Lecture Notes up to and thru 1/26

Ch 22-24

Bio 117 notes Fri, Jan 8

Nature of Science

Hypothesis - scientific claim which is falsifiable (could be proven wrong – but isn’t necessarily wrong to start with)

Experiments don’t always support hypothesis

Empirical evidence – observations made of outside world

Null hypothesis (H0) – hypothesis that there is NO difference/relationship/pattern between one event and another / data
Like any hypothesis it’s a scientific claim that could be proven wrong
EX College students today are equally as smart as students from 1990.

Alternative hypothesis (HA) – there IS a difference/relationship/pattern between data
EX College students in 2010 are smarter than college students in 1990.
Could prove this false by looking at average ACT scores. If the average ACT score in 1990 is higher, this statement is false. We must assume the test in both years is equally as difficult.

Theory – hypothesis which has been tested by many experiments, but none of the experiments prove the theory false (no certain number of experiments that have to be performed)

Jan 10

Data Presentation and interpretation

Materials and Methods

Do NOT write like a recipe (1. Blah blah 2. Blah blah)
Write in past tense, third person – don’t identify people
What question am I answering for my reader with this graph? – use this question to determine what kind of graph to use
Graph usually better than table
Pie graph used when percentages equal 100 percent
Axis labels are important to graphs
Do not leave “series 1” on the graph

Nature of Science and Evolution (supplements text)

Falsifiability and Scientific Method
Human beings have more DNA than bacteria do – not falsifiable – too vague
Reworded: A human being has more DNA than a bacteria. – falsifiable
KU will beat NE in men’s basketball on Wednesday – scientific statement (falsifiable and empirical evidence will be gathered during/after the game)
KU has the longest history with the sport of basketball of all Big 12 schools – not a scientific statement – can look it up
KU deserves to win the Nat’l Champ this yr – can’t gather empirical evidence because of the word “deserves”

Truth Vs Science

Scientific claims are never “true;” they can’t be true
If the statement is true, then it can’t be falsified
All scientific claims are potentially false.
Some things we believe to be true, but aren’t scientific (faith)
Don’t use the word “belief” when talking about empirical evidence

Questions that science can’t answer (not subject to empirical evidence)
What is good or bad?
What should people do?

Evolution and science
Evolution is a theory, not hypothesis
Lots of experiments have been performed, but none of them have proven evolution false
Theory of evolution – common descent (things share ancestors), selection on randomly-occurring heritable variation in a population leads to diversity of organisms
Evolution – change in population over time
Hard to disprove evolution
Evolution only conflicts with religious faith if you let it - both Catholics and Methodists say evolution and biology does NOT conflict

What the theory of evolution does NOT say
Some organisms are better or worse than other organisms - can’t falsifiable because of the word “better”
Humans are more “highly evolved”
Individuals evolve
Acquired traits (chop off arm working out a lot) can be passed from one generation to the next
Whether or not our lives have purpose

Common descent
Living things share ancestors (siblings share ancestors – parents)
Support for common descent of all life
DNA (stores instructions for ALL cells) is used as molecule of heredity for all cells
Same relationship between DNA, RNA, and protein production exists for all cells (transcription and translation)
ATP is used as “energy currency” by all cells
Phospholipid bilayer is used as a cell membrane by all cells
Transcription – RNA is made from DNA template; synthesis of RNA using strand of DNA as the template; transcription begins with a strand of DNA. It is divided into several important regions. The largest of these is the transcription unit. This portion of the DNA will be used to produce RNA. Several complexes, known as transcription factors, are required for successful transcription. These complexes prepare the DNA for the successful binding of RNA polymerase. One RNA polymerase is bound, and other transcription factors complete the mature transcription complex. Now, energy must be added to the system for transcription to begin. This energy is provided by the reduction of ATP into ADP and Pi. RNA polymerase then synthesizes an RNA template from the strand of DNA. Most factors are released after transcription begins. When the end of the transcription unit is reached, the RNA polymerase dissociates, and the newly formed strand of RNA is released.
Translation – synthesis of a protein (polypeptide). Takes place on ribosomes, using the information encoded in messenger RNA; transforms the code contained in DNA and later mRNA into the proteins necessary for cellular life
ATP (adenosine triphosphaate) – an energy-storage compound containing adenine ribose, and three phosphate groups. When it’s formed from ADP, useful energy is stored; when it it’s broken down (to ADP or AMP), energy is released to drive endergonic reactions
Phospholipids – lipid containing a phosphate group; important constituents of cellular membranes
Phospholipids bilayer cell membrane - a thin membrane made of two layers of lipid molecules.; these membranes are flat sheets that form a continuous barrier around cells.
What observations would falsify the theory of common descent?
Something that’s alive, but doesn’t have phospholipid bilayer

