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What is Spontaneous generation?

Study Guide Test One 

I. History of Genetics

A. The relationship of Science to Society- Science an shape and drive  social ideas, but society can limit science by determining what is  ethical or not (ex. Stem cells)

B. Humans first genetic usage occurred when we domesticated animals  for transportation, hunting, and livestock. To get the best product (of  both animals and plants), humans used genetic manipulation, which is the recognition of the most desirable traits and using that information  to breed ideal generations.

C. Theories of Heredity

 1. Spontaneous generation- the formation of living organisms without  the presence of parent organisms in s sterile environment

 2. Preformationism- also known as Ovism; organisms develop from  smaller versions of themselves; ex. A tiny man located inside a  sperm

 3. Pangenesis- every organ of the body releases tiny fragments of  itself (called gemmules), which accumulate in reproductive organs  4. Evolution by Nature Selection- over time, certain traits of  organisms increase or decrease in occurrence based on the ability  to survive in their given environment

What is Preformationism?

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Don't forget about the age old question of To find the probability that exactly 25 of the computers will require repair, one would use what type of probability distribution?
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 5. Lamarckism- an organisms can pass characteristics it has gained  through its lifetime to its offspring; additionally, if a characteristic is not used, it will slowly be lost over time

 6. Epigenesis- the embryo is not pre-formed in the sperm or ovum;  instead, the embryo is formed and developed during reproduction  and will be susceptible to environmental factors after 8 weeks II. Introductory Vocabulary

 A. Genetics- the branch of biology that deals with heredity and trait  expression

 B. Heredity- the transmission of traits through the passing of alleles

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 C. Expression- the conversion of genetic information into actual  characteristics

D. Life- a complex organism with the ability to convert energy, respond  to stimuli, tend towards equilibrium, and must have a biological  requirement (such as a nervous system or respiration)

What is Pangenesis?

 E. Macromolecules- large molecules that are found in all living cells and  are the building blocks of cells ; Comprised of C, N, P, O, H, and S 1. Carbohydrates- provide energy and support  If you want to learn more check out cardiorespiratory endurance def

2. Lipids- provide support, energy, and insulation

3. Nucleic Acid- controls all cellular activities (DNA and RNA) 4. Proteins- many functions such as metabolism and transport III. Structures and Properties of DNA

 A. Steps of discovery that led to the final accurate configuration of DNA  1. Comprised of sugar, phosphate, and base

2. DNA is the molecule of heredity

3. Stacked base composition Don't forget about the age old question of clayton state university nursing

4. Base ratio is the same for Guanine to Cytosine and Adenine to  Thymine

5. DNA has a crystal structure

6. DNA is a helical shape

7. DNA attracts water molecules

8. Phosphates are on the outside of the helix (where water can get to  them)

9. How many bases are in a twist

10. The diameter

11. Shape and distance of the bases

IV. Chemical Composition of DNA

A. Nucleotide composition If you want to learn more check out chem 365 sdsu

 1. Nitrogenous base 

a) Purine- a two rigid heterocyclic base

(1) 9 atom structure

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(2) Adenine and Guanine are purines 

b) Pyrimidine- a single ringed base

(1) 6 atom ring

(2) Thymine (DNA only) and Cytosine and Uracil (RNA only) are  pyrimidines

 2. Sugar 

a) Deoxyribose (DNA)

(1) Carbons are numbered, starting with the carbon on the right  of the molecule, going clockwise to the fourth carbon on the  ring, then the fist carbon branching from the fourth 

(2) Deoxy- lacks an oxygen on the 2’ Carbon

b) Ribose- RNA (has an oxygen off 2’)

 3. Phosphate 

a) Phosphoric acid located off the 5’ carbon

 b) Phosphodiester bond- holds the nucleotides together from the 5’ carbon of one sugar to the hydroxyl group off 3’ of another  sugar (comprised of the phosphates)

 4. Difference between Nucleoside and Nucleotide- nucleosides lack  phosphoric acid (has 2’ in the name) and nucleotides have  phosphoric acid (has 2’ and 5’ in the name)

5. N-glycosidic bond- holds the base to the sugar (on the 1’ carbon)  a) Anti configuration- large carbon ring on the outside of the sugar  b) Syn configuration- most of the large carbon ring is located in the middle and over the sugar  

