AP Bio Summer Notes
Unit 1
Biological Macromolecules (Biomolecules)
Biomolecules: Amoeba Sisters
What make up all of life
Monomer: building blocks/what make up biomolecules
Carbohydrates/Carbs
Important, fast source of energy
Monomer: monosaccharides
Cho (Carbon, Hydrogen, Oxygen)
Lipids/Fats
Monomer: Fatty Acids & Glycerol
Ex: Butter, oil, cholesterol
Provide insulation/warmth; Source of long term energy; Make up cell membranes
Cho (Carbon, Hydrogen, Oxygen)
Proteins
Great for muscle building, ex meats & any types of beans
Monomer: amino acids
Important for working in immune system & acting as enzymes
Enzymes are made of proteins
Dna codes for protein important for structure and body function
Chon (Carbon, Hydrogen, Oxygen. Nitrogen)
Nucleic Acids
Include DNA & RNA, involved in coding of traits
Monomer: nucleotide
All types of life must have nucleic acids to direct cells activities
Chonp (Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorous)
Protein Structure
How do Genes Produce Proteins/Traits
Chromosomes made of DNA, has many genes
Gene = segment of DNA; determines structure of a protein
DNA double stranded, made up of subunits called nucleotides or bases (A, T, C, G)
DNA = code for protein (group of 3 bases = code; each code = subunit of amino acids)
4 categories/properties of Amino Acids
Positive + (charge)
Negative - (charge)
Hydrophobic (HATES water) (phobic - a fear of something (avoids))
Hydrophilic (LOVES water) (philic - a fondness for something (loves))
Positive attracted to negative Aa, & vice versa, usually on/near surface of protein
Hydrophobic repelled by water, usually on inside of protein
Hydrophilic attracted to water, usually on outside of protein
Proteins have 3d structure; Aa cause certain folds/shapes; protein’s structure related to function
Mutations can:
Change DNA sequence, can cause change in amino acids
Amino acid changes change protein structure (shape) & function
Overview of Protein Structure & Folding
Proteins made 24/7 through a process called protein synthesis
Changes/modifications are added to proteins to make them functional
Can be adding certain chemical groups, ex. Phosphorylation, or folding
Protein Shape 🤝 Protein Function
Proteins have different levels of structure with different ways of folding
1. Primary Structure
Sequence of Aa Peptide bonds hold; genes determine Aa order/number
In protein synthesis, Aa form polypeptide chains; proteins made of 1+ pcs
Aa have a carboxyl group, amino group, & R group/side chain
2. Secondary Structure
Aa sequences fold differently, Alpha Helix & Beta-pleated Sheet most common
Folds depend on Aa arrangement, shapes due to hydrogen bonds
3. Tertiary Structure
Folding occurs in 3D shape due to R groups, which vary Aa’s
3D shape due to other interactions: Ionic Bonds, Van Der Waals, Disulfide Bonds/Bridges, Hydrogen Bonds
4. Quaternary Structure
Looking at protein w/ 1+ pcs; each can be a subunit, interactions between pcs like HB or DB can keep them together
Interactions occur depending on protein’s Aa
Proteins have help - chaperonins proteins help w/ folding process
Have barrel shape, where proteins go in, have ideal environment for folding
Each protein has ideal environment, includes ideal temperature & pH range
If out of environment, it disrupts multi-level interactions
Can denature protein, disrupting shape and function
Nucleic Acid Structures
DNA vs. RNA
RNA sends genetic messages so DNA can make proteins
RNA is hypothesized as coming before DNA in the RNA World Hypothesis
Similarities
DNA & RNA are in all living cells
Eukaryote cells: DNA found in nucleus, & RNA both in & out of nucleus
Prokaryote cells DON’T have nucleus
Both
Nucleic Acids, have nucleotides made of 3 parts: Phosphate, Sugar & a base
Contrasts
DNA is double stranded, having 2 strands of nucleotides running antiparallel
RNA single stranded, having 1 nucleotide base
Sugar in DNA is Deoxyribose; sugar in RNA is ribose
DNA bases: Adenine + Thymine, Guanine + Cytosine
RNA bases: Adenine + Uracil, Guanine + Cytosine
3 types of RNA
mRNA (messenger RNA) carries messages based off DNA
Eukaryotic cells: DNA stays in nucleus, mRNA can leave & send messages to ribosomes
