Review Sheets

Here you go. Idk how helpful but whatever

1) Mendel was super far ahead of his own time, so all the way up until the 1900s, people just looked at it and were like wtf? What he did was cross Pea plants. He would take a true breed homozygous dominant (purple flower) and a true breed homozygous recessive (white flower). When crossed, he would get a 3:1 ratio of Purp to cracka. This was because PP Pp pp. With this he came up with the Conclusions: a) Each individual must carry 2 hereditary factors for each allele b) These hereditary factors segregate during gamete formation such that each gamete only contributes one factor to the offspring c) One factor may mask/dominate the other in expression.
This guy is a bamf. But the legit laws: A) There are alternate versions of genes that account for variations inherited characters. B) For each trait, an organism inherits 2 alleles, one from each parent. C) If 2 alleles of an inherited pair differ, then one determines the organisms appearance and is called the dominant allele. The other allele will have no noticeable effect on the organisms appearance and is called recessive. D) A sperm or egg carries only one allele for each inherited character because allele pairs segregate from each other during the production of gametes.
2) Pea plants were ideal because: a) the separate traits were distinguished, eg: tall-short, purple-white, happy-angry... b) short reproduction time c) produced large offspring. They were also able to self-pollinate. This is when the flower contains both the sperm on the stamen and the eggs on the carpel and can thus reproduce by itself. Cross-pollination is when one flower supplies the sperm and another provides the eggs. Mendel would cut the stamens off of one pea plant and brush pollen off the other one onto the first to cross-pollinate.
3) Genotype - the hereditary factors ( same as alleles) of an individual that are it’s carriers for a given trait. Or as the book says- It’s genetic makeup...thanks book
4) Phenotype - The physical expression of the genotype
5) Know homozygous, heterozygous...aka don’t be retarded
6) Be able to determine genotype/phenotype ratios of crosses ( monohybrid, dihibrid) Just be able to do that stuff AaYy x AaYy...
7) A test cross is used to determine an unknown individual’s phenotype. Breed unknown genotype individual with a homozygous recessive individual. Like with wittle puppies! B_ x bb
An allele is a variation of a trait. A locus is the location of a specific allele of a trait on the chromosome.
9) A gene is a trait inherited from an individual’s parents
10) Incomplete dominance is when both alleles are expressed resulting in an intermediate phenotype. Know how to do this. Red + White = Pink
11) Co-Dominance is when both alleles are expressed fully. Like AB blood.
12) Multiple alleles is when there are more than two alleles that exist for a gene.
13) Epistasis is when multiple genes code for one phenotype. Deafness! “What?” DEAFNESS hahaha oh I’m soooo funny. But ya there’s an inner ear and a middle ear. Both have to be screwed up to make the person deaf.
14) Pleiotropy is when one gene affects multiple phenotypes. Marfan syndrome - makes people extremely lanky, Ethan, but seriously to the extreme. I think I saw some guy with it at swimming once. Longer fingers, toes, di-... Outward or inward chest.
15) Be familiar with sex determination in humans. Like Y-linked traits and X linked traits and all that. It’ll be pretty obvious if he does it.
16) So sex-linked traits are traits specific to the X or Y chromosomes, which are sex chromosomes. Everything is sexy. X is the most common because guys have XY and girls have XX. 3:1. Thomas Hunt Morgan discovered this in his studies with his students (Alfred H. Sturtevant in particular) on Drosophila Melanogaster, aka fruit flies! Recombination frequency is the number of recombinants over the number of offspring. So lets say 200 of 1000 babies have x-ray vision and can fly. 20% chance of this specific recombination frequency. X-ray vision gene is 20 centi-morgans (or map units) from the gene of flight.
17) Be familiar with chromosomal basis of inheritance. Genes at specific loci and meiosis, mitosis, etc.
18) What is meant when genes are said to be linked? Genes located on the same chromosome, inherited together more often than not. Discovered through the frequency of them being inherited together.
19) Genetic recombinants are genes resulting from genetic recombination (cross-over). Recombination frequency is the number of recombinants over the number of offspring. So lets say 200 of 1000 babies have x-ray vision and can fly. 200/1000 ----> 20% chance of this specific recombination frequency. X-ray vision gene is 20 centi-morgans (or map units) from the gene of flight.
20) Chromosome mapping. Example, p gene is 50mu from q gene and z gene is 25mu from p and 75mu from q so is must go z –> p –> q.
21) Pedigree stuff. There are a few methods of gene transfer. A) Autosomal Recessive = a) affected individuals can have unaffected parents. b) males and females equally affected c) typically not prevalent in pedigree. B) Autosomal Dominant - a) affected individuals have at least one affected parent b) males and females equally affected c) often more prevalent in pedigrees. C) X-linked Recessive - a) affected individuals may have unaffected parents b) guys more likely affected than girls c) carrier mom –> affected son is a hallmark D) X-linked Recessive - a) affected individuals have at least one affected parent b) girls more often affected than guys c) All daughters with affected dads are affected, but none of the sons. E) Y- linked - Father to Son F) ??? - Mitochondrial Inheritance - If it doesn’t make sense at all, it’s mitochondrial.

