
Protonated*form*dissociates*into*H+*and*its*deprotonated*form
AH*(protonated)*<->*A-+*H+*(deprotonated)
§
○
•
Strong$acids
Completely*dissociate*in*water,*smaller*pKa
○
All*A- +*H+
○
•
Weak$acids
Partially*dissociate*in*water,*larger*pKa
○
Most*A-+*H+
○
Some*AH
○
•
Each*acidic*group*in*a*molecule*has*its*own*pKa,*inherent*value
•
pKa*is*how*particular*acid*will*behave*at*a*particular*pH
•
Comparing*pH*and*pKa
pH=pKa:*protonated*and*deprotonated*states*are*present*at*equal*
concentrations
○
pH<pKa:*protonated*state*in*excess*(AH)
pH*is*low,*acid*wants*to*balance*out*lots*of*H+*and*hang*onto*it
§
○
pH>pKa:*deprotonated*state*in*excess*(A-+*H+)
pH*is*high,*add*more*H+*into*solution*to*balance
§
○
•
Chapter 2: Part 4 (Energy)
Chemical Reactions in Organisms
Metabolism
All*chemical*reactions*occurring*in*organism
○
•
Anabolic Reactions
Link*simple*molecules*to*form*complex*ones
○
Monomers*to*polymers
○
Requires*energy
○
Endergonic
○
+deltaG*naught
○
Entropy*decrease
○
•
Catabolic Reactions
Break*down*complex*molecules
○
Polymers*to*monomers
○
Releases*energy
○
Exergonic
○
-deltaG*naught
○
Entropy*increase
○
•
Entropy
Characterize*reaction*in*terms*of…
Energy-Is*energy*released*or*required?
○
Entropy-Is*disorder*increased*or*decreased?
○
•
Factors*contributing*to*increasing$disorder (entropy)
Addition*of*heat*(increase*molecular*motion)
○
Phase*changes*(S*to*L*to*G)
○
Breaking*molecules*(polymer*to*monomers)
○
•
Spontaneous*reactions*increase*total*entropy
•
Natural*tendency*for*highly*ordered*systems*to*become*disordered
•
Catabolic*and*anabolic*reactions*linked
Energy*released*in*catabolic*drives*anabolic
○
•
Requires*energy-positive*delta*G*naught
•
Releases*energy-negative*delta*G*naught,*spontaneous
•
Reversible Reactions
Most*chemical*reactions*in*living*organisms*are*reversible
•
Which*direction*overall?*Delta*G*naught
•
Which*direction*at*moment?*Delta*G
•
Interpretation
DG =
negative
Reaction proceeds from left to right
as written until equilibrium is
reached.
DG =
positive
Reaction proceeds from right to left
as written until equilibrium is
reached.
DG =
zero
Reaction is at equilibrium, will not
proceed in either direction.
Move*towards*equilibrium-releases*energy
•
Move*away*from*equilibrium- requires*energy
•
Powerpoint*Notes
Tuesday, September 26, 2017
4:23 PM
Chapter 1
Timeline of Life
Prokaryotes*(3.8*by*ago)- nucleic*acids,*synthesis*of*proteins,*membrane*
enclosed*proteins*and*molecules,*reproduce,*ocean
•
Photosynthesizers- led*to*more*oxygen*and*ozone*layer
•
Eukaryotes- nucleus*first*formed,*organelles*other*than*chloroplast*formed,*
single-celled
•
Multicellular*organisms- eukaryotic*cells*didn’t*separate,*groups*of*cells*
started*working*together
•
Organisms*on*land*(800*my*ago)- UV*radiation*too*intense*before*ozone*
layer*formed*from*more*photosynthetic*organisms
•
Land*plants
•
Land*animals- plants*as*food
•
Dinosaurs*
•
Mammals
•
Extinction*of*dinosaurs*(65*my*ago)
•
Scientific Method
Observations1.
Questions2.
Hypothesis3.
Predictions4.
Testing5.