rRNA (ribosomal RNA) are major components of ribosomes
tRNA (transfer RNA) transfers Aa to match the correct mRNA codon
When Aa join, makes a polypeptide chain
Unit 2
Cell Organelles: Structure and Their Function
Organelles in Eukaryotic Cells
Inside Eukaryotic cells are membrane-bound organelles
Cell Ingredients/membranes
Cell membrane (outside of cell)
Nuclear membrane
surrounds DNA; Pores inside connect to endoplasmic reticulum
Endoplasmic reticulum
Layered membranes come out/surround nucleus
Ribosomes
mRNA travel from nucleus to get to ribs
Sometimes in endoplasmic reticulum, sometimes floating in cytoplasm
Called rough endoplasmic reticulum if connected
Called smooth endoplasmic reticulum if not
Golgi Bodies
Look like endoplasmic reticulum, but detached from Nuclear membrane
Good @ packaging molecules/newly-produced proteins send outside cell
Mitochondria
Have own DNA, comes maternally; where ATP’s produced
Chloroplasts (used in plants/algae for photosynthesis)
Vacuole
Tends to be big in plants, can give structure, more visible than in animals
Contains water & enzymes; viewed as a storage compartment
Contains enzymes helping digest/break things down to be used
Lysosome
Associated with animal cells, also exists in plant cells & a compartment
Contains enzymes useful for lysing/breaking down cell waste products/foreign substances
Endomembrane System
-> group of membranes/organelles in eukaryotic cells modify, package, & transport lipids & proteins
Does have: nuclear envelope, lysosomes, endoplasmic reticulum, Golgi, & plasma membrane
DOESN’T have: mitochondria, chloroplasts, or peroxisomes
The Endoplasmic Reticulum (ER) helps modify proteins & synthesize lipids
has membranous tubules & flattened sacs; discs/tubules hollow, space inside called lumen
Rough ER (name from bumpy ribosomes attached to cytoplasmic surface)
Feeds new-formed protein chains > lumen, some to ER, some anchored in membrane
Inside ER, proteins fold/modificate, incorporate to cell mem or secreted from cell
Proteins not staying in ER, packed into vesicles, shipped to Golgi
Also makes phospholipids for other cell mem, transported when vesicle forms
Smooth ER (continuous w/ rough ER, but has few/no ribosomes on cytoplasmic surface)
Synthesizes carbs, lipids, steroid hormones, detoxes meds/poison, stores calcium ions
Muscle cells have special type: sarcoplasmic reticulum, responsible storing calcium ions
Tiny smooth ER patches in rough ER, exits for vesicles leaving ER, called transitional ER
The Golgi Apparatus (made up of flattened membrane discs; sorts, tags, packs, & distributes lipids & proteins)
Receiving side: cis face; opposite side: trans face
Transport vehicles travel to cis face, fuse, empty contents into Golgi lumen
Traveling, proteins/lipids change more, sorted, then packaged in vesicles from trans face
Some sent other parts of cell or fuse with plasma membrane
Lysosomes (organelle containing digestive enzymes, like animal cell organelle-recycling facility)
Breaks down old/unnecessary structures so molecules can be reused (some vesicles from Golgi bound for)
Can also digest foreign particles brought into cell form outside
Process called phagocytosis: part of macrophage’s pm folds inward, surrounds pathogen, branches off, forms structure called phagosome -> fuses w/ lysosome, forming compartment which digestive enzymes destroy pathogens
Vacuoles (in plant cells)
central area stores water/wastes, isolates risky mat, has enzymes break down macromolecules/cellular components
function in water balance; may used store compounds (toxins/pigments (colored particles)
Lysosomes vs. Peroxisomes
Both break down molecules/remove cell hazards; show up small round blobs
Peroxisomes house oxidizing enzymes (produces hydrogen peroxide), detoxifies some substances entering the body
Peroxisomes not part of endomembrane system, don’t receive vesicles from Golgi
Cell Membrane
Structure of a Plasma Membrane (PM)
Has consistency of salad oil; defines borders of cell, allows controlled cell interaction w/ environment
Cells able to exclude, take in, excrete substances, talk w/ other cells; pm needs lipids proteins & carbs
Lipids barrier for cell; proteins cross-membrane trans., carbs so both recognize other