thanx aidan

haha i looked at first line and broke out laughing
"they all looked at it and were like wtf?"

hahaha wtf

FILL IN THE BLANKS QUIZ
I suggest you copy this into word and print out multiple copies and try to answer it right next to the question by writing it out. And then check you answers. I’ve included a section on possible new fill in the blanks. Feel free to point out errors. ~~~~Machak

Mendelian & Human Genetics

There is no matching for this test but I suggest you look at some key terms and how to solve genetic problems!

DNA as the Genetic Material

1. Enzyme that open the double helix in replication-
2. Isotope used to label the phage DNA in the Hershey-Chase experiment
3. Determined that A=T and C=G in any given organism
4. Term used to describe the fact that the two strands of DNA run in opposite directions
5. Scientist(s) that published a brief article in Nature in 1953 that described the chemical structure of DNA
6. Scientist(s) that provided the X-ray diffraction pattern of DNA that was instrumental for the Watson and Crick model
7. Location on chromosome where replication begins
8. Year DNA was discovered.
9. Scientist credited with discovery of DNA
10. “starting block” for DNA replication
11. Enzyme used in PCR
12. Scientist who invented PCR
13. Isolated from seaweed, used to make gels fro DNA electrophoresis
14. “safe” stain used for staining DNA

Transcription, Translation, Regulation of Gene Expression, & Microbial Genetics

1. A deletion or insertion results in this type of mutation
2. Region of DNA that directs the binding of RNA polymerase
3. Two types of mutation according to cell type
4. Means of bacterial genetic variation that was discovered by Griffith in 1928
5. Describes an operon that is usually turned “off”, but can be turned “on”
6. Region of DNA to which a repressor protein binds in prokaryotes
7. Part of an operon that code for proteins with related functions
8. DNA-directed RNA synthesis
9. A point mutation that does not change the amino acid coded for
10. Term for the phage cycle in which the DNA is incorporated into host cell chromosome, and is thus “dormant”
11. Extrachromosomal DNA in prokaryotes that may confer and advantage
12. The corepressor in the trp operon
13. General term for gut-dwelling bacteria such as E. coli
14. Enzyme found in retroviruses
15. Three consecutive bases of mRNA that code for an amino acid (or a termination factor)
16. Site where initiation of transcription occurs
17. Part of tRNA that corresponds to #15

Evolution and Speciation

1. Type of prezygotic reproductive isolating mechanism exhibited by cicadas
2. Type of natural selection that selects for the extreme traits
3. The movement of genes into or out of a population
4. Reproductive isolation that occurs before fertilization
5. Movement of individuals out of a population
6. Another term for nonrandom mating
7. Phenomenon in which the two genders of the same species vary significantly in outward phenotype; common in birds
8. The study of the geographical distribution of fossils and of living things
9. A measure of an individual’s relative reproductive success
10. Wrote an essay arguing that organisms tend to produce man more offspring that the environment can support, leading to a struggle for existence, an argument that influenced Darwin’s ideas of natural selection
11. The change in allele frequencies over time as a result of random chance
12. Proposed the notion of inheritance of acquired traits as a mechanism for evolution.

ANSWERS

Test 1
No matching!

Test 2
1. helicase
2. P32
3. Chargaff’s Rule
4. Antiparallel
5. Watson and Crick
6. Wilkins and Franklin
7. Origin of Replication
8. 1869
9. Miescher
10. RNA primer
11. taq polymerase
12. Dr. Kary Mullis
13. Agarose Gel
14. Methylene Blue

Test 3
1. Frameshift Mutation
2. Promoter
3. Somatic and Germline
4. Transformation
5. inducible
6. operator
7. regulatory genes
8. transcription
9. silent/synonymous mutation
10. lysogenic
11. plasmid
12. tryptophane
13. endemic
14. Reverse Transcriptase
15. codon
16. promoter
17. anticodon

Test 4
1. temporal isolation
2. disruptive selection
3. gene flow
4. prezygotic isolation
5. emigration
6. sexual selection
7. dimorphism
8. biogeography
9. fitness
10. Thomas Malthus
11. genetic drift
12. Jean-Baptist de Lemarck

