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TULANE / Biology / BIOL 2050 / Prokaryotes can also have, what?

Prokaryotes can also have, what?

Prokaryotes can also have, what?


School: Tulane University
Department: Biology
Course: Genetics
Professor: Meenakshi vijayaraghavan
Term: Winter 2016
Cost: 50
Name: Final Exam Study Guide
Description: All Notes from the Semester Compiled into Chapter Divisions as Well as Additional Study Sheets of Specific Topics
Uploaded: 04/26/2016
192 Pages 24 Views 9 Unlocks

Overview of Genetics

Prokaryotes can also have, what?

Chapter 1: Overview of Genetics

Scientific Advancements 

Human Genome Project

∙ A General Overview of Facts

o National Institute of Health and the Department of Education  implemented the Human Genome Project from 1990 to 2003

o Haploid set has 3 Billion Base Pairs, so a Haploid Human Cell has 6  Billion Base Pairs

o The Molecule is 2 Meters Long

o Codes for about 20,000 – 25,000 Genes

New Technologies From the Project

∙ 1. DNA Fingerprinting – criminal investigations, parental information,  genetic defects

How does antibiotics work?

Don't forget about the age old question of What type of error will occur if a static method attempts to access an instance variable?

∙ 2. Cloning – advanced organisms

o Dolly the Sheep

o Copy Cat

∙ 3. Genetic Engineering – various applications

o Gene injection for therapy

o Insulin production through animals

o GFP to mice (shows up on skin)

▪ Technique used to identify, sterilize, and eradicate mosquitoes  and stop pesticide use

Genes and Traits 

Important Overview

∙ Gene

o Basic Definition – basic unit of biological information; a functional unit  of heredity

What is the eukaryotic stages?

o More Applicable Definition – segment of DNA that encodes for a  functional polypeptide

o Structural Gene – segment that encodes for a protein Don't forget about the age old question of In biological evolution, how are populations changing through time?

▪ As opposed to RNA encoding genes

∙ Cell Overview

o Definition – basic unit of life (membrane enclosed)

o Macromolecules: Genes code for Macromolecule Production in Cells ▪ 1. Proteins

▪ 2. Lipids

Overview of Genetics

▪ 3. Carbohydrates

▪ 4. Nucleic Acid

DNA’s Properties and Considerations

∙ Central Dogma: DNA ???? RNA ???? Proteins

∙ Proteins and Traits

o Proteins – work horses of the cell; tools of gene expression If you want to learn more check out What stock market means?

o Traits – characteristics an organism expresses; often looking at the  phenotypic expression

∙ Building Blocks

o Nucleotide monomers for a strand

o Two strands are held together by Hydrogen bonding

∙ Additional Pieces

o Histones attach in order to make Chromosomes

o The Chromosomes for the Genome

∙ Accessing DNA

o DNA can only be accessed during gene expression

▪ The process during which information present in genes is used to  change characteristics in an organism

o Transcription – a copy is made into mRNA to be later read and  translated

o Translation – amino acid sequence is encoded in the cytosol


∙ Type of Traits:

o 1. Morphological Traits – a displayed phenotype

▪ Physical appearance

▪ Ex: color of a flower Don't forget about the age old question of What is the purpose of reparation?

o 2. Physiological Traits – the capacity of an organism to function,  mechanisms reliant on genes

▪ Process depends on genes and propagates life

▪ Ex: Cellular Respiration

o 3. Behavioral Traits – a behavioral response contingent on a genetic  pathway

▪ Response to a given environment

▪ Ex: mating calls

∙ How Does Molecular Composition Affect Traits? – The Butterfly Example o Color in the wing is contingent on the translation of pigmentation o Gene Classes with Traits:

▪ Normal Gene – makes the right gene in the right amount in  the right cell

▪ Abnormal Gene – a mutation causes the balance to be thrown off o The Butterfly that has properly functioning genes creates a large  amount of pigmentation Don't forget about the age old question of Why is a membrane potential important?

▪ It is seen as very dark because of high pigment concentration

Overview of Genetics

o This observation can be expanded to the population level – how  much of the gene is present?

