Sunday, December 15, 2013

12/13 Mitosis and Meiosis

Mitosis
1. Interphase: Period of cell growth
2. Prophase: Nucleus disappears
3. Metaphase: Chromosomes line up in the middle
4. Anaphase: They separate to opposite sides
5. Telophase: Separate into two nuclei
Cytokinesis: Two actual cells

Meiosis (two big steps)
Meiosis I
Prophase I
Metaphase I
Anaphase I
Meiosis II
Prophase II
Metaphase II
Anaphase II

Meiosis:
G1- The cell begins at 2n (1 mom, 1 dad) 8
S- DNA Replication 4n 16
G2- 4n 16


Reading Assessment: Chapter 6 Your Inner Fish

What the reader learned in the first couple pages was every animal goes through the same stages of development as embryos. Every animal originated through one of the three layers of tissues called germ layers. During fertilization, a sperm and egg fuse together and the egg divides and forms a ball. For humans, the cell body divides four times (16 cells). The cell ball is called a blastocyst. The blastocyst implants itself in the moms uterus halfway and the baby's body forms from the top part of the blastocyst. When the cells divide, the baby becomes a "tube". It is called a "tube within a tube structure". The outer layer of the tube is the ectoderm (skin and nervous system), the middle later is the mesoderm (forms tissue in between guts and skin) and the inner layer is the endoderm (inner structure of the body, digestive tract and glands). 


Hans Spemann, an embryologist found that some cells can form a whole new individual on its own. He used newt eggs and pinched one side of an egg from its other side and the embryo formed twins. Hilde Mangold transplanted a tissue from one embryo to another embryo specie. She put the patch where the three germ layers are. She discovered a small patch of tissue, called an organizer, that was able to tell other cells what to do. All mammals, birds, amphibians and fish have organizers and it is possible to swap one species organizer for another. 

Flies have crazy mutations because they have an error in their DNA. Genes are stretches of DNA that are on the chromosome. 8 genes called hox genes are responsible for the development. Versions of the hox genes appear in every animal with a body. Many genes interact in the organizer to organize the body plan. 


12/11 Project and Microscopes

Today we worked on our Unit 5 Project (Tour through the cell on prezi)
We also learned how to use the microscopes. Here is a picture of a plant cell

12/9 Unit 4 Test

we had a test on genetics for unit 4
swaggie

Tuesday, December 3, 2013

12/2 Special Genetics

Today in class we covered codominance, incomplete dominance, and sex-linked problems. 

Codominance: both traits show. both dominant. 


Incomplete dominance: 1:2:1 ratio 

(P) red x white 
they make pink (F1)
F1 x F1
create white, pink, pink, red

Epistasis- product of genes make phenotype


Puppies! 

eebb and eeB_ = yellow
E_bb= chocolate
E_B_= black

BBEE x bbEE

F1= BbEe
F1 x F1

B_E_ black

bb_ _ choc. 
_ _ ee yellow 



Blood 

A and B are dominant over O
A and B completely dominate over each other 
AA and AO = A
BB and BO= B
AB=AB
OO= O

A man with a type A blood marries a woman with type A blood. They have the first child as blood type O. 


Genotypes

Father: AO
Mother: AO
Baby: OO

Friday, November 22, 2013

11/21 Genetics: Dihybrid Crosses

Dihybrid crossing is when you cross two different traits. In this example, we crossed two butterflies. Each butterfly's genotype was AaBb.

A=black body          B=spots
a=white body           b=no spots

Wednesday, November 20, 2013

11/18 Genetics: Monohybrid Crosses

Genes
1. DNA
goes through transcription- RNA polymerase 
2. mRNA- processing... introns out/cap and tail
goes through translation- ribosome (5-3)/tRNA bus system
3. Amino Acid
4. Polypeptides- proteins make traits 

Physical and biochemical (inside of you)
Example. lactase- enzyme
break down lactase

Lactose intolerant -no lactase
gene malfunction: mutation, point base, deletion, insertion (jumping genes)

Traits "Alleles"
Dominant- always shows (A_)
Recessive- (Aa)

2 types of cells 
Somatic- body cells
Mitosis: cell division 23 pairs(1/2 mom 1/2 dad) creating identical daughter cells (DNA replication)
Gametic- sex cells (gender)
Meioses

