AP Biology Notes

Unit 1: Chemistry of Life

Unit 2: Cell Structure and Function

Unit 3: Cellular Energetics

Unit 4: Cell Communication and Cell Cycle

Unit 5: Heredity

Unit 6: Gene Expression and Regulation

Unit 7: Natural Selection

Unit 8: Ecology

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Unit 5: Heredity

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LIFE CYCLES

Sexual Life Cycle: alteration of halving and doubling chromosome count in each generation

Meiosis: halving chromosome count in testes and ovaries to make sperm and egg, makes germline cells (all about halving chromosomes and creating variation)

Fertilization: doubling chromosome count, sperm meets egg, creates a zygote

Every single life cycle contains both of these events

but only applies to organisms that reproduce sexually with male and female, not asexuals who require only mitosis (no variation, with redwoods or hydras) without a mate, so without mutation there is no evolution. Asexual reproduction keeps species going without available mates

Haploid (n): cells with half of the number of chromosomes (sperm and egg/ova)

Gametes: sperm and egg created thru meiosis

Diploid (2n): cells with two sets of chromosomes

Number of chromosomes varies per species

Somatic Cells: (normal) body cells, that have 46 chromosomes, half from mom half from dad, really 23 pairs of chromosomes

Each pair is a homologous pair, NOT sister chromatids, each chromosome is duplicated, two sister chromatids on either side of the X held together by a centromere. Homologous means they have the same genes located in the same regions not necessarily the same versions of the genes

Allele: different versions of the same gene

Locus (loci): exact location of a gene on a chromosome

Karyotype: picture showing 23 pairs of chromosomes (only visible in mitosis because of condensing)

Autosomal pairs (22): all of the genes for normal traits

Sex chromosomes (23rd): XY male and XX female

What changes for organisms to organism, one or the other, either diploid or haploid stage is dominant

Animals are mainly diploid because their body cells are somatic and not germline

Fungi usually haploid with only one set of chromosomes, can’t cut one set of chromosomes in half so they do not have meiosis use mitosis is reproduce asexually to make haploid spores (like a gamete but do not fertilize each other) spores find a good environment and grow into a new fungus (everything is haploid and no variation)

However, if two fungi come into contact, they will fertilize each other to produce a zygote, and then goes thru meiosis to produce more haploids for variation (evolution)

Plant Life Cycle:both haploid and diploid split equally there is no dominant stage, for every species of plant there is a haploid and diploid form of that plant

Alternation of generations: one gen is haploid and the next may be diploid, it flips every gen

Sporophyte:diploid (2n) generation of a plant, (e.g. ferns that we usually see), goes through meiosis next → produces haploid (n) spores

Gametophyte: spores grow into a haploid (n) generation, produces GAMETES BUT THRU MITOSIS (sperm + egg) that create a zygote to reenter the sporophyte stage: haploid egg + haploid sperm = diploid plant

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MEIOSIS

Meiosis I: chromosome number is cut in half

Two types of meiosis: I and II

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Only germline cells go thru mitosis (ovum and sperm) but ova are already produced at birth, whereas sperm is produced all thru a male’s lifetime

Prophase I: mitotic chromosomes form, nuclear envelope disappears, spindle fibers reach out (e.g. four total chromosomes and 2 homologous pairs)

Homologous pairs have the same gene in the same place (locus) one from dad and one from mom

Tetrads: homologous pairs come together (4 sister chromatids) during PROPHASE I

Chiasma: where the homologous pairs overlap, the pairs exchange pieces of chromosomes, through crossing over important to create genetic variation

The areas that cross over are completely random

Metaphase I: tetrads line up on the equator of the cell using spindle fibers, not like mitosis, they line up in their homologous pairs, but in mitosis has the chromosomes lined up single file not in pairs

Anaphase: cell splits in half

Meiosis I: 2n diploid parent splits to two n haploid daughters

Meiosis II: anaphase II the sister chromatids are pulled apart

End with four haploid variable gametes

VARIATION

Genetic recombination: put back together after mixing the genes “genetic lottery”