▪ This then becomes an ethological question

▪ How does evolution and environment change gene translation? Thought Process of a Geneticist – It Moves Backwards

∙ The butterfly example also shows a sort of backwards movement of the  thought process

o Look at the Organism, look at the Cellular factors, the go back to  the Population 

∙ It starts with observation of the organism and goes backwards to figure  out what’s happening

∙ A “Symptom to Cause” methodology

An Evolutionary Perspective 

∙ Evolution Definition – accumulation of changes over time

o Neutral and Beneficial mutations accumulate

∙ Horse Example

o Displays Vertical Evolution, the only type when tracing small  mutations actually matters

o The development of a small, goat-like animal to the strong horse we  know today

o Specific differences are selected for that change the appearance ∙ What Are Morphs? If you want to learn more check out Why does polyphemus say he doesn’t need zeus or his laws?

o Morphs are members of the same species that look dramatically  different, representative of evolutionary changes

▪ What makes a Species?

∙ 1. Similar Genetic Makeup

∙ 2. Capability to Interbreed

▪ But Morphs are dramatically different

o Panther Example

▪ Panthera onca is the Panther and the Jaguar

▪ And their differences are representative of their environments ∙ Chromosome Changes: another method of genetic change and evolution  that can only remain present through natural selection

o 1. Chromosome Aberration – any sort of change in the Chromosome ▪ Breaks

▪ Duplications

▪ Inversions

▪ Transmutation

o 2. Genomic Mutation – change in the Chromosome number

▪ Diploidy – a duplicate chromosome  

▪ Polyploidy – a ubiquitous change in all the cells

Overview of Genetics

∙ The Most Important Part?

Genetic Fields and Studies 


∙ 1. Molecular – change of genome leads to changes in the proteome ∙ 2. Cellular – the nature and composition of the cell’s proteins identify that  cell

∙ 3. Organismal – the cellular composition is reflected in the observed traits ∙ 4. Population – what are the composition of those trait variants in the  population?


∙ 1. Transmission – process by inheriting traits

o Quantitative Mendelian analysis of gene expression

∙ 2. Molecular

o Biochemical composition of genes and their expression

o DNA/RNA composition

o Functional Aspects and the Central Dogma

∙ 3. Population

o Allele distributions in a population

o Ethological considerations of environmental effects

Mendelian Genetics

Chapter 2: Mendelian Genetics

Who Was Mendel? 

Why the Pea Plant?

∙ Overall Reasons

o Easy to observe

o Short harvest time (30-40 Days)

o Small space required to grow

o Large flower is easy to manipulate and handle

∙ Anther/Reproduction Manipulation

∙ Isolate Traits

Overall Process of His Experiments

∙ 1. Self-Fertilization

o His initial step involved insuring that his plants were indeed true  breeding

o Self-fertilization for 9 Generations to achieve true breeding parents ∙ 2. Hybridization

o Those parents were then crossed to produce the organisms in  

which he was truly interested  

o The F1 Generations

o Observed that there were generally speaking two variables of the  trait

∙ 3. Self-Fertilization (of the Hybrids)

o He then self-fertilized the F1 Generation to get the F2

o Removed the anther in this process

Mendel’s Studies

∙ Traits Studied

o 1. Flower Color – PURPLE, white

o 2. Flower Position – AXIAL, terminal

o 3. Seed Color – YELLOW, green

o 4. Seed Shape – ROUND, wrinkled

o 5. Pod Shape – INFLATED, condensed

o 6. Pod Color – GREEN, yellow

o 7. Height – TALL, short

∙ Methodology

o Mendel’s method was not strictly scientific

▪ He simply performed experiments and analyzed his numbers

▪ He did not have a hypothesis

o His methodology is known as “Quantification”

Mendelian Genetics

▪ Involved a mathematical analysis of his findings to search for  


▪ Used an empirical approach to deduce laws

Mendel’s Laws 

I. Law Number One: Law of Segregation

∙ Diagram of Mendel’s Characteristic Cross

o Terms to Know:

▪ Parent Generation

▪ Cross Fertilization

▪ Single Factor Cross

▪ Monohybrid  

▪ F1 (First Filial) Generation

▪ Self-Fertilization

▪ F2 (Second Filial) Generation

∙ Summary and Observations

o Unit factors of inheritance will segregate during crossing

Mendelian Genetics

▪ These “unit factors” are now known as “Genes”

▪ The variants of these are called Alleles

∙ Having the same alleles is known as Homozygous,  

different alleles is Heterozygous

∙ This composition is now known as Genotype

▪ Mendel observed the Phenotype, the observable  


∙ Punnett Squares

o Mendel didn’t explicitly use Punnett Squares, but his predictions  can be neatly displayed in Punnett Squares

o Punnett Squares have their limitations, though, due to practicality ▪ General Hybridization:  

∙ Possible Gametes = (#alleles)(#traits)  