Mendel
pea plants 
traits- smooth or wrinkle 
color: green/yellow
shape
height: tall/dwarf
flower color 

Ratios
-math data 
"trends" something being passed
-didn't know DNA

Vocab 
homozygous- same AA(p2) aa (q2)
heterozygous- different Aa (2pq)
dominant- A_
recessive- aa
phenotype- physical traits
genotype- genes Aa (letters)
F1- first offspring/generation
     carrier or hybrid- heterozygous
     pure- homozygous
Backcross- F1 mate w/parents

Sunday, November 17, 2013

Monday, November 11, 2013

11/11 (Make a Wish) The Operon System

The operon system goes through the replication process.
Heres a recap of replication
First, helicase breaks the hydrogen bonds
RNA primase goes in with its RNA nucleotides and adds an OH- to the 3 prime side to make it polar
DNA Poly III reads it
DNA Poly I replaces RNA nucleotides with DNA nucleotides
Lastly, DNA Ligase goes in and fills those fragment gaps with phosphodiester bonds

Operon System- regulatory gene creating a key

Trp Operon System (creating Amino Acid Trp)
DNA goes through transcription, mRNA goes through translation and creates a protein
The protein is the key (repressor) to unlock the door (the operator)
The RNA polymerase reads it
Tryptophan is made
This whole area of the system is the promoter (open door)

Lactose Operon (Creating enzyme lactase; disaccharide)
Glucose and Galactose- we cannot digest
Protein is inserted with Allolactose (inducer) which makes it inactive 
The protein unlocks from operator and the RNA polymerase is able to read it and make Lactase

Saturday, November 9, 2013

11/6 Snork Lab

Today we analyzed a Snork's genes of its DNA and determined the traits of the Snork based off of that. Protein Synthesis determines the physical or chemical trait.

Protein Synthesis in order-
Gene
DNA
mRNA
Amino Acid
Polypeptide
Protein (gives us trait)
Enzyme

Example of what we did-
We converted the DNA base to mRNA base
CAT AGG GAG to...
GUA UCC CUC

Every gene's beginning starts with a Start Codon (AUG) and ends with a stop codon (UAA)

We then used this wheel to find the Amino Acid sequence based off of the mRNA sequence.
The Amino Acid sequence coded for a specific trait, and we used those traits to draw the Snoopy Snork. 

Tuesday, November 5, 2013

Explaining Pictures

Edgar Zwilling and John Saunders discovered two patches of tissues that controlled the development of bones inside limbs. One strip of tissue at the end of the limb bud is essential- without it the development stops. 
Mary Gasseling experimented with chicken eggs and took the patch of tissue from the pinky and put it on the first finger. The chicken resulted in having a new set of fingers that were mirror images of the normal set. The gene inside the tissue was able to control the development of the pattern of the fingers. (mirror image duplication)
The patch of tissue is the zone of polarizing activity (ZPA) How did it control the formation of fingers and toes? There is the concentration-dependent idea which explains that there is a high concentration of ZPA.
Denis Summerbell experimented with the idea and put foil between the ZPA patch and the rest of the limb. The foil was a barrier to prevent any molecule from diffusing to the other side. It resulted in cells on the ZPA side forming digits and the opposite side had barely formed digits. Something spread out of the ZPA that controlled how digits formed.
That something was the sonic hedgehog gene. It is what causes the ZPA tissue to do what it does. When things go wrong with sonic hedgehog, like in this picture, hands become messed up because the gene is not turned on properly during the 8th week of human development. 

Errors sometimes happen when the DNA is copied from the parent to the daughter cell. The error is called a mutation and it is not done randomly. Evolution favors a mutation that helps an organism discover adaptations to help it survive. So this flower's mutations were triggered by outside influences. McClintock discovered "jumping genes" (transposons) that proved that mutations are not just random. They remain in an active gene after inserted and make a difference. There are two different ties of jumping genes: DNA transposons which cut and paste, and Retrotransposons which copy and paste. This flower was affected by the DNA transposons where the code of the gene splits and it loses its trait which causes a change in the physical trait. 