Crossing Over: in meiosis

Independent Assortment of Chromosomes:

Pairs that line up in metaphase determines the combination of chromosomes that end up in the gametes, completely random order of lining up

2# of homologous pairs=number of possible combinations(typically 8M combos)

Random Fertilization: random chance decides which sperm gets to each egg

Each sperm is 1/8M combos and each egg 1/8M combos, each person is 1/64 trillion combos, not even considering crossing over events

All new variation came about/created from mutation at some point, but a limited role in genetic variation, variation is about mixing up preexisting genes

MENDELIAN GENETICS

Gregor Mendel: Austrian monk who is the father of modern day genetics

Worked with Pisum satium plant

Came up with laws of inheritance based off pea plant experiments

Characters: big overarching things (color, height, shape, etc.)

Trait: different form of a character (tall, short, blue, yellow)

Controlled which pea plants breed with other pea plants, or he self-pollinated and bred the pea plant with itself

Self-bred pea plants became purebred/true breeding, 100% the same organism without any variation

Mendel’s First Cross:

P generation: Parental generation, crossed a purebred purple with a purebred white plant

People used to believe in blending inheritance: traits are mixed so tall person mates with short person would equal a medium height baby

F1 generation: created only purple plants, traits didn’t blend, so it proves blending inheritance wrong

Hybrids: combination of two organisms, half-purple and half-white

F2 generation: bred purple hybrids and created 75% purple and 25% white flowers

Traits do not blend together

Traits can be hidden and come out in a later generation

Genotype: genetic makeup of an organism containing all of the alleles

Homozygous Dominant

Heterozygous (shows Dominance)

Homozygous Recessive

Phenotype: the physical appearance

If someone has a dominant phenotype, you cannot figure out the genotype, either AA or Aa

Dominant (heterozygous, homozygous dominant)

Recessive (homozygous recessive)

One allele cannot suppress another allele, every allele is always expressed

AA making correct proteins → dominant trait

Aa making enough correct proteins → dominant trait

aa making defective proteins → recessive trait

Don’t need two functioning alleles, only one is necessary

Mendel’s LAWS OF INHERITANCE:

Laws of Segregation: for every character there are two different forms/versions called alleles (two different versions of a gene, but Mendel didn’t know that)

During formation of gametes, the two alleles for each character separate. (During anaphase)

Each gamete gets one of the alleles randomly

Homozygous: (same) two of the same allele are inherited

Heterozygous: (different) two different alleles are inherited

One allele will be expressed → dominant

One allele will not be expressed → recessive

Punnett square demonstrates that two alleles from one character (for example Aa) segregate and can match up with the other parent’s segregated alleles to make percentages of possible combinations

Genotypic Ratio: 1:2:1 if (AA, Aa, Aa, aa) homozygous dominant:heterozygous:homozygous recessive of the possible combinations

Phenotypic Ratio: 3:1 dominant(D):recessive(R) expressing of the possible combinations

For dihybrids, the ratio is D/D : D/R : R/D : R/R

Double Heterozygous (AaBb) x Double heterozygous = 9:3:3:1

Double Heterozygous x Double homozygous (aabb) = 4:4:4:4

Double Homozygous x Double homozygous = 0:0:0:16

Law of Independent Assortment: inheritance of one character doesn’t affect the inheritance of another character, each is inherited independently

Each pair of alleles segregates into gametes independently

ASSUMES EVERY GENE IS FOUND ON A DIFFERENT CHROMOSOME

E.g. brown hair doesn’t mean you’ll get brown eyes

Dihybrid Cross: a cross involving two characters to find all of the possible allele results (16 squares, there are also trihybrid crosses with 64 square and quadra hybrid crosses) (SEE PHOTO ON GOOGLE DRIVE)

Testcross: find out the unknown dominant allele that corresponds with the dominant phenotype of an organism

Cross the dominant organism with a homozygous recessive organism, if any of their offspring are recessive, then the dominant organism is heterozygous (Bb) because you need a recessive copy from this parent in order to have recessive (bb) offspring.