∙ Possible Offspring = (#gametes)2 

▪ Monohybrid Cross

∙ Gametes = (2)1 = 2

∙ Offspring = (2)2 

▪ Dihybrid Cross

∙ Gametes = (2)2 = 4

∙ Offspring = (4)2 = 16

▪ Trihybrid Cross

∙ Gametes = (2)3 = 8

∙ Offspring = (8)2 = 64

o But for Monohybrid and Dihybrid Crosses they are useful

▪ Monohybrid









o Dihybrid










Mendelian Genetics
















∙ So how, using these techniques (considering Genotype, Phenotype, an  Punnett Squares), can you determine genotypes from phenotypic  observations?

o 1) Back Cross

▪ The given organism displaying the dominant trait is crossed  back with another from the generation before (usually  

another dominant)

▪ This is practiced most in agricultural circles to produce mass  amounts of a given trait

▪ Here the genotype is irrelevant and only the phenotype is  desired

o 2) Test Cross

▪ This is the true test to determine the Genotype of an  

organism by only viewing its Phenotype

▪ The F Generation Monohybrid with a Dominant Phenotype  (Often assumed to be Heterozygous) is crossed with the P  

Generation Recessive 

▪ Depending on the Genotype of the Dominant Phenotype,  

we’ll see a certain number of recessive offspring from the  


II. Law Number Two: Law of Independent Assortment

∙ Diagram of the Experiment - Standard Test to Display Independent  Assortment

o Terms to Know

▪ Two Factor Cross

▪ Dihybrids

o Process

▪ Initial

▪ Hypothetical

▪ Actual

Mendelian Genetics

∙ Genes assort independently of one another during separation o Independent Assortment deals with Genes and Multiple (Two  Factor or More)

▪ Segregation deals with alleles, Assortment deals with  


▪ Genes Assort independently and the segregation process  

does not link their alleles

▪ In essence, Dominant alleles don’t have to stick together in  different genes

o Refers to the Segregation of alleles, but with Multiple genes

Mendelian Genetics

∙ Occurs in Anaphase I of Meiosis (four in a line, homologues split) ▪ They are independent of each other on different loci in the  


▪ The chromosomes are in lines of four, with homologues and  duplicates (sisters) being present

Modern Genetics 

“What is the relation with molecular mechanisms?”

∙ How do external and even internal observations relate to genetic  mechanisms?

∙ A lot of this methodology involves detecting defects and tracing them  back to discover the genetic origin

o This method, though, only goes so far, considering not all defects  can be easily phenotypically detected

o This has found, however, that small genetic mutations in defective  alleles are a source of overall deficiencies

Dominant and Recessive Genes

∙ Overall

o Most genes have two variants

o Defects in the alleles cause the rise of diseases

∙ Relation to Diseases

o Recessive Genetic Disease – two of the allele must be present o Dominant Genetic Disease – only one of the allele needs to be  present

▪ These types of genetic disease are almost always fatal  


▪ Known as “de novo” mutations

▪ They randomly occur during gamete formation

Mendelian Genetics


∙ Examples to Consider

1. Two Carrier Parents (25% Infected) 2. Two Infected Parents (100%  Infected) 

∙ Two Odd Pedigree Symbols

o 1. Fraternal (Dizygotic) vs. Identical (Monozygotic) Twins

o 2. Consanguineous (Cousins)


Eugenics vs. Euthenics

∙ Eugenics – the aim of improving the genetic quality of humanity o Counseling aimed towards preparing and informing women on  genetic possibilities and dangers

o Important with aged mothers as well

o A maintenance of strong genes in the human population

Mendelian Genetics

∙ Euthenics

o This is the improvement of functioning and wellbeing through the  improvement of living conditions and external factors

o These factors increase the reproductive rate by increasing survival Some Broad Notes

∙ 1. Simple Probability

o Measuring times something occurs against the times it could have  occurred

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���������� ���������������� ������������ =�������������� ��������������������

���������������� ��ℎ����������������

∙ 2. Accuracy

o Very dependent on sample size

o Error should be small

▪ Error is between observed and expected

▪ Ensures error is by chance, not an external affecter

▪ Random Sampling Error is Minimized by Large Sample

∙ 3. Sum Rule

o You can add mutually exclusive probabilities

o Looked at as an “Either/Or” event

▪ They are mutually exclusive

o Mutually Exclusive or Independent

Mutually Exclusive


*Event = Brown and  Blue Eyes

*These types of events  can be summated

*Event with 2 People,  Eye Color

*The outcomes are  

unrelated to each other *These types of events  are multiplied in some  fashion

∙ 4. Product Rule

o Independent Set of Events in a Given Order

▪ What is the probability of the First and Second being…

o The event is in a given order

∙ 5. Binomial Expansion

o Independent Event in No Order

o Say five events are happening, one can search for the possibility of  the event simply occurring three times