For those wanting some additional fill in the blank…

1. passing of traits from parents to offspring
2. scientific study of heredity
3. the actual alleles an individual has for a given trait
4. the physical expression of #3
5. both alleles are expressed, resulting in an intermediate in the physical expression
6. both alleles are expressed (but maintain their individual identity in the physical expression)
7. More than two alleles exist for a certain gene
8. A single gene effects multiple physical expressions
9. Two or more genes interact to affect a single physical expression
10. traits determined by a gene on the X and Y chromosome
11. genes located on the same chromosome (relatively close). Typically inherited together
12. viruses that attack specific bacteria
13. Includes Cytosine, Uracil in RNA, and Thymine, 1 ring base
14. Includes Adenine and Guanine, 2 ring base
15. “seals the gap” between nucleotides left by proofreaders
16. Means of separating fragments of DNA or proteins by SIZE
17. The harmful stain used in #16
18. Premature termination of translation due to a STOP codon
19. Usually “on” but can be turned “off”
20. DNA or RNA surrounded by a protein capsid. Not a cell
21. Change in living things over time
22. Differential reproductive success as a result of heritable traits
23. Study of large-scale changes over long periods of time, that lead to a new species
24. Study of change in allele frequency of population over short periods of time
25. By preventing gene flow, allows for genetic divergence

ANSWERS
1. heredity
2. genetics
3. genotype
4. phenotype
5. incomplete dominance
6. codominance
7. multiple alleles
8. pleiotropy
9. epistasis
10. sex-linked traits
11. linked genes
12. bacteriophages
13. Pyrimadines
14. Purines
15. ligase
16. Gel Electrophoresis
17. Ethidium Bromide
18. Nonsense Mutation
19. Repressible
20. Virus
21. Evolution
22. Natural Selection
23. Macroevolution
24. Microevolution
25. Reproductive Isolating Mechanism

is there even a fill in the blanks section on the test?

good contribution alex

Thank you very much for this as well as everyone else who made review sheets for anything. especially newcomb who decided he'd go crazy and write lots of reviews. but annnyway thanks sooooo much

i hope not but thanks anyways machak

DAMNT.

there was on the last final so why wouldnt there be one on this one

thanks for the quiz and there is a fill in the blank on the final

hahahahaha

on a more serious note, does anyone have the answers for the scantron for the second test, DNA as the genetic material? much obliged

ya its:
1 c
2 a
3 b
4 e
5 e
6 d
7 e
8 d
9 b
10 e
11 d
12 d
13 c
14 e
15 d
16 a
17 e
18 c
19 b

c
a
b
e
e
d
e
d
b
e
b
d
c
e
d
a
e
c
b

thanx to both of you

well since you already did that it would be helpful if you did the scantron for the transcription and mendelian tests also

just in case any1 wants to review even more after all the other reviews, i found my old ones so here they are:

Mendelian Genetics

1. Mendel did crosses for seven different characters: flower color, flower position, seed color, seed shape, pod shape, pod color, and stem length
a. Crossed true breeding dominant (NN) with true breeding recessive (nn) which made up the P generation. The offspring made up F1 generation. They were all heterozygous for the trait (Nn). Their offspring make up the F2 generation. The genotype ratio was 1 NN: 2 Nn: 1nn, so the phenotype ratio was 3 Dominant trait: 1 Recessive trait.
i. Concluded that alternative versions of genes account for variation in the character. These are now called alleles.
ii. Concluded that for each character, there are 2 alleles
iii. Concluded that if two alleles that differ are inherited, one determines the phenotype.
iv. Concluded that allele pairs (homologous chromosomes) separate during gamete formation (law of segregation)
b. Did a dihybrid cross between homozygous plants. One had yellow round seeds (AABB) and the other had green wrinkled seeds (aabb). The F1 generation were all dihybrids (AaBb). The F2 generation resulted in 9 round yellow: 3 round green: 3 yellow wrinkled: 1 green wrinkled.
i. Concluded that each pair of alleles segregates independently of other pairs of alleles during gamete formation (law of independent assortment).
2. Pea plants were ideal for crosses because there were many different characters, they had short generation times, and they produced a large number of offspring.
a. Cross-pollination – pollination of one plant by the pollen of a different plant
b. Self-pollination – pollination of a plant by the pollen of the same plant
3. Genotype – the alleles an individual carries for a trait; the genetic makeup
4. Phenotype – physical expression determined by the genotype
5. Homozygous dominant – having two dominant alleles for a character: homozygous recessive ¬– having two recessive alleles for a character: heterozygous – having a dominant and a recessive allele for a character
6. Genotypic and phenotypic ratios
7. Test cross – a cross between an individual with dominant phenotype (unknown genotype) and an individual with recessive phenotype (and recessive phenotype).
a. Used to determine the genotype of the individual with the dominant phenotype
8. Allele – an alternative version or genetic factor of a trait: locus – particular site where a gene is found on a chromosome
9. Gene – a pair of alleles that determines a phenotype
10. Incomplete dominance – when both alleles are expressed in a heterozygous individual resulting in an intermediate phenotype
a. Ex: Red snapdragon X white snapdragon results in pink snapdragon
11. Codominance – when both alleles are expressed in a heterozygous individual, but they both retain their own identity
a. Ex: in blood type, IA and IB are codominant, and IAIB results in red blood cells with A and B antigen
12. Multiple alleles – when multiple alleles exist for a gene. Ex: blood type
a. In blood type, there are 3 alleles: IA, IB, and i. Type A blood makes A antigens, makes anti-B antibodies, and is the genotype IAIA or IAi. Type B blood makes B antigens, makes anti-A antibodies, and is the genotype IBIB or IBi. Type AB blood makes A and B antigens, doesn’t make anti-A or anti-B antibodies, is the genotype IAIB, and it is the universal recipient. Type O blood makes no antigens, makes anti-A and anti-B antibodies, is the genotype ii, and is the universal donor
13. Epistasis – when 2 or more genes interact to affect a single phenotype. Ex: the Bombay phenotype
a. In Bombay phenotype, a gene codes for whether or not an individual presents the protein from the blood type, no matter the genotype from the IA, IB, and i alleles. E results in the presence of the proteins. e results in no presence of protein. If one is dominant for the gene, then he shows the phenotype from the blood type alleles. If one is recessive for presentation of protein, he presents type O blood.
14. Pleiotropy – when one gene affects multiple phenotypes
a. Ex: sickle cell anemia, defective dynein, and marfan syndrome
15. Sex determination – Males: XY and Females: XX
16. Sex-linked traits – traits determined by a gene on a sex chromosome
a. X-linked and Y-linked traits
b. Most common are the X-linked traits because if not everyone has a Y chromosome, then there cannot be any major life-determining genes on it
17. Chromosomal basis of inheritance
18. Linked genes – genes located on the same chromosome, therefore inherited together more often than not. This was discovered when William Bateson and Reginald Punnett observed a dihybrid cross between two sweet pea plants. They crossed a double heterozygous plant and a homozygous recessive plan. After doing the cross, they did not get the 9:3:3:1 phenotypic ration. They got a disproportionate amount with a ration of 284: 21:21:51
19. Genetic recombination – the production of offspring with allele combinations different from those in the parents, as a result of crossing over or independent assortment
20. Chromosome mapping – the ability to determine the distance between linked chromosomes based on the recombination frequency
21. Pedigree symbols are: unshaded square=unaffected male, unshaded circle=unaffected female, dark square=affected male, and dark circle=affected female.