11/4 DNA Replication Enzymes

Steps to replication-
1) Helicase- breaks hydrogen bonds "unzips"
2) RNA Primer- primes it with RNA nucleotides, reads 3-5, OH on 3
3) DNA Pol III- reads 3-5, adds nucleotides to synthesizing strand
4) DNA Pol I- Replaces RNA nucleotide with DNA nucleotide (new DNA)
5) DNA Ligase- Lagging strand has Okazaki fragments, ligase creates phosphodeister bond (bond between phosphate and sugar in nucleotide) and seals gaps


Sunday, November 3, 2013

Reading Assessment: Chapter 3 Your Inner Fish


body made up of hundreds of cells
cellular diversity gives tissues and organs functions and distinct shapes
despite their differences, there is a similarity= exact DNA
-individual genes turning on and off inside each cell during development
makes protein that can affect how the cell behaves 
making hands
Edgar Zwilling and John Saunders
experiment on chicken eggs
-how the pattern of the skeleton forms
discovered: two patches of tissue control the development of the pattern of bones inside limbs

strip of tissue at end of limb bud is essential- without it, the development stops

Mary Gasseling
experiment on chicken egg
-took patch of tissue from pinky and put it on first finger
result: new fingers mirror images of normal set
-gene inside tissue able to control development of pattern of fingers
(mirror image duplication)

patch of tissue: zone of polarizing activity (ZPA)
-tissue that causes pinky side to be different from thumb side
-control formation of fingers and toes
how?
concentration-dependent idea- high concentration of ZPA

Denis Summerbell
foil between ZPA patch and rest of limb
-use barrier to prevent any molecule from diffusing to other side
results: cells on ZPA side formed digits
cells on opposite side barely formed digits (malformed)

something spread out of ZPA that controlled how digits formed (hedgehog gene)


the DNA recipe

one molecule started whole thing

fly experiment
-pattern of gene activity that makes body of fly from a single celled egg

hedgehog gene- made one end of body segment look different from the other
(similar to ZPA)

hedgehog gene has a specific DNA sequence
-scientists found sequence in other animals

animal version of gene= sonic hedgehog 
(mimics activity of ZPA)
active in ZPA tissue

vitamin A cause s.h to turn on in the opposite side of limb

-make fingers distinct from one another-depends on how close finger is to gene

-when things go wrong with sonic hedgehog- hands messed up
not turned on properly during 8th week of human development=extra fingers


giving sharks a hand

sharks: earliest creatures that have fins with skeleton inside
mermaid’s purses- skate embryo

(cartilage)
-apply same experiments as they did to chickens
sonic hedgehog’s role in its limb?: YES
similar effect to fin (duplicate)



experiment
a skate embryo with a bead inside that leaks mouse s.h protein

result: develop different from one anther (responded to gene, like chickens did)
-s.h does something similar in skates and in humans
-genetic recipe similar

recipe that builds our hands has deep roots in other creatures
“inner fish”- biological tools that build fins
-all appendages are built by similar genes
-connections among creatures

Wednesday, October 30, 2013

Reading Assessment: Chapter 6 Survival of Sickest


First vaccine
cowpox
resistant to smallpox

make other people resistant by putting it on teenage boys
-worked

how vaccination works
begins with harmless version of virus 
-bodies will recgonize but not enough to cause seriou disease
-immune system produces antibodies that defnd against virus
-then if we are exposed to harmful version, our bodes are prepared to fight

different antibodies to fight off different attacks

First cell
-genetic instruction to mnufacture proteins to build human being
instructions carried out by nucleotides
-nucleotides= dna base pair
-genes  organized in 23 pairs
every pair except 23rd (sex chromosome) is a matched pair
-chromosome carries the same instructions 
-always have dominant gene over recessive

germ cells-cells that combine to provide offspring

3% dna is meant for building
97% isnt active in building

97% portion of genome plays role in evolution 
-called noncoding DNA
-made up of jumping genes
-related to viruses

mitochondria= produce energy to run cells
-live in all cells
-own heritable DNA

evolution shaped by integration and adaptation of viruses

Theory
genetic chnages product of accidental mutations (rearrange DNA)
-mutations happen when there is an error
-mutations happen when organism exposed to radiation or powerful chemicals
-sun cause mutation
sunspot peaks- energy leaked through magnetic field
occurred during massive flu outbreaks
-antigenic drift- mutation occurs in the DNA of a virus
-random mutation= advantage on its carrier, better chance to live
one species advantage could be anothers disadvantage (ie. virus to humans)

theory wrong: evolution favor a mutation that helps an organism discover adaptations to help survive

single genes have capacity to produce different proteins at once
shuffle/reshuffle to produce array of proteins

complexity- combining parts of one gene with another

not instructions anymore, scientists learn genes are an intricate network of info