∙ 6. Chi-Squared Test

o Tests “goodness of fit,” or how much variance is due to random  sampling

Mendelian Genetics

Probability Rules 

I. Sum Rule

∙ Ex: Considering two traits, Tail Length and Ear Type

o Each event is a Mutually exclusive – you cannot have a normal  and abnormal tail/ear

o So, because each is Mutually Exclusive, you can summate their  probabilities

o What is the probability of having a Normal Eared, Normal Tailed  Organism?

▪ Find the total possibilities (16)

▪ Find the specific possibilities (9)

II. Product Rule

∙ You want a specific order of events with independent events

∙ Can consider two individuals now

∙ Ex: Cystic Fibrosis

o Chances of one child = ¼  

o Chances of not one child = ¾  

o Chances of children 1,3 out of 3: ¼ x ¾ x ¼  

III. Binomial Expansion

∙ Not a specific order, but still independent

∙ Ex:

�� =��!

2! (3 − 2)!(14)2(34)1 

⇒ �� =3!

��! (�� − ��)!��������−������������������ ������������


Total number of  


3 Kids


Desired Event

2 Kids Recessive


Probability of individual  event



Probability of “not p” for  individual event


IV. Chi-Squared

∙ Displays variance of expected versus observed and determines how  random the results are

∙ An assumption must be made to count as the hypothesis o 1 Trait, Segregation (3:1, Two Phenotypes)

Mendelian Genetics

o 2 Traits, Assortment (9:3:3:1, Four Phenotypes)

∙ Ex: Assessing Chi-Squared for wing shape and body color

o 1. Propose Hypothesis (as above, to eventually determine  


o 2. Analyze the Observed Values

o 3. Use expected values based on hypothesis

o 4. Use formula (smaller value is better)

o 5. Compare to Degrees of Freedom

∙ Null Hypothesis: occurs merely because of chance

∙ Degrees of Freedom

∙ Always equals (n-1)

Cell Division

Chapter 3: Cell Division

Viewing the Cell 

Genetic Material

∙ Eukaryotes

o Double stranded, Linear DNA

o Well defined organelles are present

o Chromosomes are made of the Chromatin complex (60% protein  (histones), 40% DNA

∙ Prokaryotes

o Double Stranded, Circular DNA

o Naked DNA (no protein)

∙ Somatic Cells vs. Germ Cells

o Somatic Cells are Diploid (have two sets of chromosomes)

▪ These sets are comprised of pairs, called Homologous Pairs

▪ These pairs are identical in many ways

o Germ Cells are Haploid (have one set of chromosomes)


∙ Definition – examination of the chromosomal compaction and composition  of an organism

∙ Process for Examination

o 1. Addition of Division Inducing Agent (condenses and duplicates  Chromosomes)

o 2. Allowance of Replication

o 3. Centrifuge to Stop Replication and Collect Sample (forms sample  pellet)

o 4. Addition of Hypotonic Solution (swells up cells)

o 5. Drop Cells on a Slide and Fix Them (no more changes can occur) o 6. Stain Cells With Geimsa (stains different components differently) o 7. Addition of Trypsin (breaks down histones, reveals DNA bands) o 8. Photo Imaging (computer or camera)

o 9. Karyotype Arrangement

∙ Karyotype Arrangement – the entire chromosome complement of an  organism arranged from tallest to shortest

o Homologue Identification

▪ 1. Size

∙ While size can help identify Homologues, it is no  

suggestive of overall genomic complexity of an  


▪ 2. Centromere Position

∙ 1. Meta-Centric – in the middle

Cell Division

∙ 2. Sub-Met-Centric – closer to the middle

∙ 3. Acro-Centric – closer to one end; ‘p’ is short, ‘q’ is  


∙ 4. Telo-Centric – only one arm

▪ 3. Banding Patterns

∙ Banding is induced by the addition of the Trypsin

∙ This can identify and differentiate based on Loci, not  

based on Alleles

∙ Why are Karyotypes important?

o 1. They Allow for Evolutionary Comparisons

▪ Chimps have 48 Chromosomes, with Chromosome 2A and  2B each adding up to the total of Human Chromosome 2

▪ Banding with Chimps is also seen to have high similarities to  that of humans  

∙ So the Chromosomes are Similar, but not identical

o 2. They Can Identify Abnormalities in an Organism

Eukaryotic Chromosomes 


∙ Homologues form the Diploid number

∙ Cell Division

o Why do Cells Divide?