Selection on heritable variation
Heritable variation – differences between individuals that are genetic – passed down from parent to child
Where heritable variation between individuals comes from:
Changes to DNA can happen by chance when DNA is being copied (mutation)
Those changes to DNA are then inherited by descendants

Artificial Selection
Breed animals for traits we want
Humans control what genetic traits are most prevalent in populations of domesticated animals and plants
Restricting breeding to those with most desired
Killing those with least desired traits
Phenotype vs genotype
Phenotype – set of observed/physical traits
Genotype – set of genes (DNA)
Phenotype and genotypes aren’t always the same because of recessive genes in organisms with more than 1 set of chromosomes
Selection for friendliness
Select animal for friendliness, its coat and skin color will change

Most fit organism passes genes on next generation and is surving

Natural Selection
Observation: all organisms produce more offspring than needed to maintain population if all those offspring survived
Observation: But populations of organisms, aren’t, generally, increasing exponentially
Observation: This is because huge numbers of organisms die before they can reproduce

Darwin/Wallace insight
Hypothesis: which organisms survive to reproduce and which ones die is not just a matter of chance
Organisms that are better able to compete in a given habitat will be more likely to reproduce
Competition for: limited resources, hiding places, mates
This is analogous to artificial selection

Hardy-Weinberg equilibrium
Based on organisms with dominant and recessive traits
Way of calculating how many organisms survive with no mutations and no evolution – only survived by random chance
There ARE mutations
Mutations to cells’ DNA occur every time a cell divides
Most of these mutations are neutral; some affect phenotype of organism
Mutations occur randomly, so rarely at same site in DNA in one organism
Mutations are NOT usually bad

Examples of natural selection
Antibiotic resistance (Flu is a virus – antibiotics kill bacteria)

Falsifiable – can be falsified by gathering empirical data

29 colonies on 10^8 plate
29 * 10^8 in .1 mL of original sample
10 mL of original broth
approxiamately 29 *10^10 bacteria/ original tube

Jan 18

Natural Selection Cont.

Take online quizzes to stay up to date on the material
We can take online quizzes as many times as we want
For investigation problems
Hypothesis needs to be falsifiable
Positive and negative controls
Negative control: one field with no treatment
Positive: field you know is going to be destroyed
Most of the time will have to design experiment (most important part of question)
Need to be specific (don’t use words like: some, a lot)
Can workshop answers on wiki
Will need to know what would falsify hypothesis

Kinds of Selection
Stabilizing selection
Natural selection towards a mean
Ex: More advantageous to be average than very tall or short
Figure 22.13
Why two y-axes? Two graphs on one graph
Bars represent percent of population
Most babies born between 5-8 lbs – most of them live
Testable hypothesis between mortality and birth-weight: Babies of average birth weight have stronger hearts than babies either above or below the average birth weight.
Could falsify if: all the fetal heartbeat data is the same, no matter the birth weight
Does NOT lead to speciation

Disruptive selection
Advantageous to being an extreme – really big or really small; no advantageous to being average
Can lead to speciation by creating barriers to breeding
Speciation – population has been divided into two different species (can’t breed with each other)

Genetic drift and population bottlenecks
Population bottlenecks – most likely to occur in small, isolated populations. A small, random selection of a larger population results from a bottleneck. When this random selection breeds, the genetic makeup is different than the original population.
50 % of cats on Key West are polydactyl
dominant trait, but it’s very rare in most cats (less than 5 %)
Due to founder effect – Ernest Hemingway’s cat was polydactyl. They lived in Key West. The cat founded a new population of polydactyl cats.
Evolution vs. Intelligent Design
Evolution posits common descent plus natural selection on heritable variation
Evolution predicts: traits of organisms alive today are limited by genetic traits of ancestors; Organisms evolve workable, but not perfect, solutions to problems because of natural selection
Intelligent design posits that organisms were created as they recently appear by a super-intelligent rational designer
Intelligent design predicts perfectly working features of organisms – not restricted by past