and heres

DNA as the genetic material:

1. DNA was first discovered in 1869 by Frederick Miescher when he isolated the nuclei from pus cells and purified the chemical nuclein.
2. Chromosomes are comprised of
a. DNA
b. Associated proteins
3. The Griffith experiment
a. Discovered 2 strains of streptococcus bacteria
i. “S” strain – formed smooth colonies and produced protective capsules around the cells
ii. “R” strain – formed rough colonies and did not produce the protective capsules
b. Injected the S strain into the mice, and they died of pneumonia because the protective capsules protected the cells from the mice’s immune system. Live S was found in the blood of the dead mice
c. R strain was injected into the mice and they lived. Live R was injected into the mice
d. He boiled the S strain and injected it, and the mice lived
e. Then he boiled S, mixed it with live R, and injected it, and the mice died. Found live S in the blood, so he concluded that a transforming factor converted the R into S
f. The experiment showed that the R used a transforming factor from the dead S to produce protective capsules and become S
g. Left the unanswered question: what is the transforming factor?
4. Avery, McLeod, and McCarty experiment
a. Took S strain bacteria and removed the protein coat, mixed it with the R, and the R transformed
b. Removed the rest of the protein and mixed the S with the R, and R still transformed
c. Removed the RNA with an RNA enzyme (RNAase) and mixed the S with the R, and the R still transformed
d. Removed the DNA with Deoxyribonuclease and mixed the S with the R, and the R did not transform.
e. This showed that DNA was the genetic material that the dead S used to transform the R
5. Hershey-Chase Experiment
a. They got bacteriophages to infect some e coli. They believed that the bacteriophages injected their genetic material into the e coli which contained the instructions for the e coli to make new phages.
b. The phages were composed of DNA surrounded by a protein capsid
c. They knew that DNA has phosphorus and no sulfur, and protein has sulfur and no phosphorus. Phosphorus and sulfur can be radioactive isotopes, so you can use them as tracers
d. The bacteriophages with radioactive DNA injected the genetic material into the bacterium
e. The bacteriophages with radioactive protein injected the genetic material into the bacterium (into a different tube than step d)
f. They used a blender to pull the bacteriophages from the e coli.
g. Used a centrifuge to pull the bacterium to the pellet at the bottom of the tube. In the first tube, the pellet was radioactive and the liquid was not, so they knew that the DNA was inserted and is therefore the genetic material. In the second tube, the liquid was radioactive and the pellet was not, so they knew that protein was not inserted
h. The experiment confirmed that the DNA is the genetic material
6. They already knew that the genetic material had to be able to
a. Replicate on its own
b. Code for specific proteins
7. In 1953, Watson and Crick determined the chemical structure of DNA from the evidence from
a. Edwin Chargaff’s A pairs with T and C with G
b. Rosalind Franklin and Maurice Wilkins’ x-ray crystallography
8. The DNA nucleotide is made up of a 5-carbon sugar, a phosphate group, and a nitrogen base
9. DNA replication – process by which 2 strands of DNA are made from one strand of DNA
a. Helicase binds to the origin of replication and pulls apart the double helix
b. Primase places RNA primers as starting blocks for the replication
c. DNA polymerase adds new DNA polymers to the 3’ end of the strand. It keeps adding to that in continuous replication. To go the 5’ direction, you keep placing primers in front of the previous okazaki fragment and add polymers to that in discontinuous replication
d. Proofreader enzymes (special DNA polymerase) replace the RNA primers and incorrect polymers with correct DNA polymers
e. Ligase seals the gap between the 3’ and 5’ of adjacent okazaki fragments
10. In DNA gel electrophoresis, you place DNA or protein samples into the wells of the porous gel. A current runs through the gel with one side positive and the other negative. DNA or protein is on the negative side and is negative, so it moves to the positive side. Larger fragments of DNA or protein have more trouble moving through the gel, so the smaller fragments move farther. It is used to separate the fragments of DNA or protein according to size. The gel used is called agarose and the DNA is stained with methylene blue
11. DNA fingerprinting is matching a person’s DNA and a sample DNA to see if they are the same. It is used to place a person at a crime scene, etc.
12. PCR is polymerase chain reaction and is an amplification of DNA; makes billions of copies of DNA. It was invented by Kary Mullis. It is valuable because one is able to make one billion copies of a small sample of DNA
a. First, the temperature is raised to 94-96 C. This denatures the DNA and breaks the hydrogen bonds, so the strands are separated
b. Annealing of primers to the ends of the desired DNA
c. An unusually heat-stable DNA polymerase (called Taq polymerase from thermus aquaticus) adds new DNA polymers and duplicates the strands in continuous replication
32P and 35S are the isotopes used in the Hershey Chase experiment
Chargaff’s rule – Adenine pairs with thymine and cytosine with guanine
Rosalind Franklin and Maurice Wilkins – x-ray crystallography
Antiparallel – the 2 DNA strands are equal, but they go in the opposite direction (5’ to 3’ and 3’ to 5’)
Origin of replication – where helicase binds to unzip the double helix
Semiconservative replication – each strand of the original double helix is used as a template for replication

heres transcription, translation....