Rule of Multiplication: likelihood of multiple genetic events happening consecutively which depends on the individual likelihoods of each individual event.

E.g. have four male children in a row = 6.25% chance, because each child is a 50/50 chance, so ½ * ½ * ½ * ½ = 1/16

Complete Dominance: simple dominance, one allele is expressed over another allele BUT not all characters are completely dominant

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Incomplete Dominance: one allele is not dominant over the other, you cannot use capital and lowercase letters (GREY OR PINK)

The heterozygote is an intermediate phenotype (sort of like blending == pink) half way between the two alleles

Codominance: both alleles are equally expressed (both red and white) it creates spots on organisms only thing that really exists at the level of the protein

BLOOD TYPES: use multiple alleles to decide type, but only inherit two alleles like normal

A allele (I^A)

B allele (I^B)

O allele (ii)

O is recessive to both A and B, but A and B are codominant

Phenotypes:

Type O: OO

Type A: AA, AO

Type B: BB, BO

Type AB: AB (codominance)

If you’re blood type A you have A antigens (glycoprotein MHCs) on blood cells, if you’re blood type B you have B antigens, if you are blood type AB you have both A and B antigens, and if you are type O then you have no antigens

You have antibodies that fight off foreign blood, if type A, you have B antibodies, if type B you have A antibodies, if you are type AB, you have no antibodies, bec. You would target your own cells with A or B antigens, and if you are blood type O you have A and B antigens

O is the universal donor because it has no antigens, cannot read blood type O as being foreign, AB is the universal receiver because it has no antibodies to detect and fight off foreign blood

RH Factor: important antigen another way to detect foreign blood, either positive (+) if you have it or negative (-) if you don’t

O negative is the real universal donor because it’s an extra antigen on cells

AB positive is the true universal receiver because it has no RH factor

RH factor is controlled by complete dominance you can only be RH negative if you’re are (nn, but if you’re Nn or NN) you’re positive

Do not need to have the same blood type as your parents

In reality the only type of dominance that exists at the molecular level is codominant (two different alleles, half of one protein and half of another)

Two characters control blood type, A/B/O and RH

Pleiotropy: when one gene has multiple phenotypic effects (most human genes are pleiotropic)

E.g. PKU, caused by a single gene, causes severe mental impairment and reduced skin pigmentation (gene involved in skin and in brain, does multiple things in the body) Most genetic diseases have multiple effects

Epistasis: when one gene directly affects another gene

E.g. one gene B/b in mice determines if fur coat is brown or black, another gene determines if B/b pigment is deposited in skin if homozygous recessive (cc) for second gene, B/b dominant or recessiveness doesn’t matter → creates albinism

Polygenic Inheritance: multiple genes work together to create a character

Quantitative Characters: characters that vary along a continuum, not caused by one gene, but caused by multiple genes that add up

E.g. three genes produce melanin, if you get two dominant alleles and one recessive, two genes are producing melanin, and one is producing nothing → determines skin color

Any human character that is polygenic, cannot be predicted (like eye color)

Norm of reactions: Environment plays a large role in converting genotype to phenotype, norm is the normal phenotype that goes with a genotype

But sometimes your environment can change your phenotype away from the original norm prescribed by the genotype

Some genes are not affected by the norm of reactions (environment plays no role)

E.g. affects height if you work out too much early on you stunt growth

Multifactorial Character:

E.g. hydrangeas color depends on pH of soil even though they have the same genotype, so color is considered multifactorial

Trait determined by the effects of multiple genes

Pedigree Analysis: information about the presence/absence of a particular phenotypic trait is collected from as many individuals in a family as possible and across generations.