Fluid mosaic model
Currently accepted model for plasma membrane structure, first proposed in 1972
Pm many components: phospholipids, cholesterol, protein move free in membrane plane
Principal components: lipids (phospholipids, cholesterol), proteins, & carbohydrates
Phospholipid made of glycerol, 2 fatty acid tails, & phosphate-linked head group
Biological membranes: 2 layers w/ tails pointing inward, called phospholipid bilayer
Cholesterol made of 4 fused carbon rings; found w/ pholipid in core of membrane
Membrane proteins extend partway into pm, cross m, or attached in/outside face
Carb group outer surface of pm, attached proteins/lipids, forming glycoproteins/glycolipids
A human cell has 50% protein, 40% of lipids, & 10% carbs
Phospholipids
Made in bilayer, make up fabric; are amphipathic: have hydrophilic /hydrophobic regions
Head: Hydrophilic, has - charge w/ charged/polar group; face outward, contact watery fluid in/outside cell
Hydrophobic has long/nonpolar fatty acid tails, easily link w/ nonpolar mol. not water
Tuck away fatty acid tails into interior get away from water
Phospholipid bilayer formed by interaction; makes barrier between in/out cell
If phospholipids small tails form micelle (small single-layer sphere); if bulkier tail form liposome (hollow droplet of bilayer membrane)
Proteins
2 main categories: integral & peripheral
Integral membrane proteins integrate into membrane, one hdpb anchors core of bilayer
Some stick partway to membrane, others stretch side to side, called transmembrane proteins
May cross membrane 1, maybe have twelve membrane sections
Peripheral membrane proteins found out/in mem surfaces, attached > integral proteins/phospholipids
Don’t stick to hydrophobic core, more loosely attached
Carbohydrates/Membrane Fluidity
Carbs found outside surface bound to proteins (forming glycoproteins)/lipids (forming glycolipids)
Carbs help identify cells from each other
Structure of phospholipids’ fatty acid tails important determine fluidity & other prop.
Saturated fatty acids no double bonds, so straight tail, pack together in cold temps.
Unsaturated fatty acids 1+ double bonds, bend/kink tail, doesn’t pack together tight
Stay more fluid because less tight
Most cell mem contain mixture of phospholipids sometimes 2 straight tails, some not
Fish can change proportion of unsaturated fatty acids, making more fluid
Low temps: Cholesterol increases fluidity (keeps pplp packing tight); high temps: reduce fluidity
Cholesterol expands range of temps to maintain functional healthy fluidity
Diffusion
Amoeba Sisters Diffusion
ICH: ichthyophthirius multifiliis: something aquarium fish get
Caused by parasitic protist; contagious
Treatment option contains antiparasitic: methylene blue
Medicine move on own; process called: diffusion
Diffusion: net movement of a substance travelling down its concentration gradient
Moves from high concentration to low concentration
Doesn’t just happen in water
“Net” movement: overall movement
Molecules could move other directions nor stop moving
Molecules continuously moving, even when equilibrium is reached
Diffusion is a PASSIVE transport
An energy input NOT needed
Concentration gradient a form of potential energy
Another type of diffusion called facilitated diffusion
When molecules have net movement of high concentration -> low concentration
Can be too large/other characteristics stopping them directly traveling through selective cell membrane, have to go through protein channel
Factors affecting rate of diffusion
Distance: greater the distance, slower the diffusion
Temperature: high temperature means more molecule movement so more diffusion
Characteristics of solvent: density slows molecules down
Characteristics of substance traveling: greater mass lower diffusion rate than small mass
Characteristics of barrier: ex cell: small and/or nonpolar easy pass; large and/or Polar hard to pass
Surface area/thickness of cell also alters diffusion rates
Large sa/thin mem fast diffusion than small sa/thick membrane
Helps get things in & out of cells
Unit 3 & 4
Photosynthesis
Amoeba Sisters: Photosynthesis