1. RNA vs. DNA
a. RNA has ribose instead of deoxyribose
b. Has Uracil instead of thymine
c. Is typically single stranded instead of double stranded. Therefore it is less chemically stable and can’t function by itself for very long (is temporary)
2. Crick’s central dogma: DNA is transcribed into mRNA which is translated into polypeptides
3. Transcription – DNA directed RNA synthesis; almost always occurs in the nucleus (can occur in the mitochondria)
a. Initiation – RNA polymerase recognizes and binds promoter, unwinds the double helix, and begins making RNA transcript complementary to the template strand of DNA
b. Elongation – RNA polymerase continues making RNA transcript complementary to the template strand of DNA
c. Termination – RNA polymerase recognizes the termination sequence of DNA, stops transcribing, and “falls off” the DNA
4. Promoter – DNA sequence to which RNA polymerase binds; “beginning of a gene”. Tells the RNA polymerase to begin transcription
5. Types of RNA
a. Messenger RNA – read by ribosome to make protein (after transcription)
b. Ribosomal RNA – part of the ribosome that catalyses protein synthesis (catalyses the dehydration reaction to bind the proteins: peptide bond)
c. Transfer RNA – the adapter which reads the binds its anticodon to the complementary codon on the mRNA, bringing with it the corresponding amino acid
6. The genetic code:
a. Is universal for all organisms
b. Is redundant: more than one codon can code for an same amino acid
c. Is not ambiguous: a given codon always codes for the same amino acid
7. Translation – RNA directed protein synthesis; occurs in the cytoplasm on a ribosome which has a small and large subunit
a. Initiation – the ribosome binds to the 5’ end of the mRNA and moves until reaching a start codon (AUG) which tells the ribosome to begin translation. The tRNA with the anticodon which binds to AUG (start codon) attaches to the P site of the ribosome bringing the amino acid met.
b. Elongation –A new tRNA with an anticodon complementary to the next codon attaches to the A site of the ribosome and brings with it a corresponding amino acid. The amino acid binds to met in a peptide bond catalyzed by rRNA, and the first tRNA translocates and leaves the ribosome. The second tRNA moves to the P site (as it carries the polypeptide) so that a new tRNA can bind to the ribosome’s A site
c. Termination – is triggered by a stop codon which acts as a signal to stop translation
8. tRNA – is stable even though it is RNA because it folds back on itself and base pairs with itself. It is an adapter because one side is the amino acid attachment site, and the other side is the anticodon. The amino acid attachment site carries an amino acid and the anticodon binds to the codon on the mRNA. So it is an adapter because it connects the nucleotide language with the amino acid language
9. be able to determine the amino acid sequence from a DNA template
10. mutation – a change in the nucleotide sequence of DNA
a. Somatic cell mutation – mutation in a somatic cell
b. Germline cell mutation – mutation in a gamete (this affects the offspring)
11. Two types of point mutation:
a. Base substitution – when the nitrogen base of a nucleotide is switched with another
b. Frameshift mutation – when a nitrogen base is inserted or deleted; this changes each codon that follows after the insertion/deletion; it shifts the bases
12. Spontaneous mutations – mutation that occurs naturally and randomly. Induced mutation – mutation when the environment affects the DNA structure (from mutogen or carcinogen: gamma rays, X-rays, etc.)
13. Reasons for regulating gene expression
a. For prokaryotes, efficiency: they save resources like ATP, nucleotides, and amino acids. Used by e coli: when there is an abundance of lactose, the bacteria can turn on the genes to break it down, and when there’s no lactose, then the e coli can turn the genes off to not make enzymes and not waste resources
b. Cell specialization: so that certain cells can turn off genes that they will never use (ex: a cardiac muscle cell will never turn on the genes needed to be a kidney cell)
c. Developmental stages: at different points in life, we need different amounts of proteins
14. Levels where gene regulation can occur:
a. DNA level – we could regulate replication, but it is always good to replicate DNA just in case we ever need it
b. Transcription – ideal regulation stage because you don’t waste anything
c. RNA level
d. Translation
e. Protein, polypeptide
15. Operon – a cluster of genes with related functions and a promoter, operator, and terminator.
a. Promoter – DNA sequence where RNA polymerase binds to begin transcription
b. Operator – DNA sequence to which a repressor binds to inhibit the RNA polymerase from binding to the promoter and therefore inhibiting transcription
c. Structural genes – genes that code for related proteins with related functions (all transcribed)
d. Termination – DNA sequence that tells the RNA polymerase to end transcription