B. Two Nucleotide Chains

1. Double helix

2. Anti-parallel 

a) One strand’s phosphodiester bonds go from 3’ to 5’, while the  other’s go 5’ to 3’

b) 3’ side begins with the OH off the 3’

3. Base Pairing

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a) Bases linked by hydrogen bonds between oxygen and nitrogen  atoms

b) Purines aways bond to pyrimidines 

 c) Adenine to Thymine- 2 hydrogen bonds  

d) Guanine to Cytosine- 3 hydrogen bonds (stronger than the AT  bond)

e) Because the base pairs are pseudosymmterial (all H bonds are  the same length), that gives DNA the ability to “stack” them I. Physical Structure of DNA 

A. Bases are projected at right angles to the phosphate-sugar backbone  (perpendicular)

B. Bases are not perfectly co-planar and flat- slight shift in the planes  when stacked caused by energetically non-compatible hydrophobic  interactions, cause partial overlap helping to cause twisting of the DNA (results in hydrogen bonds with slightly different lengths

C. Because of base pairing, shift in backbone structure as well results in  twisting of DNA

D. IF deoxyribose sugars attached 180degrees to each other- would have  similar sized grooves

1. However, it is not flat 

2. Results in major grooves and a minor grooves (where proteins  interact with DNA)

3. Major groove side 

4. Minor groove side 

E. Three main forms of DNA structures- all are double stranded, have  bases pointed inwards, and strands are antiparallel and complimentary  1. A-DNA 

a) Dehydrated for of DNA- bases are not stacked, they are tilted b) Wider and shorter than the B-Form 

c) Often found in replication 

 2. B-DNA 

a) Right handed helix 

b) Hydrated form of DNA- contains H2O molecules 

 3. Z-DNA 

a) Left handed helix 

b) Zig-zag pattern of structure 

4. Not individual molecule structures; forms just found at different  locations

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 II. Replication- duplication of our genetic information 

A. Cell division- process where a parental cell divides into two or more  ought cells

1. Cell size is limited due to the ability of the cell to transport food and oxygen from the cell membrane to the interior of the cell

2. Surface area : volume ratio == outside of the cell unable to keep up with the inside because the inside grows at a faster rate 

B. Replication process- ensure that each cell in an organism has a  complete and correct copy of the organism’s genome or genetic data,  not just half the DNA present in the parent cell

1. G0- resting phase/ cell senescence 

2. G1- growth phase; cell increases in size and prepares for DNA  synthesis

3. S- DNA replication  

4. G2- growth phase; cell increases in size and prepares for mitosis  and cell division

 5. Mitosis- cell growth stops and cell divides into two daughter cells;  PMAT 

C. Three different mechanisms proposed for replication 

1. Semi-conservative model- the double stranded DNA contains one  parental and one daughter stand following replication (Watson and  Crick’s model)

2. Conservative model- both parental stats stay together after DNA  replication and the daughter molecules contain all new nucleotides 3. Dispersive model- parental and daughter DNA are interpreted in  both strands  

a) consists of old and new stands 

b) consistent with “crossing over” 

c) Randomized process 

4. Meselson-Stahl Experiment (1958) 

a) Analyzed E .coli 

b) Added an extra neutron to all nitrogenous bases in DNA by  growing them in N15 culture; compared them to some grown in  N14 (original nitrogen consistency in E coli)

c) After the N15 E coli replicated, they recognized two different  types of stands in one DNA molecule  

 d) After that, all of the strands created were N14; therefore, one  can come to the conclusion that the parent stands are passed

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down to F1, which then go to F2, and so on == Semi

conservative 

e) DNA replication- use of an existing strand of DNA as a template  for the synthesis of the new identical strand

f) It takes E.coli less than an hour to copy approximately 5 million  base pairs in a single chromosome and divide into two identical  daughter cells

g) A human cell can copy its 6 billion base pairs into daughter cells  in only a few hours

h) Process is remarkably accurate with only about one error  occurring every 1 billion nucleotides- high fidelity 

D. Four major stages of replications: 

 1. Initiation 

a) Origin of replication (OriC in bacteria) 