Chapter 15
Evolutionary Theory
Charles*Darwin
First*to*back*theory*of*evolution*with*scientific*observation
○
Species*change*over*time,*divergent*species*share*common*ancestor,*
mechanism*that*produces*change*is*natural*selection
○
•
Alfred*Russel*Wallace
Helped*develop*theory*of*natural*selection,*similar*to*Darwin's*theory,*
developed*around*the*same*time
○
•
Both*knew*principal*cause*of*natural*selection*is*the*environment
•
Natural Selection
Adaptation*refers*to*both*the*processes*of*evolution*and*the*characteristics*
themselves
•
Gene$pool- sum*of*all*copies*of*alleles*at*all*loci*in*a*population
•
Migration*of*individuals*between*populations*results*in*gene*flow,*which*
can*change*allele*frequencies
•
Genetic$drift- changes*in*allele*frequencies*from*one*population*to*the*next*
due*to*random*sampling;*small*sample*forms*new*population,*leading*to*
genetic*drift
•
Population$bottleneck-large*reduction*in*size*of*a*population*with*
reduction*in*genetic*variation
•
Hardy-Weinberg
Five*Assumptions*of*Hardy*Weinberg*Equilibrium
Mating*is*random
○
Population*size*is*very*large
○
No*migration*between*populations
○
No*mutation
○
Natural*selection*doesn’t*affect*alleles*under*consideration
○
•
No*population*will*meet*requirements
•
Useful*for*predicting*approximate*frequencies
•
Types of Natural Selection
Chapter 16
Phylogenetic Trees
Taxon- any*group*of*species*that*we*designate*or*name
•
Clade- a*taxon*that*has*all*of*the*descendants*of*a*common*ancestor
•
Ancestral$traits- shared*traits*inherited*from*a*common*ancestor
•
Homologous$trait- feature*shared*by*two*or*more*species*descending*from*
a*common*ancestor
•
Derived$trait- trait*that*differs*from*its*ancestral*form
•
Synapomorphies- derived*traits*shared*among*a*group*and*viewed*as*the*
evidence*of*the*common*ancestry*of*the*group
•
Homoplastic$trait- similar*traits*generated*by*convergent*evolution*and*
evolutionary*reversals*(bat*and*bird*wings)
•
Biological Classification
Binomial$nomenclature- Linnaeus*two*name*system
First*name*is*the*genus,*second*name*is*the*species
○
•
Monophyletic-one*taxon*contains*an*ancestor*and*all*descendants*of*that*
ancestor
•
Polyphyletic- group*that*doesn’t*include*its*common*ancestor
•
Paraphyletic- group*that*doesn’t*include*all*descendants*of*a*common*
ancestor
•
Chapter 17
Speciation
Caused*by*disruption*of*gene*flow,*gene*flow*required*to*maintain*a*species
•
Biological$species$concept-Ernst*Mayr,*species*are*groups*that*can*
interbreed*and*are*reproductively*isolated*from*other*groups
•
Allopatric$speciation-when*populations*are*separated*by*a*physical*
barrier*(geographic*speciation),*dominant*mode
Also*when*members*cross*barrier*to*form*new*population- founder$
effect
○
Founder*effect*group*has*incomplete*representation*of*the*gene*pool
○
•
Sympatric$speciation-does*not*require*physical*isolation
May*be*by*multiplication*of*chromosome,*resulting*polyploid*
organisms*cannot*interbreed*with*the*parent*species
○
More*common*among*plants
○
•
Reproductive Isolation
Prezygotic$barriers
Mechanical$isolation- male*and*female*cannot*physically*reproduce
○
Temporal$isolation-differences*in*breeding*seasons
○
Behavioral$isolation- different*mating*behaviors
○
Habitat$isolation-in*different*habitats,*can't*interbreed
○
Gametic$isolation- sperm*and*egg*don't*bind*into*zygote