16. Lac operon – is an inducible operon because the genes are usually “off” but can be turned “on” (native repressor is usually active)
a. lac operon contains the genes Lac Z which codes for lactose permease, Lac Y which codes for ß-galactosidase, and Lac A. Lactose permease lets in the lactose, and ß-galactosidase breaks the glycosidic bond between glucose and galactose. The regulatory gene Lac I codes for the repressor
b. first, with the lack of lactose, the repressor binds to the operator of the lac operon inhibiting the transcription of the operon
c. in the presence of lactose, the repressor is deactivated, and the genes are transcribed so that the lactose can be broken down. The lactose binds to an allosteric site of the repressor, allosterically inhibiting the binding to the operator by changing the shape of the repressor’s active site. When the repressor cannot bind to the operator, RNA polymerase is free to bind to the promoter initiating transcription.
d. After the lactose has been broken down, the repressor is again active and the genes are turned “off”
17. Trp operon – is a repressible operon because the genes are usually “on” but can be turned “off” (native repressor is usually inactive)
a. The trp operon contains the genes trp A, trp B, trp C, trp D, and trp E. these genes code for enzymes 1, 2, 3, 4, and 5 which are used in the metabolic pathway for creating trp which is very uncommon. The regulatory gene (trp R) codes for the trp repressor.
b. With the lack of trp, the repressor cannot bind to the operator, so the RNA polymerase begins transcription. The enzymes 1-5 are synthesized and are used in the anabolic pathway to build trp.
c. in the presence of trp, the repressor is activated. Trp binds to an allosteric site of the repressor, changing the shape of the repressor’s active site and allowing it to bind to the operator. This prevents RNA polymerase from initiating transcription so that the genes are turned “off” and trp is not made
18. virus – protein capsid surrounding RNA or DNA; some have phospholipid envelopes, it is an obligate intracellular parasite, they are small (few – few hundred nm), and they are not cells.
a. Are not living
i. Not a cell
ii. Cannot reproduce on their own
iii. Do not require energy
b. Have living characteristics
i. Have DNA or RNA
ii. They reproduce
19. Viral reproduction
a. Lytic cycle
i. Enter cell and inject DNA or RNA
ii. Transcription and translation of viral genes
iii. Assembly of new viruses
iv. Lysis of the cell (cell is killed and the virus spreads)
v. Process starts over
b. Lysogeny (latent viruses)
i. DNA integrates into host chromosome and is replicated with it (prophage or provirus)
ii. Can cycle or go lytic
20. Retrovirus – RNA virus that carries reverse transcriptase: enzyme that allows the RNA to be converted into DNA in reverse transcription. All cells have the same DNA, but the mRNA that is transcribed represents the transcribed DNA that is actually used uniquely by each cell, so we can use reverse transcription to convert the mRNA back into DNA to find out what DNA is actually being used by each individual cell
21. Bacteria reproduce asexually through binary fission.
22. Plasmids – extrachromosomal circular DNA in bacteria that are not necessary for life, but may confer an advantage
a. Antibiotic resistance (R plasmid)
b. Fertility – ability to get sex pile and conjugate (F plasmid)
c. Ability to utilize unique food sources
23. Three ways in which bacteria acquire genetic variation:
a. Transformation – bacteria acquire DNA from environment and incorporate it into its chromosome (ex: when the live R bacteria was mixed with the dead S bacteria and injected into the mice in Griffith’s experiment, the live R acquired the DNA from the environment)
b. Transduction – when bacteria acquire new bacterial DNA from a phage that is carrying DNA from the previous host cell (previous infection)
c. Conjugation – a donor bacterium (is male and has sex pili) transfers DNA to a recipient bacterium through a cytoplasmic bridge. The donor bacterium copies its DNA and sends it through the bridge. F factor conjugation occurs when the F factor is integrated or in plasmid form. When it is integrated, some genes from the donor might be attached to the F form, and the f form might not be completely donated for the cytoplasmic bridge could break. When it is integrated, is always sent.
RNA polymerase – enzyme that adds new nucleotides to the mRNA strand complementary to the template DNA
Promoter
Template strand – the strand of DNA or RNA that is being transcribed or translated
Termination sequence
Introns – internal noncoding regions that are removed during gene splicing
Exons – the parts of the gene that are expressed by the amino acid
Codon – sequence of three nucleotides that codes for an amino acid
Anticodon – sequence on the tRNA that binds to the codon to bring a specific amino acid
Amino acid attachment site – site on the tRNA to which the amino acid is bound
Archaea – lived better in extreme environments (thermophile, halophile, and methanogen)
Eubacteria – all common bacteria