(1) AT rich regions 

(2) DNA-A proteins will wind to DNA at origin sites; forms a  complex of proteins called boxes; this can cause stress on the DNA, causing it to open up at weak A+T bonds

(3) GATC methylation sites 

b) Initiator proteins- origin binding proteins 

c) Replication bubbles 

d) Replication occurs 

e) Replication forks 

f) Replication occurs bidirectionally  

2. Unwinding of dsDNA strand 

a) Topoisomerase- (gyrase) massages the DNA, making it relax b) Helicase- causes the DNA to separate, unwinding it by breaking  hydrogen bonds between paired nucleotides

c) Single strand binding proteins- keep the DNA from closing back  up; stabilizes ssDNA until elongation begins

 3. Primer Synthesis 

a) Primase- RNA polymerase that adds a ribonucleotide primer to  ssDNA

b) Primers- typically 10-12 bases in length; as soon as DNA  polymerase binds to it, it removes itself from the original strand  and is replaced with DNA nucleotides  

 4. Elongation

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a) DNA polymerase- enzymes that catalyze attachment of  nucleotides to make new DNA during replication; multiple types,  but pol 3 is most important

(1) DNA pol 1- removes RNA primer 

(2) DNA pol 3- responsible for most of the replication process (3) DNA pol 2, 4, 5- repairs DNA 

b) Limitations 

(1) DNA polymerase can only synthesize DNA in 5’ to 3’ direction (2) DNA polymerase cannot initiate DNA synthesis by itself;  requires addition of RNA primer 

c) Watson and Crick model 

(1) 2 stands of DNA 

(2) Run anti-parallel to each other 

(3) Sugar phosphate backbone- hydrophilic sugar and phosphate  backbone on the outside with nitrogenous base inside  

(4) Nucleotides joined by phosphodiester bonds (5’C to 3’C) (5) AT and CG bas pairing  

d) Process 

(1) New DNA is synthesized from deoxyribonucleoside  

triphosphate (dNTPs- contains 3 phosphate similar to ATP, but also has a sugar and a base) 

(2) The 3’-OH group of the last nucleotide on the strand attacks  the 5’-PO4 group of the incoming dNTP

(3) Two phosphates are cleaved off of the incoming dNTP,  

releasing energy used to bond the next step

(4) A phosphodiester bond forms between the two nucleotides  (5) The leftover phosphate ions are released 

e) Summary 

(1) Semi-conservative (one parental strand and one daughter  strand)

(2) Bi-directional (both parental strands are replicated at the  same time)

(3) Leading strand synthesis 

(a) As the helicase opens the DNA, DNA pol 3 follows on the 5’ strand of the parent

(b) DNA pol 3 begins the on the new strand’s 5’ side at DNA  pol 1 and moves towards the 3’ side (towards the helicase) (4) Lagging strand synthesis

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(a) DNA polymerase moves away from the replication fork 

(b) Pol 3 does not attach to double stranded DNA 

(c) DNA ligase joins the newly synthesized DNA strands by  creating a covalent phosphodiester bond

(5) Proofreading 

(a) High fidelity- mistakes are very rare (1 in every 10^8  

bases)

(b) Reads the intensity of the bond 

(c) Recognizes instability of is matched base pairs 

(d) Configuration of DNA pol active site 

(e) proofreading/exonuclease activity of DNA pol 

E. Prokaryotic vs. Eukaryotic replication 

 1. Prokaryotic 

a) Single circular plasmid DNA 

b) Circular DNA- one origin 

c) DNA free in cytoplasm- easy access 

 2. Eukaryotic 

a) Multiple large linear chromosomes 

b) Linear DNA- multiple origin sites 

c) DNA tightly packed around histone proteins 

d) Telomeres- complex of repetitive DNA and proteins found at the  terminal ends of eukaryotic chromosomes

(1) Small piece of DNA that never gets turned into a double  strand at the very end of strands

(2) Telomerase fills in the holes with the correct nucleotides F. KEY FACTS 

1. KNOW THE ENZYMES 

2. REPLICATION ONLY OCCURS ON SSDNA 

3. REPLICATION ALWAYS OCCURS IN 5’-3’ DIRECTION 

4. REPLICATION IS SEMI-CONSERVATIVE 

5. REPLICATION IS BI-DIRECTIONAL 

III. Mendelian Genetics 

A. Intro 

1. Key Vocab 

a) True breeding/pure breeding- breeding the same homozygous  parents, creating a known control

b) Reciprocal cross- cross between the male of one strain or trait  with the female of another strain or trait, and vice versa