Photosynthesis: Process that uses light, carbon dioxide & water to make sugar
Some types of protists & bacteria can & plants can
Amoebas and animals can’t, but use oxygen produced
Can be carried out in variety of environments
Animals & plants need glucose to make ATP through cellular respiration
Photosynthesis formula: Carbon Dioxide + Water + Light Energy = Oxygen + Sugar
Reactants on left (Carbon Dioxide, Water, Light Energy), are inputs
Products on Right (Oxygen & Sugar) are outputs
Formula needs to be balanced: 6CO2 + 6H2O ->Light = 6O2 + C6H12O6
Plants have light capturing molecules called pigments
Visible light has different wavelengths, which have different colors
Pigment used for photosynthesis: Chlorophyll
Expert @ absorbing red/blue light, but not green, so it reflects
Found in chloroplast of plant cells; 2 major reactions making up take place here
Light dependent reaction (LDR) & light independent reaction (LIR)
LIR also called “calvin cycle” or “Dark Reaction”
LDR happens in thylakoids
Thylakoids are tiny compartments in chloroplast, contains pigment, nicely stacked
In LDR, light converted through complex process via photosystems -> chemical energy (ATP & NADPH)
Water is split into electrons, protons, & oxygen (which also product)
LIR also occurs in chloroplast; needs products from LDR, so happens @ same time
DOESN’T happen in thylakoids, but stroma (fluid outside thylakoid)
CO2 must be fixed (w/ help from enzyme, CO2 changed to usable form)
ATP from LDR helps supply energy; NADPH helps reducing energy
NADPH adds high energy electrons to process
CO2, ATP, & NADPH can then be converted into Glucose
Plants are producers providing energy for consumers (animals)
Cellular Respiration
Amoeba Sisters: Cellular Respiration
Cells need energy: ATP energy (ATP = adenosine triphosphate; a nucleic acid w/ 3 phosphates)
When 3rd phosphate broken, releases a lot of energy, converted into ADP
then converted into ADP (Adenosine Diphosphate)
Eukaryote and Prokaryote cells have to make ATP, but different processes
One way: Aerobic Cellular Respiration (specifically in Eukaryotic cells)
Formula: C6H12O6 + 6O2 = 6CO2 + 6H2O + ATP energy
photosynthesis formula swapped reactant & product
Has 3 major steps (focusing on Eukaryotic cells)
Glycolysis (takes place in cytoplasm; doesn’t require oxygen)
Glucose converted into pyruvate (takes some ATP to get process started)
Krebs cycle/“Citric Acid” cycle (involved mitochondria, requires oxygen)
Pyruvate converted to Acetyl-CoA (?) then oxidized, & CO2’s produced
Then produce 2 ATP, 6 NADH, & 2 FADH2
Electron Transport Chain (still in mitochondria, requires oxygen)
Electrons transferred NADH & FADH to electron carriers, used create proton gradients
Protons used to power enzyme called ATP Synthase
Oxygen final electron acceptor (when adding 2 hydrogens, get H2O)
Makes more ATP than the other steps
Textbooks say produces 34 ATP; add to other steps = 38 ATP
If no oxygen available, cells have ability to perform process called fermentation
Importance of ATP: helps organisms live; without it organisms cannot function
Steps of Cellular Respiration
Electron carriers: NAD+ & FAD become NADH & FADH2
Electron-carrying form conversion:
NAD+ + 2e- + 2H+ -> NADH + H+
FAD + 2e- + 2H+ -> FADH2
Glycolysis
Glucose undergoes transformation, converting into 2 molecules of pyruvate
In the reaction ATP’s made & NAD+ is converted to NADH
Pyruvate oxidation
Each pyruvate goes into the mitochondrial matrix, converting into two-carbon molecule bound to Coenzyme A, aka acetyl CoA
Carbon dioxide released & NADH generated
Citric Acid cycle
Acetyl CoA made before combines w/ four-carbon molecule, goes through cycle of reaction, ultimately regenerating four-carbon starting molecule.
ATP, NADH, & FADH2 produced, & carbon dioxide released
Oxidative phosphorylation
The NADH & FADH2 deposit electrons in electron transport chain; as electrons move, energy’s released & used to pump protons out of matrix, forming gradient.
Protons flow back into matrix through an enzyme called ATP synthase, making ATP
@ end of electron transport chain, oxygen accepts electrons & takes up protons to make water
Glycolysis can take place w/o oxygen during fermentation process.