Why was the standard keyboard more fit than the Dvorak keyboard?
Dvorak keyboard jammed more often than standard because a person can type faster on Dvorak typerwriter than standard typewriter – kept old design
Why do we still use this keyboard design today?
Would have to relearn how to type
Why is keyboard design analogous to a heritable trait in an organism?
Body hair is something we still have, but don’t really need anymore
Cercadian rhythms – we’re wired to be awake and asleep at certain hours of the day

Jan 19

Evolution predicts imperfection
Sicklecell anemia – red blood cells don’t do a good job transporting oxygen throughout body because they don’t more quickly – get blocked in capillaries easily
With aggressive modern medical treatment, sickle cell anemia patients can live to be 48
No treatment, die as kid
8% of blacks carry the sickle cell allele (1 version of a gene when there are multiple versions of the gene)
We have recessive and dominant traits because we possess 2 sets of chromosomes
1 brown eye allele, 1 blue eye allele = brown eyes
2 hemoglobin alleles
Sickle cell allele– makes allele that interacts differently with cytoskeleton – changes shape of red blood cells
Sickle cell allele carries are resistant to malaria
Don’t have to be sick with sickle cell anemia – just have to be a carrier
Malaria kills about 1 million people, mainly children and pregnant woman, every year
Sickle cell is most common in Americans whose ancestors came from high malaria areas
Fitness tradeoff – malaria is worse than sickle cell anemia – better to have 1 sickle cell allele and one normal allele and be resistant to malaria than get sick with malaria
Does the persistence of sickle cell anemia alleles in blacks falsify the idea of an intelligent designer?
Scientific – good for ancestors to be resistant to malaria

Experimental design
Question: Can the eccoli become resistant to the T4 phages which kill them?
Falsifiable hypothesis: The eccoli will not become resistant to the T4 phages (null hypothesis)
Falsify by: If at least 1 eccoli becomes resistant
Eccoli will become resistant (alternative hypothesis)
How can we distinguish between acquired immunity and randomly-occurring mutations leading to 74 resistance?
Had chicken pocks once and fought them off – can’t get them again – acquired immunity
Randomly resistant – born resistant
How to distinguish: randomly occurring (would be passed onto offspring); acquired immunity (is not passed onto next generation)

Hexagon – t4 phages
Football – eccoli
T4 attach to protein at surface of bacteria – inject their dna into eccoli. Eccoli copy dna. T4 then kills eccoli. 100 percent of bacteria which are attached to die.

Make cultures – put T4 phages on entire petri dish. Then add eccoli to whole plate. Zone of inhibition will not form if the alternative hypothesis is correct.

Day 1 (Tues)
Plate of bacteria – individual colonies
If Colony of bacteria killed by t4 phages – all bacteria will likely die (bacteria are clones of one another)
Take colony off plate and expose it to to t4 phage. Rest of colony should be used to inoculate flask of sterile broth bacteria can grow in. all bacteria in broth will be descents of original bacteria. Put some bacteria/broth mix from flask into test tube with phages. If test tube bacteria die (THEY DIED), we know all bacteria couldn’t grow because of t4 phages – if bacteria from plate were killed by phages. Grab one colony off plate and put it in broth – will grow in flask because there are no viruses (phages) Inoculate flask and test tube of phages – expect nothing to grow in test tube, but lots in flask.
Shaking broth cultures allow the original phenotype of bacteria to dominate the population while in cultures that aren’t shaken new phenotypes of bacteria evolve.
Should we have shaken or static E. coli cultures?
Half shaken, half not shaken

By having a bottlenecked population and a not bottlenecked population, we can possible observe random genetic drift

Day 2 (Weds)
Subdivide flask – take small amount from flask of broth. Dilute broth. Then take little bits of diluted broth and put in numerous test tubes- could lead to new traits.
Could enoculate another flask – has same volume as all test tubes put together.

Made 1/50K dilution from flask. Put broth in test tubes – same dilution in all test tubes.