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c) Self cross- crossing one parent with another parent with the  same allele combination, ex. Aa x Aa

d) Filial generation- the first generation of offspring, represented as  F1

e) Dominance- the characteristic of a gene that masks the  presence of the other allele  

f) Probability method- finding the probability of some event  described using the Multiplication Rule (used when independent  events, like multiple characteristics, occurring together are  calculated by multiplying their probabilities) and the Addition  Rule (the addition of independent probabilities in order to find  any one of multiple exclusive events) 

g) Gene- particle of inheritance/DNA sequence (no such thing as a  dominant gene, just a dominant trait) 

h) Allele- alternative forms of a gene (R vs. r) 

i) Locus- physical location of any gene on a chromosome 

j) Loci- physical location of any two or more genes on a  

chromosome

k) Genotype- combination of alleles an individual has (ex. RR, Rr,  rr)

l) Phenotype- physical appearance of a trait (ex. Round, wrinkled)  m) Homozygote- individual having the same alleles (RR or rr) n) Heterozygote- individual having different alleles (Rr) 

o) Mendel’s First Law- Segregation of Alleles; every individual has  two alleles for a trait (diploid). During formation of gametes, the  alleles separate and offspring randomly receive an allele from  each parent.  

p) Mendel’s Second Law- Independent Assortment; during gamete  formation, when two or alleles are inherited, individual alleles  assort independently of one another giving different traits an  equal opportunity of occurring together  

q) Mendel’s Third Law- Idea of Dominance; the trait from one allele  will mask the trait of another allele

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r) Monohybrid Cross- mating between two individuals with different alleles at a single locus/for a single trait/for a single allele (from  each parent)

s) Dihybrid cross- crossing two sets of traits 

t) Mendel’s Big Six Crosses 

B. Meiosis  

1. Intro 

a) Chromosome Theory of Inheritance- correctly explains the  underlying mechanism of Mendelian genetics by combining  chromosomes with the paired facts postulated by Mendel

b) Genes are located on the chromosomes, which are what passed  to the next generation 

c) Homologous chromosome- paired chromosomes having genes  

Parent’s Alleles

Name

Genotype

AA x AA

Pure A

All AA

aa x aa

Pure a

All aa

AA x aa

Parental

All Aa

Aa x Aa

F1 cross

1 AA : 2 Aa : 1 aa

Aa x aa

Backcross recessive

1 Aa : 1 aa

AA x Aa

Backcross dominant

1 Aa : 1 AA

Phenotype 

All AA (Dom.) All aa (Rec.) All Aa (Dom.) 3 Dom. : 1 Rec. 1 Dom. : 1 Rec.  All A_ (Dom.)

for the same trait located at the same place on the chromosome (1) Genes are in the same order in the same place

(2) The two chromosomes in a homologous pair are NOT always  identical to each other (can be a heterozygous combo or  homozygous combo)

d) DNA Replication

(1) Cell Cycle- series of events that take place in cells leading to  cell division and DNA duplication

(2) Mitosis- when one cell divides and form two IDENTICAL cells (a) Interphase Prophase Metaphase Anaphase Telophase

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(b) Cytokinesis- process during cell division when the  

cytoplasm of a single cell is divided to form two daughter  

cells

(c) 2n => x2 (2n)

(3) Meiosis- process in which the number of chromosomes in a  cell is halved during the production of germ cells (gametes) (4) Type of cell division that reduces the number of chromosomes in the parent cell by half and produces four reproductive cells  2. Consists of two successive nuclear divisions (look at picture below) a) Meiosis I (2n)

 (1) Prophase I 

(a) Takes a diploid cell and goes through replication, creating  exact copies in sister chromatids 

(b) Sister chromatid from mother and sister chromatid from  father (homologous chromosomes) overlap each other in  

the middle of the cell, called crossing over 

(c) Tetrads- two homologous chromosomes

(2) Metaphase I

(a) The homologous chromosomes pair up along the middle of  the cell

(b) How each pair of homologous aligns and separates is  

independent and random  

(3) Anaphase I

(a) The tetrads split open

(b) The sister chromatids go to opposite sides of the cell,  

notice that the chromosomes randomly pick a side to go to (4) Telophase I

(a) The cells split apart

(b) First meiotic division ends with two daughter cell, both  haploid (n)