Square is male, circle is female, painted in means they have that trait

Sex-linked trait: genes inherited only on the X-chromosome (males have one X and females have two Xs) only get one allele, males can’t be carriers

Hemophilia: not able to form blood clots

Sex-linked diseases are more common for males because there are less combinations, females get two alleles which one could be dominant good

Male pattern baldness

Muscular dystrophy

Color blindness

DISORDERS

Recessively inherited: must be homozygous recessive

Heterozygotes are disease carriers, you yourself are normal, but carrying a recessive allele that causes the disease and can pass it to the offspring.

Cystic Fibrosis: recessively inherited, caused by a mutated Chloride channel gene

Dominant allele codes for functional protein

Recessive allele codes for a misfolded protein

Heterozygote: dominant allele will make enough correct channels and ignore the bad ones

Homozygous Recessive: no chloride channels work, you have CF

Homozygous Dominant: All chloride channels work

Mucus builds up in your lungs and get choked over time.

Sickle Cell Anemia: mutated hemoglobin gene also recessively inherited

Heterozygotes have the Sickle Cell Trait, can have problems at high altitudes, where there is less oxygen, since you’re making half normal and half defective hemoglobin, so they can have anemia symptoms

Tay Sachs Disease: mutated gene codes for a mutated lipid breakdown protein in the brain, also recessively inherited, but at the molecular level, is incomplete dominance, only digest half the amount of enzymes

Consanguineous Mating:inbreeding, creates diseases because it brings out recessive and bad traits, because you’re more likely to mate two carriers to create recessive expressing bad offspring

Achondroplasia: dwarfism, dominantly inherited

Lethal Dominant (Huntington’s Disease): only need one dominant allele to kill you/make you diseased

Genetic Testing:

Probability: just look if the parents are carriers and find the percentage/likelihood of what the kids might get

Pedigree: use for members of a family to determine who is a carrier of a genetic disease

Genetic Tests: available for over 2000 genes, before having children to find out if you are a carrier

Use gel electrophoresis, run your alleles next to dominant or recessive alleles, if dominant, your fingerprint would match the dominant banding patterns, but if you’re a carrier it would be different that both the dominant and recessive allele.

Fetal Testing: if something in the ultrasound indicates something is wrong, so they test within the uterus, both invasive can cause harm to mom and child

Amniocentesis: (safer) 4-16 weeks into pregnancy, 2nd trimester,

Big needle to go through stomach and into the amniotic fluid in uterus, look at fetal cells in the fluid

Test karyotype → down syndrome?

Genetic tests/ Gele electrophoresis

Chorionic villus sampling (CVS): much more invasive, more potential harm, can be done earlier between 8-10 weeks in pregnancy

Take a piece of the chorionic villus through the cervix

Newborn Screen:

Heel prick: test for PKU (can’t break down amino acid phenylalanine) can cure this if they just put them on a special diet

CHROMOSOME THEORY OF INHERITANCE

Females have two copies of sex-linked genes, and males only have one sex-linked copy

T. H. Morgan: discovered sex-linkage of genes

Flies display white eyes instead of normal dominant red eyes are more common in males

Must be sex-linked, on the X chromosome

Y chromosome is much smaller than the X chromosome

SRY Gene: makes males male, directs development of male anatomical features

LINKED GENES: two genes found on the same autosomal chromosome

***goes against Mendel’s Law of Independent Assortment (every character inherited on its own, but ASSUMES EVERY GENE IS FOUND ON A DIFFERENT CHROMOSOME)

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If two genes are found on the same chromosome, the characters are inherited together

If you have GG, you might also have RR.

The only thing that can separate two genes is when crossing over occurs, only way to separate two genes.