Day 3 (Thurs)
Test tube and flask should have bacteria growing in them. Hockey stick phages onto plates. Hockey stick bacteria from test tubes and flasks onto plates. Will see if any bacteria are resistant to phages. Plated bacteria onto petri dishes from tubes and flasks. (Bacteria are not exposed to phages until final step – Thurs) (Bacteria exposed to phages on Day 1 were not plated)

Day 4 (Fri 1/22)
Count t4 resistant colonies

Will t4 resistance occur in e. coli? (clas vote)
79 percent said will become resistant
21 percent said will not become resistant

Why would t4 resistance occur, if it did?
47 percent random
47 percent it will caused by exposure of e. coli
3 percent resistance will not occur, so there’s no reason
Interpret data before looking at data. That way we won’t interpret our data in favor of our original thoughts.

If null hypothesis is true (resistance occurs randomly) how should number of resistant colonies from tubes compare to those from flask? Why?
Flask is like the US
Each test tube is like a small town population of the US
All genetic diversity occurred between Tues and Fri (1/22)
E. Coli divides every 15 min (96 duplications)
Every time a cell divides, it could undergo a mutation
If resistance occurs randomly, all test tubes will be different – some might have resistant bacteria in them, while all other cells in a test tube might not be resistant. (If we see this, we will reject the alternative hypothesis)
If there’s a mutation in the flask, all the flask plates will have the same number of resistant colonies because all of the bacteria are from the same flask. (If this is true, we will reject the null hypothesis)
If alternative hypothesis is true (resistance occurs because of exposure to phages), how should number of resistant colonies from tubes compare to those from flask? Why?
If there is the same amount of resistant bacteria on each plate, then the alternative hypothesis is “true” – all exposed to same amount of phages at same time

Number of resistant bacteria (in test tubes):
Tube 5 (Shaken)
Tube 3 (Shaken)
Tube 2 (Shaken)
Tube 1 (Shaken)

Number of resistance bacteria (in flask):
Every plate was contaminated with bacteria other than E. Coli, so we couldn’t count individual colonies.

January 25, 2010

There will be lots of problem solving questions on exam. Will be some stuff from book that isn’t covered in class. Lab and lecture come together on tests and on a day-to-day basis.

Definition of “genome”
Genome – full set of genes plus noncoding regions of DNA
Genes = DNA which code for proteins
Includes DNA in genes and mitochondria and chloroplasts
Noncoding DNA = doesn’t code for protein
Multicellular organisms tend to have lots of noncoding DNA (more than 80% of human genome)
In eukaryotes, most genes are on the chromosomes, but some are in mitochondria and chloroplasts. These genes are transmitted in the egg cytoplasm in sexually reproducing organisms
Genome is complex set of integrated genes and regulatory sequences, and stretches of noncoding DNA
Positions of genes, as well as their sequences, are subject to change
Genome sequencing has contributed to our understanding of evolution

Mutations = change in DNA sequence
Mistakes in DNA replication result in mutations – these are the raw material for evolutionary change (could change proteins/amino acid chain)
Without the genetic variation provided by mutations, organisms could not evolve
Most mutations are completely neutral; they have NO effect on the phenotype of the organism
Many nucleotide substitutions have no effect on phenotype
Most amino acids are specified by more than one codon; so if amino acids change when replicated, same protein will be coded for since there are many amino acid combos
“codon” – set of 3 mRNA bases that correspond to a particular amino acid
Substitution that does not change the amino acid that is specified is a synonymous or silent substitution – doesn’t change phenotype
When copying DNA to RNA, it’s a one to one ratio so it’s hard to screw it up

DNA – instructions
Cells made out of mostly proteins, not DNA
Proteins do all of the work – they’re able to do work because of their shape and chemical makeup
Shape and chemical makeup are determined by sequences of amino acid
Work the protein does is determined by shape and chemical make up
20 different amino acids – each has different structures and chemical properties
DNA to RNA to protein
DNA copies instructions into RNA before proteins can be made
RNA has instructions on how to make proteins
Cell four course meal – DNA is like cook book; use cook book to know how to make meal; each dish has different sets of instructions; going from instructions to food is analogous to just one protein

Instructions for Ftsz : Dna that codes for proteins. Copied into RNA. Rna knows amino acid sequence for protein Ftsz.