McClintock
corn plants experiment
when they were stressed: DNA moving from one place to another (inserting themselves)
-affected nearby genes- turned them on and off

method:
  1. relocated to specific parts of genome
  2. mutations triggered by outside influences (environment)

discovered “jumping genes” (transposons)
-suggested evolution could be faster than imagine
-mutations aren’t just random

Remain in an active gene after inserted and make a difference

Example: jumping gene one one line of fruit flies turned them into superhero fruit flies
-resist starvation 
-withstand high temp
-life expectancy that was 35% longer

genome gambles on mutation

Cairns 
E coli- digestive workhorse in humans 
*cannot digest lactose
-starvation is a big threat to bacteria

experiment: deprived E coli of any food except lactose
  • bacteria developed mutations that allowed them to lose their lactose intolerance
idea: bacteria targets specific area of their genome where mutations could be an advantage to them



argument idea:
hypermutation- mutation on steroids
helped bacteria produce mutations 100 times faster
-suggests genome has ability to order mutations on demand

Weismann barrier

germ plasma theory- divides the body’s cells into groups
every cell (except germ cell) is a somatic cell

theory: info in somatic cell is never passed on to germ cells
but: some viruses may be able to penetrate the barrier and carry DNA fro somatic to germ cells 

germ line mutations- mutations result in a different gene in egg or sperm that produces new trait in offspring

cancer- uncontrolled cell growth caused by mutation in the gene that is supposed to control the growth of cancerous cells

jumping genes help humans in two ways (diversity):
  1. very active in brain development 
  2. immune system 

Antibodies 
b-cells- building blocks for antibodies

V(D)J recombination: b-cells seek out instructions for antibody in their DNA, snip away line of instruction for other antibodies and sew rest together
(unlike jumping genes because leaves a little loop) 

once antibodies are developed, you always have them 
-immune to future infections 

Viruses
cannot produce on its own
hijack hosts cellular machinery

retrovirus-offspring born with virus permanently in DNA

HERVs-permanent place in DNA


two different types of jumping genes:
DNA transposons- cut and paste
retrotransposons- copy and paste

Tuesday, October 29, 2013

10/28 DNA Structure y'all

Today in class, we went over the lesson about DNA structure and function. 

Some basic concepts-

Erwin Chargaff found:
1) Composition of DNA varied from one species to another- bases= A, C, T, G
2) A=T (straight edge letters)
C=G (curved letters)

The base pairs (A to T, and C to G) are held together by hydrogen bonds

C and T are pyrimindines 
G an A are purines 

The nucleotide is made up of phosphate, sugar and a base. 
The phosphodiester is the bond between the sugar and phosphate.

The structure has two ends 
1) phosphate= 5 prime
2) sugar=3 prime (3 carbon)

The sugar molecule has an OH attached to it. It only recognizes it because it is polar (negative). 

It is a little hard to explain, so here is a picture of what I am talking about. 



In class, we also made our own paper DNA structures. 

Sunday, October 27, 2013

"From Atoms to Traits" Questions

Explain the significance of Mendel

Mendel’s breading experiment with the peas changed the general perception of heritable genes from blendable to exact genes passed from parents to the offspring. The inheritance patterns of the peas were mirrored by the behavior of chromosomes in the nucleus. Genetic information was finally becoming a physical appearance in the threads inside the nucleus. 

Draw the structure of DNA and who discovered this structure 
James D. Watson and Francis Crick 