When OBSERVED amounts do not match the EXPECTED offspring phenotypes, → genes must be linked

AaBb x aabb = 4:4:4:4 (1:1:1:1) expected amount

Parental Type: offspring same as the parents

Recombinant Type: offspring different from the parents (nonparental type)

Result of crossing over

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Determine the percent recombination: add up the recombinants 2016+185m = 391, divide by total number of results (2300) = 17% were created through crossing over

Divide percent recombination by 2 to get map unit distance btwn. genes (high map units = high percent recombination)

4:4 arrangement of spores no recom, 2:2:2:2 means recombination

The percent recombination (aka rate of crossing over) is directly proportional to the distance between the two linked genes

If genes are farther apart (either end of the chromosome), there’s more of a chance they will cross over

If closer together, more unlikely to inherit them separately through crossing over

Chromosome/Linkage Map: Percent recombination can be used to create this, provides the locus (location) of each linked gene on a chromosome

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CHROMOSOMAL DISORDERS

Nondisjunction: occurs when chromosomes fail to separate during anaphase I or anaphase II

Both pairs (of sister chromatids or homologous pairs) can go to one side, and the other cell doesn’t have another chromosome

One gamete will have one more chromosome, one will have one less chromosome

Aneuploid: abnormal number of chromosomes

Trisomy 21 (Down Syndrome): 21st pair went thru nondisjunction, would have three chromosomes for the 21st pair (47 chromosomes instead of 46)

Klinefelter’s Syndrome: nondisjunction of the sex chromosomes (XXY - still male, as long as you have the Y chromosome still have SRY gene), have some female attributes → makes them sterile

Wider hips, minor breast development *****lack of (facial/leg) hair*****

When your chromosomes are screwed up you’re always sterile

Turner’s Syndrome: XO (normal female that’s sterile) 45 chromosomes

Cannot reproduce because they don’t have the right number of chromosomes

Barr body: Second X chromosome is inactivated (still have two x chromosomes) turned off through DNA methylation

Sometimes, the one X chromosome can be active, but sometimes the other x chromosome can be active

Males cannot exhibit these features because they don’t have mutually exclusive inactivated chromosomes

Alterations to Chromosome Number:

Crossing over errors:

Duplications and Deletions: caused by the same event, at cross over, one chromosome takes (deletions more harmful) the WHOLE part of the other that crossed over and the other one is left shorter

Cri du chat: cry of the cat, caused by deletion in chromosome 5, have a cat-like cry, severely mentally impaired, microcephaly, die in infancy

Inversion: piece of chromosome that is crossed over goes on backwards, order of the genes matters (not as harmful as a deletion)

Translocation: when two nonhomologous chromosomes cross over which shouldn’t

Chronic Myelogenous Leukemia: caused by unusual crossover of chromosome 9 and chromosome 22; chromosome 22 is translocated a piece of 9 becoming a Philadelphia chromosome

Genomic Imprinting: GOES AGAINST EVERYTHING, sometimes you only use the allele inherited from the mom or from the dad, doesn’t deal with dominance

For IGF (growth factor) gene ONLY the paternal allele is the only one that matters, maternal allele is shut off completely through methylation throughout the body

If you get a bad allele from dad for IGF, you get dwarfism

Same genotype doesn’t even matter

CHI SQUARE ANALYSIS

Tells you if your results are valid or not, determines if genes are linked or not, must do a statistical test; analyzes difference between actual (observed) to expected outcomes, tell you if they are different or the same

EQUATION RETURNS THE VALUE NOT THE PROBABILITY

MUST ADD UP VALUES THEN COMPARE TO THE CHART

You almost never get a perfect ratio (9:3:3:1, e.g.)

Null Hypothesis = H0

NO difference between observed and expected, 27;23 is no different from 25:25 when flipping a coin

Alternate Hypothesis: There is a difference, more likely to flip heads than tails

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x^2: just symbol for chi square, not actually squared

x2=(O-E)2/E

0.05: ALWAYS the cutoff

If value is greater than number that corresponds with 0.05 value, then there IS a difference (alterative hyp.)

If the value is smaller than the number that corresponds with 0.05, then there’s NO DIFFERENCE (null hyp.)

Probability that chance alone creates your results

https://www.youtube.com/watch?v=WXPBoFDqNVk

Degrees of Freedom: number of groups minus 1 (heads, tails - 1 = 1)

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