○
•
Postzygotic$barriers
Hybrid$zygote$abnormality- zygote*can't*mature*anymore
○
Hybrid$infertility- many*hybrids*are*infertile
○
Low$hybrid$viability- may*not*get*to*sexual*maturity
○
•
Reinforcement- more*effective*prezygotic*barrier*may*evolve*if*hybrid*
offspring*survive*poorly
•
Factors Influencing Speciation Rates
Ecological*specialization*(diets)- environment*around*you*shapes*organism,*
allopatric*in*most
•
Population*bottlenecks- few*genes*expressed*more*frequently,*causes*
speciation
•
Type*of*pollination*(animal*vs*wind)- depends*on*physical*structure*of*
female*parts,*can't*be*pollinated*with*other*types*of*reproductive*plants,*
reproductive*barrier,*species*remain*separate
•
Environmental*changes- cause*natural*selection
•
Sexual*selection
•
Chapter 2: Part 1
Atoms and Molecules
Electrostatic$attraction-protons*and*electrons*experience*this*force
•
PONCHOS- 98%*of*dry*weight*of*biological*molecules
Phosphorous
○
Oxygen
○
Nitrogen
○
Carbon
○
Hydrogen
○
Sulfur
○
•
Bonding
Strongest*to*weakest:
Covalent
○
Ionic
○
Hydrogen
○
Dipole-Dipole*interactions
○
Van*der*Waals-hydrophobic
○
•
Covalent$$bond- two*atoms*share*a*pair*of*electrons
Molecules*can*interact*through*non-covalent*interactions
•
Nonpolar*vs.*Polar*Covalent*Bonds
Nonpolar-electronegativity*difference*less*than*0.5
○
Polar-electronegativity*difference*of*0.5*or*greater
○
•
Polar*molecules*are*hydrophilic
•
Nonpolar*molecules*are*hydrophobic
•
Ionic$bond- two*atoms*trade*electrons
Anion-net*negative*charge
•
Cation-net*positive*charge
•
Formal$charges- when*total*number*of*electrons*differs*from*protons
•
Ionic*interactions*typically*between*two*ions*present*in*a*solvent*(water)
•
Interactions*Between*Nonpolar$Molecules
Van*der*Waals*
•
Hydrophobic*Interactions
•
Chapter 2: Part 2
Macromolecules
Proteins,*nucleic*acids,*carbohydrates,$lipids
•
Polymers*form*through*condensation*and*break*apart*through*hydrolysis
•
Carbohydrates
Stored*energy*(starch,*glycogen),*short*term
•
Structural*molecules*(cellulose)
•
Recognition*molecules*in*membrane
•
Monomers- monosaccharides
Covalently*linked*through*glycosidic*bonds
○
Two*common:*pentoses,*hexoses
○
All*monosachharides*have*hydroxyl$groups
○
•
•
Polymers- polysaccharides
Three*main*types
Starches- polymers*of*glucose,*storage*in*plants
§
Glycogen- highly*branched*polymer*of*glucose,*energy*storage*
in*mammals
§
Cellulose- most*abundant*C*compound,*structural
§
○
•
Lipids
Composed*mainly*of*hydrocarbons
•
Nonpolar,*insoluble
•
Major*functions
Store*energy,*long*term
○
Cell*membranes*(phospholipids)*
○
Thermal*insulation
○
•
Three*Classes
Triglycerides
○
Phospholipids
○
Sterols
○
•
Triglycerides
•
Fatty*Acid^,*carboxyl*group*is*polar
Amphipathic-hydrophilic*end*and*hydrophobic*tails
§
○
Include*fats*and*oils
○
Carboxyl*and*hydroxyl*groups
○
Three*fatty*acids*(carboxyl*groups),*glycerol
○
Phospholipids
Two*fatty*acid*chains,*phosphate*group*and*glycerol
○
•
Chapter 2: Part 3 (Acids)
Acidic$molecules
Capable*of*giving*up*one*or*more*H+*ions*(protons)
AH*<->*A-+*H+
§
Usually*breaking*of*very*polar*covalent*bonds*between*H*and*
electronegative*atom
§
○
•
Basic$molecules
Capable*of*forming*covalent*bonds*with*one*or*more*H+*ions*
(protons)
B*+*H+*<->*BH
§
Due*to*presence*of*lone*pair*electrons
§
○
•
Measurements*Related*to*H+*Ions