Explain each of the five examples of variations that occur to DNA and give an example of each.
  1. Point Mutation (Class of Mutation)- A single base pair change. A whipper dog can vary between a small version and a big version of itself. The mutation stops the signaling molecule gene that regulates muscle growth. The muscle growth is uncontrolled because it does not have a stop signal. 
  2. Insertion- One or more extra nucleotides are inserted into replicating DNA. In a pea plant there is a base pair sequence that makes peas wrinkled. The inserted base pair stops starch synthesis which then changes the peas’ sugar and water content. 
  3. Gene Copy Number- Entire gene is duplicated by copying errors during cell division, leading to differences between species and variation among members. Chimps normally have a single gene for the starch digesting enzyme, whereas humans can have 10 copies of the gene. 
  4. Duplication- Sequences that contain the same base pair repeated 8 or more times (homopolymers). A pig’s gene of two additional C-G pairs in a sequence stops the signal in pigment cells, producing a light colored coat. Copying mistakes within cells can cause the sequences to lose bases, letting the gene signal pigment cells and producing dark spots on the pig. 
  5. Regulatory- Mutations in the DNA that controls when and where genes are activated that can produce trait alterations by changing the formation of body parts during the organisms development. The shape difference between the teosinte plant and the cornstalk is because the changes in the gene that controls the cell division during stem development. 
What is eve-devo?
Evolutionary development is a field of biology that compares the developments of different organisms to determine the ancestry and relationships between them. It is the understanding of how development is changed over time. 

Make a connection between human migration and the mutation of lactose intolerance. 
The ability to digest milk into adulthood, has arisen independently in groups of different continents. It provides a nutritional advantage to humans and connects to the changes of DNA sequences and human cultural evolution. Example- Mutations affecting the same gene dominate in East African and Saudi Arabian populations who herd milk-producing animals. 

Wednesday, October 23, 2013

"Does Race Exist" in a Black and White World


Do common beliefs of race correspond to underlying genetic differences among populations? No. The article, “Does Race Exist” explains that in some cases, yes, but most of the time no. People are sorted broadly into groups according to genetic DNA. Physical features that are brought about by natural selection are used to separate people into races. The article says that people with similar skin color or facial features from evolution can be different in relation to their DNA. For an example, humans from two different homelands that have a hot climate may have similar skin tones because their adaptation to the sun. However; genetically they are different. People that are similar to each other in their DNA might be exposed to different forces. The article explains how scientists figure out the correspondence between each group by relying on tiny genetic variations of the DNA called polymorphisms. Short pieces of DNA that are similar in pattern of one another are called alus, which are part of polymorphisms. They are used to determine the relationship of populations to one another. Scientists look at hundreds of these polymorphism and eventually can group individuals based off of their DNA. They have a distinct effect in one group but may vary in another group, so the traits effected by natural selection are bad predictors of detecting which individual should go in each group. The usual assumption of race do not always reflect a person’s genetic background. There has been so much genetic mixing, that there are no true races among humans. The concept of race only applies to the social aspect of humans, which is still important. Modern mapping of the human DNA can now point out the different forms of a gene that are brought up by mutation. So race does exist but it has no validity for humans at an biological perspective. 

Monday, October 21, 2013

National Geographic Article- Answering Questions

How the first modern humans reached Australia and New Guinea:


Migrated out of Africa
Went along the coast of Southeast Asia (Sunda, one land mass), and reached Australia and New Guinea (Sahul) 

Sea level was much lower

Indicating that settlers had knowledge of seafaring 

46,000 to 41,000 years ago 
If dates are correct, Australia was populated 10,000 years before Europe. 
-Humans avoided cold, and favored tropical regions to which they adapted from Africa 

Sunday, October 20, 2013

10/15 Hardy-Weinberg Problems


Today, we learned how to use the Hardy-Weinberg equation. Mr. Quick sent out a video that explains it really well, and helped me understand how to use it in different circumstances! 


Friday, October 11, 2013

10/11 Evolution and Gene Frequencies (Lab)

Today we performed a lab (to determine the effect of random mating in a population of tigers possessing a recessive gene!) where we have 25 red beads and 25 green.

Green= h
Red= H

We put them all into a paper bag and chose two beads without looking. If they were both green (hh) they were dead. (not naturally selected to survive the cold environment)
HH was the recessive trait. (no fur)
Hh was the dominant trait. (fur) 

Hypothesis- The recessive gene will eventually go away after 10 generations.


Sunday, October 6, 2013

Reading Assessment: Chapter 8 Survival of Sickest



10/4 Parents Day

During parents day, the students and parents looked at pairs of a person (with some differences) and decided which one we found attractive. Based on the data, we were able to conclude that women are more attractive to "caring and sharing" men (feminine faces) who will make good partners. However; during ovulation women are more attracted to masculine faces who will father healthy offspring.