Mutations and phenotypic change
DNA (genes) makes RNA which makes proteins (amino acid chain) – GENE EXPRESSION – DNA sequences are related to amino acid sequences
Proteins are what do the actual work of the cell because of their shape and chemical structure (if you were change to amino acid sequence, you would change the shape of the proteins)
Change in amino acid sequence can change the chemical properties and structure of a protein, and thus its function
Cells are made out of lipids, glucose, carbs , and PROTEINS – cells are mainly not made out of DNA
Evolution of nuclei acids and proteins depends on mutations
Nucleotide substitutions can result in amino acid replacements
DNA nucleotides: A (adenine), T (thymine), C (cytosine), G (guanine)
When DNA is copied, these nucleotides are copied – sometimes they’re not copied correctly – mutation
If the mutation happens in coding region which forms proteins, that may result in mutation which changes the amino acid chain
ATACCC becomes ATGCCC – nucleotide replacement
T becomes U – messenger RNA
Nucleotide substitutions are a type of mutation

E. coli versus the phages
T4 phage (virus) has to attach to certain proteins on the surface of e. coli (bacteria)
After attaching, virus can inject its DNA which the bacteria copies. Each time the bacteria clones itself, a new phage is formed.
Grew phages in cultures of bacteria
How did random DNA mutations in E. coli result in resistance to T4 phages?
What genes and gene products did it effect? (gene product = protein coded for by a particular gene)
Surface of e. coli protein’s genes mutated – easiest way for e. coli to become resistant to t4 phages is by changing surface protein
When did the mutation occur?
Happened before e. coli were exposed to t4 phages – mutation happened between last Tues and Thurs (19-21)
Test tube of phages is clear – e. coli all were killed (all susceptible on Tues)
In flask, e. coli cloned themselves over and over
Took some broth and e. coli from flask and put it into test tubes – cloned itself in test tubes = mutation occurred
How did the mutation occur?
As a result of copying itself

Eukaryotes – has a nucleus (membrane bound organelle containing chromosomes); linear chromosomes
Karyotes – nucleus
Eu – true
Prokayote – don’t have a nucleus (bacteria); single circular chromosome

Steps of bacteria cell division
1) DNA replicated – 2 chromosomes in one cell now
Single circular chromosome in each bacteria; NO NUCLEUS
Genome size between 1-10 million base pairs for entire circular chromsome (E. coli = 5 million base pairs)
Base pair – two nucleotides together (A & T, C & G)
Spontaneous mutation rate = 1 mutant base for every 10^9 bases copied
Can see colony after it’s made up of about 1 billion bacteria
2) Cell elongates – 1 chromosome goes to each end
3) FtsZ ring forms at center, between two new cells – pinches off/ separates the two cells after slightly pinching in the cell membrane
FtsZ is a homologue (genes (or proteins coded for by those genes) which are similar in function and share a history of evolution) of tubulin which is used by eukaryotic cells for same purpose
4) new cell membrane / cell wall parts built between new cells
How many spontaneous mutations occur during the cell division needed to produce a colony of 1 billion bacteria assuming colony started with one bacteria?
(5 X 10^6)(10^9)/10^9 = 5 X 10^6
given number of base pairs = 5 X 10^6
What was the rate of mutation to t4 resistance in your experiment?
Average number of t4 resistant e. coli in .1 mL/ Number of total e. coli in .1 mL

Jan 26

Comparative molecular evolution
Evolutionary changes are determined by comparing nucleotide or amino acid sequences among different organisms
The longer two sequences have been evolving separately, the more differences they accumulate
Similarities in amino acid sequences of proteins can be used to determine relatedness of organisms

Possible exam questions on molecular evolution
Interpret a set of amino acid sequences from the same protein from different organisms to draw a conclusion about relatedness among organisms
Interpret a cladogram to draw conclusions about protein similarity among organisms, or about relatedness among organisms (draw a “tree of life/phlogeny”)

Very nice! Thanks! I know I speak for many of my fellow students too when I say that!
thanks this might be handy in the future!

You're welcome. I know they need some polishing and that some of the lab info doesn't pertain to everyone, but I was trying to be nice.

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