Other steps need oxygen to occur
Oxidative phosphorylation needs oxygen directly, but other 2 stages need it to occur
Mitosis
Amoeba Sisters Mitosis
A type of cell division done by most of body cells; really important for cell division
Helps you grow, great for repair of damage; done to produce body cells
NOT process that makes sperm or egg cells
Goal: make identical cells to replace potentially what was lost, want to have same DNA
Cells aren’t dividing all the time; if they are, that’s cancer
Cell daily life is a phase called interphase, where it’s growing, replicating DNA, and doing its daily cell functions
Where cells spend 90% of time, in respect to whole cell cycle, while mitosis is 10%
Nuclei: plural of nucleus
Have to duplicate chromosomes in interphase before mitosis
Tend to count chromosomes by number of centomeres (chromatids) present
1 chromosome w/ 1 chromatid duplicated -> 1 chromosome w/ 2 chromatids
Went from 46 chromatids to 92
Mitosis Stages of Division (PMAT)
Prophase
Nucleus is still there, chromosomes are visible
chromosomes are condensing, meaning they’re thick and visible
Metaphase “Middle”
Chromosome lined up in middle of cell, waiting
Nucleus has been disassembled
Anaphase “away”
Chromosomes move away to opposite sides/polls of cell (sister chromatids separated)
Chromosomes have spindles: fibers that help move them to end
Telophase
Chromosomes @ complete opposite ends
New nuclei are forming on each side surrounding chromosomes
Cytokinesis responsible for final separation into 2 cells by splitting cytoplasm
Completes after PMAT mitosis stages
Unit 5 & 6
Meiosis
Amoeba Sisters Meiosis
Meiosis vs. Mitosis
Mitosis makes identical cells, important for body growth, repairs, old cell replacement
Meiosis is process contributing to genetic variety
DOESN’T make body cells, but sperm/egg cells, or Gametes
Gamete & Chromosome Count Compared to Body Cells
Body cells have 46 chromosomes, while gametes have 23 chromosomes
When gametes come together, adds to 46; allows fertilized eggs to become human
Meiosis is what’s called reduction division (starting cell: 46 chromosomes, end cells: 23)
Interphase
Happens before mitosis & meiosis process starts
Where cells grow, replicate DNA & carry out functions
Still going to use PMAT for both Mitosis & Mitosis
Have to divide 2 for Meiosis (reduction division); do PMAT twice
Put numbers after phases indicating whether in first/second division
Meiosis 1
Prophase 1: where chromosomes condense & thicken, line up w/ homologous pairs
Process called crossing over occurs: way for hp to transfer genetic info & exchange between each other
Makes what’s called recombinant chromosomes
Metaphase 1: chromosomes in middle of cell, but in pairs
Anaphase 1: chromosomes pulled away by spindle fibers
Telephase 1: cell splits into 2
Meiosis 2
Prophase 2: Not going to have homologous pairs or crossing over
Chromosomes there, spindles forming
Metaphase 2: chromosomes line up in middle (now in single file line)
Anaphase 2: chromatids are pulled away by spindle fibers; creates 2 cells
Telephase 2: nuclei forming, and both cells split into 2 again (4 cells)
End Result of Meiosis
Makes sperm cells for males, egg cells for females
Independent assortment & crossing over allows variety
Ex: 4 sperm cells produced all different from each other
Also have 23 chromosomes, not identical from original cell/other sperm
Sometimes chromosomes don’t separate correctly
Called nondisjunction: when cell can receive too many or too few chromosomes
Can contribute to genetic disorders
Mutations
Amoeba Sisters Mutations
Mutation: change of genetic material, specifically in a nucleic acid
Anything w/ RNA or DNA can have a mutation (animals, plants, fungi, bacteria, protists, archaea, even viruses
Neutral Mutations
Many mutations neutral in effect
Ex: if leucine code (CUU) experiences “silent” mutation, mutates to (CUC), which still codes for leucine
Many mutations can be helpful/harmful, but is random, but some factors make it more likely to occur
External factors like certain chemical types or excessive radiation
Internal factors like an event causing problems w/ DNA replication in interphase
Gene Mutations
Dna makes genes, can code for protein influences traits
Mutation in DNA means a change in 1+ DNA bases, affects proteins production
Types: substitution (wrong base is matched); insertion (extra base(s) added); deletion (base is removed)
Insertions & deletions have potential danger
If you add/delete base, # of bases changed, everything read afterward could be affected, called frameshift mutation
Chromosome Mutations
Made up of DNA & proteins, have lots of genes on them
Types: duplication (extra copies of genes generated); deletion (some genetic material breaks off); Inversion (broken chromosome segment inverses, put back on chromosome); translocation (fragment of 1 chromosome breaks off & attaches to another)