and finally..

Evolution/Speciation:

1. Evolution – the change in living things over time; the change in characteristics and traits in organisms

2. Biogeography – the geographic distribution of species; led Darwin to believe that organisms evolve from ancestral species. It is a type of evidence for evolution. It shows that species that live closer together are more alike than species that live farther away but in similar habitats

3. Lamarck’s theory of evolution – he proposed the “inheritance of acquired traits.” According to him, if an animal changed some of its traits, then it passed the changes on to its offspring. For example, he said that the ancestors of giraffes stretched and lengthened their necks to reach leaves, and this trait was passed on.

4. Darwin’s voyage on the H.M.S. Beagle lasted 5 years. He spent most of his time collecting plants and animals, as well as fossils. He looked at the diverse life in South America and compared it with other continents. He wondered why fossils found on the South American continent were more similar to present day South American species than to fossils found on other continents. Darwin realized that natural forces gradually changed the Earth’s surface. He was influenced by Charles Lyell who wrote Principles of Geology, which talked about plate tectonics and an ever-changing world. Also, he read a paper by Thomas Malthus that explained that wars, famines, and diseases were the result of the level of population. He realized that Earth and its living organisms could not have been created only a few thousand years earlier.

5. He developed his own theory of evolution, but he didn’t publish it for a while because of the controversy. The book is called On the Origins of Species by Means of Natural Selection and was published in 1859. He eventually published it because it was presented along with another naturalist’s theory about evolution to the scientific community, and they accepted it.

6. Darwin’s theory of Natural Selection:
a. Observation 1: Members of a population vary in their traits and most are heritable.
b. Observation 2: Organisms typically produce more offspring than can survive
c. Observation 3: Organisms compete for limited resources
d. Inference 1: Individuals with traits best suited for the environment reproduce more successfully, and they tend to leave more offspring
e. Inference 2: the unequal production of offspring will cause favorable traits to accumulate.
i. This is natural selection
f. Fitness – a measure of an organism’s ability to survive to reproductive age and their reproductive success

7. Population – a group of individuals of the same species living in the same place at the same time

8. Gene pool – the total collection of genes in a population at any one time; consists of all alleles in all the individuals making up a population

9. Sources for genetic variation:
a. Gene flow – movement of individuals (and therefore alleles) into or out of a population
b. Genetic drift – change in allele frequencies due to random events or causes
i. Bottleneck effect
ii. Founder effect
c. Natural selection
d. Mutations

10. Allele frequency – is the fraction of the number of a certain allele out of the total number of alleles. Its relevance to the genetic equilibrium is that it is used to calculate the frequency of the different genotypes of the next population when the population is at Hardy-Weinberg Equilibrium