How*many*H+*ions*in*solution?*pH
○
How*willing*is*acid*to*give*up*H+?*pKa
○
•
pH
Measures*concentration*of*H+*in*solution
○
pH=-log(concH+)
○
•
Buffers
Buffered*solutions*resist*changes*in*pH*when*small*amounts*of*H+*or*
OH- ions*are*added*or*removed
○
•
pKa
Acids*can*be*protonated or*deprotonated
○
Protonated*form*dissociates*into*H+*and*its*deprotonated*form
AH*(protonated)*<->*A-+*H+*(deprotonated)
§
○
•
Strong$acids
Completely*dissociate*in*water,*smaller*pKa
○
All*A- +*H+
○
•
Weak$acids
Partially*dissociate*in*water,*larger*pKa
○
Most*A-+*H+
○
Some*AH
○
•
Each*acidic*group*in*a*molecule*has*its*own*pKa,*inherent*value
•
pKa*is*how*particular*acid*will*behave*at*a*particular*pH
•
Comparing*pH*and*pKa
pH=pKa:*protonated*and*deprotonated*states*are*present*at*equal*
concentrations
○
pH<pKa:*protonated*state*in*excess*(AH)
pH*is*low,*acid*wants*to*balance*out*lots*of*H+*and*hang*onto*it
§
○
pH>pKa:*deprotonated*state*in*excess*(A-+*H+)
pH*is*high,*add*more*H+*into*solution*to*balance
§
○
•
Chapter 2: Part 4 (Energy)
Chemical Reactions in Organisms
Metabolism
All*chemical*reactions*occurring*in*organism
○
•
Anabolic Reactions
Link*simple*molecules*to*form*complex*ones
○
Monomers*to*polymers
○
Requires*energy
○
Endergonic
○
+deltaG*naught
○
Entropy*decrease
○
•
Catabolic Reactions
Break*down*complex*molecules
○
Polymers*to*monomers
○
Releases*energy
○
Exergonic
○
-deltaG*naught
○
Entropy*increase
○
•
Entropy
Characterize*reaction*in*terms*of…
Energy-Is*energy*released*or*required?
○
Entropy-Is*disorder*increased*or*decreased?
○
•
Factors*contributing*to*increasing$disorder (entropy)
Addition*of*heat*(increase*molecular*motion)
○
Phase*changes*(S*to*L*to*G)
○
Breaking*molecules*(polymer*to*monomers)
○
•
Spontaneous*reactions*increase*total*entropy
•
Natural*tendency*for*highly*ordered*systems*to*become*disordered
•
Catabolic*and*anabolic*reactions*linked
Energy*released*in*catabolic*drives*anabolic
○
•
Requires*energy-positive*delta*G*naught
•
Releases*energy-negative*delta*G*naught,*spontaneous
•
Reversible Reactions
Most*chemical*reactions*in*living*organisms*are*reversible
•
Which*direction*overall?*Delta*G*naught
•
Which*direction*at*moment?*Delta*G
•
Interpretation
DG =
negative
Reaction proceeds from left to right
as written until equilibrium is
reached.
DG =
positive
Reaction proceeds from right to left
as written until equilibrium is
reached.
DG =
zero
Reaction is at equilibrium, will not
proceed in either direction.
Move*towards*equilibrium-releases*energy
•
Move*away*from*equilibrium- requires*energy
•
Powerpoint*Notes
Tuesday, September 26, 2017
4:23 PM
Chapter 1
Timeline of Life
Prokaryotes*(3.8*by*ago)- nucleic*acids,*synthesis*of*proteins,*membrane*
enclosed*proteins*and*molecules,*reproduce,*ocean
•
Photosynthesizers- led*to*more*oxygen*and*ozone*layer
•
Eukaryotes- nucleus*first*formed,*organelles*other*than*chloroplast*formed,*
single-celled
•
Multicellular*organisms- eukaryotic*cells*didn’t*separate,*groups*of*cells*
started*working*together
•
Organisms*on*land*(800*my*ago)- UV*radiation*too*intense*before*ozone*
layer*formed*from*more*photosynthetic*organisms
•
Land*plants
•
Land*animals- plants*as*food
•
Dinosaurs*
•
Mammals
•
Extinction*of*dinosaurs*(65*my*ago)
•
Scientific Method
Observations1.
Questions2.
Hypothesis3.
Predictions4.
Testing5.