Vulnerable times: cell replication & mitosis
Ex: fruit flies make sperm/egg cells have half # of chromosomes as organism
Sometimes chromosomes don’t separate completely; called nondisjunction
Causes mutations in egg/sperm cell
Possible for offspring to inherit mutation
EX: A protist, reproduces asexually, after dividing, daughter cell can inherit same mutation
EX: fruit flies pass mutations if found in genetic material of sperm/egg cell
Human Mutations
EX: in sickle cell anemia, gene codes for hemoglobin is mutated (substitution)
If you inherit 2 copies of this gene, you get disorder
If you inherit gene from one parent, you are a carrier, usually don't have disease
If a carrier, have protective factor against malaria
DNA Replication
Amoeba Sisters DNA Replication
Makes more DNA; both eukaryotic and prokaryotic do DNA replication
Where: if in Eukaryotic cell, in nucleus
When: During interphase
Key Player Enzymes
Many key players are enzymes
Helicase “the unzipping enzyme”
Can “unzip” DNA/break hydrogen bonds
DNA Polymerace “the builder”
Replicates DNA molecules to build new strand of DNA
Primase “the initializer”
DNA Polymerace doesn’t know where to start w/o primer
Primase makes primer so DNA polymerase can start working
Primer made of RNA
Ligase “the gluer”
Helps glue DNA fragments together
Initial Steps of DNA Replication
Starts at certain part called origin; eukaryotic cells have multiple, prokaryotic have one
At origin, helicase comes, unwinds DNA
Don’t want strands come back together, SSB proteins bind to DNA keep separated
Topoisomerase keeps DNA from supercoiling
Primase comes in, makes RNA primers on both strands
DNA is antiparallel, strands don’t go in same direction
DNA goes either 5’ to 3’ or 3’ to 5’
Sugar of DNA is backbone, has carbons numbered right after oxygen in counterclockwise direction
Left side of photo runs 5’ to 3’, right side runs 3’ to 5’
DNA Polymerace builds new strands
builds new strand in 5’ to 3’ direction, moves along old, template strand 3’ to 5’ direction/adds new bases to ‘3 end on new strand
One strand usually leading strand, other lagging strand
Helicase unwinds DNA too fast while putting down new bases
Fragments known as Okazaki Fragments
Primers replaced w/ DNA bases since made of RNA
Ligase has to take care of gaps between Okazaki fragments, sealing them together
After DNA replication, have 2 identical DNA molecules from 1 original
Called semi-conservative bc each copy has 1 original strand, & 1 new strand
Polymerase has proofreading abilities, rarely makes mistakes
New treatments can stop DNA replication in harmful cells including cancer & pathogenic bacteria
Transcription and Translation
Amoeba Sisters Protein Synthesis
Protein Synthesis: how DNA can lead to making of proteins
Some DNA is noncoding DNA, some DNA make up genes that aren’t activated, & DNA make up genes that code proteins
Steps of protein synthesis
Transcription
When DNA is transcribed into a message in the nucleus
Enzyme called RNA polymerase will connect complementary RNA bases to DNA
These RNA bases bonded together to form single-stranded mRNA
mRNA: a message made of RNA based on DNA, usually not ready to go, has to go through editing
mRNA can go out of nucleus (eukaryotes) to attach to ribosome (makes protein)
Translation
Ribosome is going to build protein
In cytoplasm, lots of available tRNA molecules (carry amino acids on them)
tRNA brings amino acids to make protein
mRNA directs which tRNAs come in & which amino acids transferred
tRNAs looking for complementary bases, on mRNA
When tRNA brings amino acids, reads bases by 3’s; codons
One tRNA contains a complementary anticodon, will connect w/ RNA if corresponding
tRNA leaves amino acid behind, next anticodon comes in, amino acid connects
Held together by peptide bond
Usually there’s stop codon
Unit 7 & 8
Natural Selection
Amoeba Sister Natural Selection
Natural Selection Example
Same species of frog: can breed w/ each other, can pass down DNA to offspring, have trait variety
Some variety: some are dark green/brown, some light green
Predators find lighter frogs easier than darker frogs
Darker frogs have easier time surviving & potentially more fitness if they can breed
Fitness isn’t determined by live longevity, but by how many offspring they have
Darker frogs pass down DNA to offspring so they'll have DNA from parents
Lighter frogs being selected against; over time, higher frequency of dark frogs
If longer, frogs could become darker
Evolution
Evolution (change over time) takes place since natural selection occurred
Natural selection: mechanism of evolution
Doesn’t mean recessive allele is gone completely, carried within population