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(5) Results- two haploid daughter cells, each with half the  

number of chromosomes as the original 

b) Meiosis II

(1) Prophase II  

(2) Metaphase II  

(3) Anaphase II  

(4) Telophase II

(5) Result- four haploid gametes

c) Overview

(1) If a cell has TWO pairs of chromosomes [A and a; B and b]… (a) n= # of chromosomes (2)

(b) 2^n=number of possible arrangements  

(2) If a cell has 23 pairs of chromosomes (like humans)

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(a) Four gametes have the ability to produce 2^23 kinds of  gametes= 8 million

(b) Fertilization= 2^23 x 2^23= 70 trillion possible zygotes (3) Purpose

 (a) Maintain a constant number of chromosomes within a  

species 

(b) Genetic variation in a species

i) Random allele assortment

 ii) Crossing over (genetic recombination) 

(4) Crossing over 

 (a) Occurs between homologous chromosome pairs (non-sister chromatids) (one mother and one father chromatids) 

(b) Occurs during meiosis (prophase I)

(c) Not that rare, happens pretty frequently

(d) The chromatids are under such high pressure, it becomes  easy for them to break off and join the other chromosome

(5) The behavior of chromosomes during meiosis provides us the  physical basis for explaining Mendel’s results: shows how  

meiosis fits in Mendel’s work  

C. Allelic Interaction- how individual alleles interact with each other  1. A GENE only gives the potential for the development of a trait 2. Mendel got lucky with his pea plants because the traits he heavily  analyzed were independent of each other

3. Most genes do interact with some other gene- actually it is the gene products (traits) that interact with one another 

4. Menelian Inheritance patterns obey two laws

a) Law of Segregation- it is totally random where the allies go once  lined up in the metaphase plate during meiosis  

b) Law of Independent Assortment- different alleles come from  different parents, causing different traits in their offspring

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5. Involves a single gene with two different alleles, and those alleles  usually code for proteins  

6. Incomplete dominance- blending of traits 

 a) Expression of the heterozygote phenotype forms an intermediate that is distinct from either parent 

b) Intermediate inheritance- combination of phenotypes

c) Neither all is completely dominant over the other

d) Ex. snapdragons: RR=red petals and rr=white petals =>  Rr=pink petals

e) Since there are two distinct phenotype, you can use two different allele notations (RW= pink)

f) Expression of the heterozygote phenotype forms an intermediate that is distinct from either parent

 g) The code for the protein will always be there, it is just a matter if  it is defective or not 

h) The amount of red pigment present is dependent on the amount  of enzyme present, which is dependent on the number of wild  type copies of the gene= dosage effect 

7. Codominance- the presence of both alleles represented at original  level, but only partly shown 

a) Neither phenotype masks the other

b) Ex. Red and white petals

 c) The amount of color pigment present is dependent on the  amount of each enzyme present, which is dependent on the  number of copies of each gene 

d) No dosage effect  

e) Two traits “show” ex. Spotted horses

8. Pleiotropy- alleles of pleiotropic genes are transmitted the same  way as alleles of single trait genes; a single allele affecting more  than one trait 

a) Mendel recognized this among his plants

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 (1) A Purple (P_) flowered pea plant had brown seed coats and  red axils 

 (2) A white (pp) flowered pea plant had no seed coat color and no axil color 

b) Example: Marfan syndrome- a dominant/recessive disorder of  connective tissue

(1) rr= Marfans  

(2) Defect in the protein Fibrillin that affected scaffolding proteins (3) Scaffolding proteins allow connective tissue to form, affecting  many things

(a) Heart problems due to enlarged aorta

(b) Extra long phalanges and appendages

(c) Eye disease

c) Antagonistic pleiotropy- a single allele (gene) can cause  competing effects, some beneficial and some deleterious to the  organism 

(1) Ex. P53- tumor suppressing gene

(2) On the upside, it prevents cancer cells from dividing, resulting in decreased tumor formation

(3) On the downside, it prevents stem cells from dividing,  

preventing the body from replacing damaged tissue during  aging

9. Recessive lethal allele- alleles that are lethal when expressed in  homozygous form but allow survival when expressed as a  heterozygote

10.Dominant lethal allele- alleles that are lethal when expressed in  either homozygous or heterozygous form  

a) A true dominant lethal allele would only last a single generation a) Only the recessive form would be passed to subsequent  generations

a) How do Dominant Lethal genes exist?