Chapter 15
Evolutionary Theory
Charles*Darwin
First*to*back*theory*of*evolution*with*scientific*observation
○
Species*change*over*time,*divergent*species*share*common*ancestor,*
mechanism*that*produces*change*is*natural*selection
○
•
Alfred*Russel*Wallace
Helped*develop*theory*of*natural*selection,*similar*to*Darwin's*theory,*
developed*around*the*same*time
○
•
Both*knew*principal*cause*of*natural*selection*is*the*environment
•
Natural Selection
Adaptation*refers*to*both*the*processes*of*evolution*and*the*characteristics*
themselves
•
Gene$pool- sum*of*all*copies*of*alleles*at*all*loci*in*a*population
•
Migration*of*individuals*between*populations*results*in*gene*flow,*which*
can*change*allele*frequencies
•
Genetic$drift- changes*in*allele*frequencies*from*one*population*to*the*next*
due*to*random*sampling;*small*sample*forms*new*population,*leading*to*
genetic*drift
•
Population$bottleneck-large*reduction*in*size*of*a*population*with*
reduction*in*genetic*variation
•
Hardy-Weinberg
Five*Assumptions*of*Hardy*Weinberg*Equilibrium
Mating*is*random
○
Population*size*is*very*large
○
No*migration*between*populations
○
No*mutation
○
Natural*selection*doesn’t*affect*alleles*under*consideration
○
•
No*population*will*meet*requirements
•
Useful*for*predicting*approximate*frequencies
•
Types of Natural Selection
Chapter 16
Phylogenetic Trees
Taxon- any*group*of*species*that*we*designate*or*name
•
Clade- a*taxon*that*has*all*of*the*descendants*of*a*common*ancestor
•
Ancestral$traits- shared*traits*inherited*from*a*common*ancestor
•
Homologous$trait- feature*shared*by*two*or*more*species*descending*from*
a*common*ancestor
•
Derived$trait- trait*that*differs*from*its*ancestral*form
•
Synapomorphies- derived*traits*shared*among*a*group*and*viewed*as*the*
evidence*of*the*common*ancestry*of*the*group
•
Homoplastic$trait- similar*traits*generated*by*convergent*evolution*and*
evolutionary*reversals*(bat*and*bird*wings)
•
Biological Classification
Binomial$nomenclature- Linnaeus*two*name*system
First*name*is*the*genus,*second*name*is*the*species
○
•
Monophyletic-one*taxon*contains*an*ancestor*and*all*descendants*of*that*
ancestor
•
Polyphyletic- group*that*doesn’t*include*its*common*ancestor
•
Paraphyletic- group*that*doesn’t*include*all*descendants*of*a*common*
ancestor
•
Chapter 17
Speciation
Caused*by*disruption*of*gene*flow,*gene*flow*required*to*maintain*a*species
•
Biological$species$concept-Ernst*Mayr,*species*are*groups*that*can*
interbreed*and*are*reproductively*isolated*from*other*groups
•
Allopatric$speciation-when*populations*are*separated*by*a*physical*
barrier*(geographic*speciation),*dominant*mode
Also*when*members*cross*barrier*to*form*new*population- founder$
effect
○
Founder*effect*group*has*incomplete*representation*of*the*gene*pool
○
•
Sympatric$speciation-does*not*require*physical*isolation
May*be*by*multiplication*of*chromosome,*resulting*polyploid*
organisms*cannot*interbreed*with*the*parent*species
○
More*common*among*plants
○
•
Reproductive Isolation
Prezygotic$barriers
Mechanical$isolation- male*and*female*cannot*physically*reproduce
○
Temporal$isolation-differences*in*breeding*seasons
○
Behavioral$isolation- different*mating*behaviors
○
Habitat$isolation-in*different*habitats,*can't*interbreed
○
Gametic$isolation- sperm*and*egg*don't*bind*into*zygote
○
•
Postzygotic$barriers
Hybrid$zygote$abnormality- zygote*can't*mature*anymore
○
Hybrid$infertility- many*hybrids*are*infertile
○