If habitat/predators don’t change, dark frogs will still have more fitness
Frogs cannot will themselves to have mutations/cell changes (they’re random
Traits random, if no effect on fitness, gene will be passed down
If trait has negative effect that affect fitness, trait won’t be passed down
If trait has positive effect that affect fitness, frog may have more babies bc trait helps them survive & reproduce; more babies will have these genes
Called an adaptation
There’s variation in bacteria too; don’t will themselves to have traits
However, when taking antibiotics, environment is being altered
Bacteria w/ traits allowing survival from specific antibiotic have higher fitness, can reproduce
Bacteria w/ unhelpful traits don’t have very much fitness bc they’re dead
Bacteria can transfer genes to other bacteria, could share resistant gene w/ others
Hardy Weinberg Equilibrium
Amoeba Sisters Hardy Weinberg Equilibrium
Got its name from a physician & mathematician
States that a population’s allele/genotype frequencies are constant, unless there’s some type of evolutionary force acting upon them
This case, population = group of organisms that are same species & can breed w/ others, 7 have fertile offspring
Ex: light/dark green frogs; dark green dominant, light green recessive
There’s an allele frequency in population; 60%, frequency of 0.6 of alleles are G, 40%, frequency of 0.4 of alleles are g
Percentages add up to 100%, frequencies add up to 1
Assumptions of Hardy-Weinberg Equilibrium
No selection (no natural selection is acting upon frogs)
Neither dark/light green will have impact on reproductive fitness
No mutation (baby frogs inherit genes from parents and there are never mutations)
No migration (frogs can’t go in, frogs can’t go out)
Large population (lots of frogs; small populations vulnerable to genetic drift)
Random mating (frogs mate w/o any specific choice
ALL 5 assumptions must be kept in order for Equilibrium to happen
Generally doesn’t happen in real life, predators see lg frogs more, eaten & have less fitness
Math
H-WE gives baseline to compare evolving populations to constant ones w/o evolutionary forces acting upon them
2 equations: p + q = 1; p2 + 2pq + q2 = 1
p + q = 1
p = dominant allele frequency in the population
q = recessive allele frequency in the population
p doesn’t need to equal q
q can be larger than p; dominant alleles aren’t most common allele
p & q just have to = 1
For allele frequencies
p2 + 2pq + q2 = 1
For genotype frequencies
p2 = homozygous dominant (GG)
2pq = heterozygous (Gg)
q2 = homozygous recessive (gg)
Ex: 500 frogs, 375 dark green, rest are dark green
Determine which equation to work w/ first
Since working w/ genotypes, work w/ second equation
Figure out what value you can determine
375 frogs are dark green out of 500, meaning 125 are light green
Can’t use whole numbers since both equations = 1
Could divide 375/500, but just gives frequency, not genotype (either GG or Gg)
Recessive genotype (light green) can use bc it’s gg, can’t be anything else
125/500 = 25% or 0.25
Equation: p2 + 2pq + 0.25
Use the value from Step 2 to determine what you can calculate
If 0.25 = q2; q = 0.5 (p + 0.5 = 1)
p must equal 0.5 (0.5 + 0.5 = 1)
2nd equation now looks like: 0.25 + 2(0.5)(0.5) + 0. 25 = 1
0.25 + 0.5 + 0.25 = 1
25% of population is homozygous dominant (GG), 50% are heterozygous (Gg), 25% are homozygous recessive (gg)
Last tips for solving Hardy-Weinberg Equilibrium
Numbers may get messy! Might need calculators and rounding
Double check your work; make sure each equation = 1
Don’t make unfounded assumptions
Don’t assume too much with given info
Practice
Genetic Drift
Amoeba Sisters Genetic Drift
Change in allele frequencies due to chance
Comparing Genetic Drift to Natural Selection
Is random compared to natural selection
Organisms with traits bringing high fitness can pass them down through natural selection
In genetic drift, organisms won game of chance
Bottleneck effect (representation of Genetic Drift)
If you shake candy out, candy out not going to represent all candy frequencies
Ex: forest fire; organisms survived not better adapted, in area not directly affected
Survivors don’t represent og population alleles, new allele frequency in surviving population
Founder Effect
May have organisms that founded an island/new area
Arrived organisms start new population don’t necessarily represent og population where came from
Ex: seeds dispersed by wind end up in new area ideal for growth; seeds may not represent og population of plants
Random sample/founder effect
Population Sizes & Genetic Drift
A random event has more potential cause more change from og in smaller populations
Smaller populations more vulnerable to genetic drift; events more significant
Which type of population is more vulnerable to genetic drift?