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(1)Genes cheat-  

(a)Delayed expression of the gene product

i) ex. Huntingtin Disease

ii) Mutations develop over time

(b)Conditional expression of the gene product

i) Lethality under one condition (the restrictive or non  

permissive condition) but not another (the permissive  

condition)

ii) Sometimes it has to be very hot or very cold to activate  the gene

iii) Invisible genes

iv) Triplet genetic code  

v) Nonsense codons

a) Penetrance- proportion of individuals carrying a particular allele  or gene that also express the associated phenotype  

(phenotype=death for lethal alleles)

(1) Complete penetrance- every instance of the mutant allele will  result in phenotypic symptoms of the condition; aka death (2) Incomplete penetrance- phenotypic symptoms are not always  present in individuals who have the mutants allele  

(a)BRCA 1- females with a mutation in this gene have an 80%  chance of developing breast cancer (but 20% of not  

developing breast cancer)

I. Multiple Alleles

A. Simple Dominance- in the F1 cross, the dominant allele covers up the  recessive allele

B. Incomplete Dominance or Codominance- both alleles are shown in  some form or fashion

C. What if you have four possible phenotypes for a specific trait?- Multiple alleles are involved 

1. More than two alleles for that trait must exist in the population

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2. Only two alleles per individual 

D. A B O Blood Type- controlled by three alleles  

1. Type A, type B, type AB, type O

2. Types A, B, and AB have specific proteins on them  

3. Antibody B are in Type A blood and they kill of anything with B.  Additionally Type B blood has Anti-A.  

Blood Type

Genotype

Can be written as…

Type A

I^A.I^A or I^A.i

(AA or AO)

Type B

I^B.I^B or I^B.i

(BB or BO)

Type AB

I^A.I^B

(AB)

Type O

ii 

(OO)

4. Type O- universal donor because it will not be attacked by any  antibodies

5. Relationship of A or B to O- dominance  

6. Relationship of A to B- codominace  

7. Rh factor- specific antigens on the surface of red blood cells;  represented as a + or -; + blood has anti- bodies and - blood has  anti+ bodies

Blood Type

Genotype

Type A+

I^A.I^A Rh+_ or I^A.i Rh+

I^A +

Type AB-

I^A.I^B Rh- Rh

Type O-

ii Rh- Rh

a) 

8. Dominance- Rh+_ : Rh- Rh

9. Mn Cell Surface Antigen- specific antigens on the surface of red  blood cells (protein represented as L) (there are always two alleles,  they just might be the same) (M to N relationship is codominance)

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a) Type AL^M= I^A.I^A.L^M or I^A.i.L^M 

b) Type ABL^MN= I^A.I^B.L^MN

E. Problems

Mother

Child

Accused Male

Eliminated

Type A+

Type O+

Type AB+

Yes, the male must  have an O allele

Type A+

Type AB+

Type O+

yes, the male must  have a B allele

Type O-

Type A+

Type O-

Yes, the father must  have an A allele

Type A+

Type O-

Type B+

No, the parents could have a recessive O  allele

Type AL^MN

Type BL^N

Type BL^M

Yes, the father must  have the N allele

1. In the following cases of disputed paternity, indicate if the accused  male should be eliminated as a possible father to the child. 2. A couple decides to have a child together together. Their genotypes are listed below. What is the probability that their child will be Type  A+L^M

a) Dad- A B; Rh+ Rh-; L^M.L^N (Aa, Bb, Cc)

b) Mom- A B; Rh+ Rh-; L^M.L^N (Aa, Bb, Cc)

c) Probability

(1) 1/4 probability the child is Type AA

(2) 3/4 probability the child is Rh+__ (Rh is simple dominance) (3) 1/4 probability the child is L^M L^M

(4) Result: multiple the probabilities- 3/64