Low$hybrid$viability- may*not*get*to*sexual*maturity
○
•
Reinforcement- more*effective*prezygotic*barrier*may*evolve*if*hybrid*
offspring*survive*poorly
•
Factors Influencing Speciation Rates
Ecological*specialization*(diets)- environment*around*you*shapes*organism,*
allopatric*in*most
•
Population*bottlenecks- few*genes*expressed*more*frequently,*causes*
speciation
•
Type*of*pollination*(animal*vs*wind)- depends*on*physical*structure*of*
female*parts,*can't*be*pollinated*with*other*types*of*reproductive*plants,*
reproductive*barrier,*species*remain*separate
•
Environmental*changes- cause*natural*selection
•
Sexual*selection
•
Chapter 2: Part 1
Atoms and Molecules
Electrostatic$attraction-protons*and*electrons*experience*this*force
•
PONCHOS- 98%*of*dry*weight*of*biological*molecules
Phosphorous
○
Oxygen
○
Nitrogen
○
Carbon
○
Hydrogen
○
Sulfur
○
•
Bonding
Strongest*to*weakest:
Covalent
○
Ionic
○
Hydrogen
○
Dipole-Dipole*interactions
○
Van*der*Waals-hydrophobic
○
•
Covalent$$bond- two*atoms*share*a*pair*of*electrons
Molecules*can*interact*through*non-covalent*interactions
•
Nonpolar*vs.*Polar*Covalent*Bonds
Nonpolar-electronegativity*difference*less*than*0.5
○
Polar-electronegativity*difference*of*0.5*or*greater
○
•
Polar*molecules*are*hydrophilic
•
Nonpolar*molecules*are*hydrophobic
•
Ionic$bond- two*atoms*trade*electrons
Anion-net*negative*charge
•
Cation-net*positive*charge
•
Formal$charges- when*total*number*of*electrons*differs*from*protons
•
Ionic*interactions*typically*between*two*ions*present*in*a*solvent*(water)
•
Interactions*Between*Nonpolar$Molecules
Van*der*Waals*
•
Hydrophobic*Interactions
•
Chapter 2: Part 2
Macromolecules
Proteins,*nucleic*acids,*carbohydrates,$lipids
•
Polymers*form*through*condensation*and*break*apart*through*hydrolysis
•
Carbohydrates
Stored*energy*(starch,*glycogen),*short*term
•
Structural*molecules*(cellulose)
•
Recognition*molecules*in*membrane
•
Monomers- monosaccharides
Covalently*linked*through*glycosidic*bonds
○
Two*common:*pentoses,*hexoses
○
All*monosachharides*have*hydroxyl$groups
○
•
•
Polymers- polysaccharides
Three*main*types
Starches- polymers*of*glucose,*storage*in*plants
§
Glycogen- highly*branched*polymer*of*glucose,*energy*storage*
in*mammals
§
Cellulose- most*abundant*C*compound,*structural
§
○
•
Lipids
Composed*mainly*of*hydrocarbons
•
Nonpolar,*insoluble
•
Major*functions
Store*energy,*long*term
○
Cell*membranes*(phospholipids)*
○
Thermal*insulation
○
•
Three*Classes
Triglycerides
○
Phospholipids
○
Sterols
○
•
Triglycerides
•
Fatty*Acid^,*carboxyl*group*is*polar
Amphipathic-hydrophilic*end*and*hydrophobic*tails
§
○
Include*fats*and*oils
○
Carboxyl*and*hydroxyl*groups
○
Three*fatty*acids*(carboxyl*groups),*glycerol
○
Phospholipids
Two*fatty*acid*chains,*phosphate*group*and*glycerol
○
•
Chapter 2: Part 3 (Acids)
Acidic$molecules
Capable*of*giving*up*one*or*more*H+*ions*(protons)
AH*<->*A-+*H+
§
Usually*breaking*of*very*polar*covalent*bonds*between*H*and*
electronegative*atom
§
○
•
Basic$molecules
Capable*of*forming*covalent*bonds*with*one*or*more*H+*ions*
(protons)
B*+*H+*<->*BH
§
Due*to*presence*of*lone*pair*electrons
§
○
•
Measurements*Related*to*H+*Ions
How*many*H+*ions*in*solution?*pH
○
How*willing*is*acid*to*give*up*H+?*pKa
○
•
pH
Measures*concentration*of*H+*in*solution
○
pH=-log(concH+)
○
•
Buffers
Buffered*solutions*resist*changes*in*pH*when*small*amounts*of*H+*or*
OH- ions*are*added*or*removed
○
•
pKa
Acids*can*be*protonated or*deprotonated