11. Population genetics – the study of the change in allele frequency due to the sources of genetic variation. Microevolution is the study of small scale changes in a short period of time in one population

12. Be able to determine genotype and phenotype frequencies

13. The Hardy-Weinberg Genetic Equilibrium – a state where allele frequencies in a population remain constant over time. Where a population is not undergoing evolution

14. Conditions for Hardy-Weinberg Equilibrium:
a. Large (infinite) population – the smaller the population, the more likely that allele frequencies will fluctuate
b. No migration (gene flow, immigration and emigration) between different populations or species – when individuals move into or out of populations, they add or remove alleles from the gene pool
c. No new mutations – can add or delete genes and modify the gene pool
d. No sexual selection (mating must be random) – if there is mate preferentiality, then the organisms with those traits are more likely to reproduce
e. No natural selection – the different survival and reproductive success can altar the gene pool

15. p + q = 1 and p2 + 2pq + q2 = 1

16. Immigration – the movement of individuals into a population
Emigration – the movement of individuals out of a population

17. Gene flow – the addition or removal of alleles

18. Three types of natural selection:
a. Directional selection – a change in the environment that changes the frequency of traits or certain alleles so that one extreme is selected against and the other extreme is selected for. Typically occurs during periods of environmental change
i. Ex: in the use of pesticides, the insects that are resistant to it survive, and the ones that are not resistant at all do not survive
b. Stabilizing Selection – a change in the environment leads to both extremes being selected against. Usually occurs in relatively stable environments
i. Ex: keeps the majority of human birth weights in the range of 3-4 kg. For infants a lot smaller or smaller than this, the infant mortality rate may be greater
c. Disruptive selection – where the average phenotype is selected against. Typically occurs when the environment favors both extremes
i. Ex: finches with large beaks are able to crack large seeds, and finches with small beaks can crack small seeds, but the finches with average sized beaks have trouble cracking either the large and small ones

d. Genetic drift – change in allele frequencies due to random events or causes
19. Genetic drift – change in allele frequencies due to random events or causes
a. Bottleneck effect
b. Founder effect

20. Bottleneck effect – a rapid decrease in population size due to a random event

21. Founder effect – a small number of individuals give rise to an independent population

22. Sexual selection is process by which there is an accumulation of traits as different characteristics result in the success or failure in attracting a mate and therefore reproducing. Sexual dimorphism is when a male and female organism of he same species look different

23. Modern evidence for evolution
a. Fossil records – the study of the comparisons between structures of organisms based on their fossil
b. Biogeography – study of the distribution of organisms over the world
c. Comparative morphology (analogous vs. homologous structures) – similarity between species give signs of common ancestry, called homology. Also, similarities in different organisms where they are different but share the same function are analogous structures
d. Embryology – study of the development of different species
e. Molecular comparisons (DNA and protein sequences)¬¬ – the studying of DNA sequences of organisms. The hereditary background of an organism is documented in its DNA and proteins encoded there

24. Macroevolution – is the study of genetic changes over a long period of time; how a new species arises (speciation)
Speciation – it is the creation of new species from genetic divergence. Occurs when there is no gene flow between populations and results from reproductive barriers

25. Biological concept of species: was proposed by Ernst Mayr in 1942. Defines a species as a group of individuals that have the potential to interbreed in nature and produce fertile offspring. Classifies species based on reproductive success

26. Genetic divergence – the creation of a new species that branched out from an existing species and was developed through reproductive isolation. It is affected by gene flow because there must be a gap between the new and old species for the new species to mature and develop.

27. Reproductive isolation: prevents genetic exchange and maintains the gap between species by keeping them from breeding.
a. Prezygotic isolation: reproductive isolation that occurs before conception or the development of a zygote. The types are:
i. Temporal – breeding occurs at different times or different places (ex. Western and eastern skunks)
ii. Habitat – species live in the same area but in different habitats (ex. Water and land garter snakes)
iii. Behavioral – species court one another using specific rituals, but different species share little or no attraction (ex. Different species of fireflies light up at different rhythms)
iv. Mechanical – male and female reproductive parts are not compatible (ex. Insect species have a unique and complex reproductive structure)
v. Gametic – where the sperm is unable to fertilize or survive in the egg (ex. Sea urchin fertilization)
vi. Geographic – where there is a physical barrier keeping the two species apart (ex. A highway prevents interbreeding between two different snail species)
b. Postzygotic isolation: reproductive isolation that occurs after conception and the development of a zygote. The types are:
i. Reduced hybrid viability – most hybrid offspring do not survive (ex. Hybrid between salamander species)
ii. Reduced hybrid fertility – hybrid offspring are sterile (ex. The mule, hybrid between horse and donkey, is sterile)
iii. Hybrid breakdown – first generations of hybrids are fertile and viable, but their offspring are not (ex. Species of cotton plants)

wow go carlos!

thats my puerto rican