Ecological Relationships
Amoeba Sisters Ecological Relationships
Predation (Predator & Prey)
Predators will feed on prey
Ex: antlions (predators) eat ants (prey)
If prey population increases, so will predators bc they have more food
If too many antlions (predators), ant (prey) populations will decrease, antlions pop decrease too
Populations can go up & down frequently, it cycles
Antlions being predators not only role played, prey to birds
Competition
Antlions: consumers, have to eat other things, can’t make own food
Have to compete w/ other antlions for food (ants)
Ex of competition for a biotic (living) factor
Sometimes competing w/ other species/predators of ants, ex jumping spider
Producers make own food, doesn't mean they don’t have competition
Plants competing for sun, ex of competition for abiotic (nonliving) factor
Symbiotic Relationships
Where different species live/work together
3 types of symbiotic relationships
Parasitism: where one organism benefits, while other is harmed
Ex: a dog w/ fleas & hookworms, these parasites feed on dog’s blood
Parasite: an organism getting nutrients from another organism, causing harm to host
Many parasites need a host as part of their life cycle
Mutualism: where both organisms involved benefit
Ex: acacia trees & acacia ants
Some acacia trees form hollow thorns, are homes for acacia ants
Some provide nectar as food for ants
Acacia ants protect tree from consumers/ other competition
Commensalism: one organism benefits, other neither helped nor harmed’
Ex: some species of barnacles and whales
Barnacles (filter feeders) attach to whale, access to food, whale may travel to nutrient-rich waters
Barnacles benefit, but neither hurt nor help whales
All three can impact populations of different species living together
If species is threatened by humans, can impact other species as well
Autotrophs vs. Heterotrophs
Amoeba Sisters Autotrophs vs. Heterotrophs
Heterotrophs
hetero: other, troph: nourishment
most animals are heterotrophs, consume organic matter
Doesn’t matter if they eat meat, plants or both; also called consumers
Fungi, some protists, bacteria & protists are heterotrophs too
Autotrophs
Auto: self, troph: nourishment
Plants usually autotrophs, make their own food
Make organic substances (like glucose) from inorganic substances (like CO2)
Their source of energy is light
Also called producers (produce food (glucose) through photosynthesis & inorganic substances (CO2)
Carnivorous plants also produce own food, digest insects to obtain nitrogen
Most carnivorous plants live in areas w/ low nitrogen in soil
Some protists, archaea, & bacteria are autotrophs
It’s possible for an organism to be both autotroph & heterotrophs
Euglena can go through photosynthesis like autotrophs, can also be heterotrophs & consume organic matter if light isn’t available
Carbon makes up life
Autotrophs & heterotrophs obtain carbon differently
Autotrophs generally use an inorganic source of carbon to make their food
Heterotrophs get carbon from organic sources they consume
Other terms here: photo- (light) & chemo- (chemical)
Instead of carbon sources, terms refer to organism’s energy source
Plant is example of photoautotroph, plants use light as energy source
Not all autotrophs use light as energy source
Great ex: bacteria in deep sea vents are chemoautotrophs
Chemical chemoautotrophs use depends on species
Humans & other animals are chemoheterotrophs
Organic compounds act as energy source
Photoheterotrophs consume organic matter, but light is energy source, which they require
Mode of nutrition found in a few type of prokaryotes
These organisms will do some form of cellular respiration to generate ATP
It can be food consumed (heterotrophs) or food generated (autotrophs)
Cellular respiration processes vary, may involve oxygen, no oxygen, different electron acceptors, etc
Food Webs and Energy Pyramids
Amoeba Sisters Food Webs and Energy Pyramids
Food chains start w/ producers (autotroph) eaten by a primary consumer (heterotroph), then by a secondary consumer (heterotroph), then by a tertiary consumer (heterotroph)
Ex: starts w/ plant, eaten by a grasshopper, then by a frog, then by a snake
Can arrange same food chain into an energy pyramid
Producers at base in trophic level 1, contain most energy (ex: 10,000 kilocalories)
Primary consumers in trophic level 2, store 10% energy from producers (1,000 Kcal)
Most energy lost in heat or undigested
Secondary consumers in trophic level 3, only store 10% energy from earlier level (100 Kcal)
Tertiary consumers in trophic level 4, only store 10% energy from earlier level (10 Kcal)
If you remove one organism from food chain, would screw up domino effect
Could result in overpopulation of one organism, or decrease population of others
Ecosystems don’t have one singular food chain, have multiple, also called food web
Can show many interactions between a variety of producers and consumers
Also can show biodiversity (the variety of all types of organisms living in a given area)
Size & climate of area affect biodiversity
If one population decreases, might be harmful, but biodiversity allows options for predators
Allows ecosystems to be more resilient to changes & recover
Decomposers also important to food chains
Are heterotrophs since do eat other things, even if they’re dead
Includes fungus & bacteria
If added to food web, every organism would go back to them