○
Protonated*form*dissociates*into*H+*and*its*deprotonated*form
AH*(protonated)*<->*A-+*H+*(deprotonated)
§
○
•
Strong$acids
Completely*dissociate*in*water,*smaller*pKa
○
All*A- +*H+
○
•
Weak$acids
Partially*dissociate*in*water,*larger*pKa
○
Most*A-+*H+
○
Some*AH
○
•
Each*acidic*group*in*a*molecule*has*its*own*pKa,*inherent*value
•
pKa*is*how*particular*acid*will*behave*at*a*particular*pH
•
Comparing*pH*and*pKa
pH=pKa:*protonated*and*deprotonated*states*are*present*at*equal*
concentrations
○
pH<pKa:*protonated*state*in*excess*(AH)
pH*is*low,*acid*wants*to*balance*out*lots*of*H+*and*hang*onto*it
§
○
pH>pKa:*deprotonated*state*in*excess*(A-+*H+)
pH*is*high,*add*more*H+*into*solution*to*balance
§
○
•
Chapter 2: Part 4 (Energy)
Chemical Reactions in Organisms
Metabolism
All*chemical*reactions*occurring*in*organism
○
•
Anabolic Reactions
Link*simple*molecules*to*form*complex*ones
○
Monomers*to*polymers
○
Requires*energy
○
Endergonic
○
+deltaG*naught
○
Entropy*decrease
○
•
Catabolic Reactions
Break*down*complex*molecules
○
Polymers*to*monomers
○
Releases*energy
○
Exergonic
○
-deltaG*naught
○
Entropy*increase
○
•
Entropy
Characterize*reaction*in*terms*of…
Energy-Is*energy*released*or*required?
○
Entropy-Is*disorder*increased*or*decreased?
○
•
Factors*contributing*to*increasing$disorder (entropy)
Addition*of*heat*(increase*molecular*motion)
○
Phase*changes*(S*to*L*to*G)
○
Breaking*molecules*(polymer*to*monomers)
○
•
Spontaneous*reactions*increase*total*entropy
•
Natural*tendency*for*highly*ordered*systems*to*become*disordered
•
Catabolic*and*anabolic*reactions*linked
Energy*released*in*catabolic*drives*anabolic
○
•
Requires*energy-positive*delta*G*naught
•
Releases*energy-negative*delta*G*naught,*spontaneous
•
Reversible Reactions
Most*chemical*reactions*in*living*organisms*are*reversible
•
Which*direction*overall?*Delta*G*naught
•
Which*direction*at*moment?*Delta*G
•
Interpretation
DG =
negative
Reaction proceeds from left to right
as written until equilibrium is
reached.
DG =
positive
Reaction proceeds from right to left
as written until equilibrium is
reached.
DG =
zero
Reaction is at equilibrium, will not
proceed in either direction.
Move*towards*equilibrium-releases*energy
•
Move*away*from*equilibrium- requires*energy
•
Powerpoint*Notes
Tuesday, September 26, 2017 4:23 PM
Document Summary
Prokaryotes (3. 8 by ago)- nucleic acids, synthesis of proteins, membrane enclosed proteins and molecules, reproduce, ocean. Photosynthesizers- led to more oxygen and ozone layer. Eukaryotes- nucleus first formed, organelles other than chloroplast formed, single-celled. Multicellular organisms- eukaryotic cells didn"t separate, groups of cells started working together. Organisms on land (800 my ago)- uv radiation too intense before ozone layer formed from more photosynthetic organisms. First to back theory of evolution with scientific observation. Species change over time, divergent species share common ancestor, mechanism that produces change is natural selection. Helped develop theory of natural selection, similar to darwin"s theory, developed around the same time. Both knew principal cause of natural selection is the environment. Adaptation refers to both the processes of evolution and the characteristics themselves. Gene pool- sum of all copies of alleles at all loci in a population. Migration of individuals between populations results in gene flow, which can change allele frequencies.