▪ 1. Asexual Reproduction

∙ Bacteria reproduce through Binary Fission

∙ DNA is replicated, the Septum if formed, and the cell  

splits into two new identical cells

o FTSZ: Filamentous Temperature Sensitive Mutant  

Z responds to trigger

Cell Division

o Forms a ring and vibrates and recruits eight  

other proteins to form on the ring around the  


o The new nine protein complex forms the Septum

▪ 2. Multicellularity

∙ In complex organisms, multicellularity is achieved  

through Mitosis

o When do Cells Divide?

▪ Density determines and initiates cellular  

▪ They accumulate nutrients and proteins (increasing density) Mitosis Overview

∙ Mitosis is a highly complex process occurring in all Eukaryotic cell types o Its goal is Replication and Distribution 

o The cells maintain genetic consistency through generations o Equal distribution must occur

∙ As a random side note, ferns have a Chromosome number over 1000 o Displays how sheer volume does not directly translate into  complexity

∙ All Cells go Through Stages (Common to all dividing cells, whether  actively dividing or not)

o 1. Interphase (G1, S, G2)

o 2. Prophase

o 3. Prometaphase

o 4. Metaphase

o 5. Anaphase

o 6. Telophase

o 7. Cytokinesis

∙ Cells also differ in the time for these stages, depending on their purpose  and function

o Bone Marrow: constant replication

o Elementary Canal Cells: twice a day replication

o Liver: once a year

o Neural Cells: terminally differentiated

Mitotic Stages 

1. Interphase

∙ G1 Phase (Gap) – Key Words: Density

o Restriction point is reached, it must progress

o So progressed into the S Phase

∙ S Phase (Synthesis) – Key Words: Replication, Centromere o Chromosomes are duplicated (DNA, Histones)

o Sister Chromatids form around the Centromere

▪ Part of Chromosome (DNA locus) that forms binding site

Cell Division

o Monad is a single Chromosome, Dyad is the Sister Chromatids

∙ G2 Phase (Gap 2)– Key Words: Kinetochore, Organelles o Organelles now begin to divide

o Kinetochore now deposits itself on the Centromere (will eventually  connect with Centrosome)

∙ It then moves into the Mitotic stage (M)

∙ Now the cell has enough contents for two separate cells, so it needs to  split (92 Chromosomes and Numerous Organelles)

∙ Mitosis is the splitting process

∙ Cytokinesis is triggered during Anaphase, which starts cytoplasmic  division

2. Prophase

∙ Quick Overview

Condensation of Chromosome; Plasma membrane Breaks Down; Physical  Assembly of Spindle Apparatus

∙ All Euchromatic regions (less compacted) now become Heterochromatic ∙ Nuclear membrane breaks down into fragments

∙ The Nucleolus (area that creates rRNA) disappears

∙ Spindle Apparatus forms  

o Physical Assembly from Centrosome and Centriole, the  

microtubule forming complex)

o They are assembled, but that’s it: only assembly

▪ 1. Polar Microtubules – deviating the poles

▪ 2. Astin Microtubules – branching to the outside, holding it in  position on the Membrane

▪ 3. Kinetochore Microtubules – go on to connect with  

Kinetochore proteins on the Centromere

Cell Division

3. Prometaphase

∙ Quick Overview

Kinetochore Microtubule Connects to Centromere; Complete Nuclear Membrane  Breakdown

∙ The spindle apparatus exists to separate sister chromatin ∙ Kinetochore begins polymerizing (growing) from the Centrosome to  ‘randomly’ attach to the Centromere

o Any that fails to attach depolymerizes

o In this manner, the Spindle Apparatus becomes functional o It binds so that each sister chromatid is bound to each pole (giving  functionality)

∙ The Nuclear Membrane also completely disappears now

4. Metaphase

∙ Quick Overview

Arrangement on the Metaplate

∙ Sister Chromatids are arranged on the Metaplate of the cell and are  connected to each pole

o The equatorial plane

∙ This arrangement is random (paternal and maternal can line up on  either side) and in a single file row

Cell Division

5. Anaphase

∙ Quick Overview

Polymerization of Polar Microtubules and Depolymerization of Kinetochore

∙ The Chromosome number must be maintained, so the sisters attached at  each pole are now separated

o I. Kinetochore Microtubules Shorten (depolymerizes)

▪ This pulls the chromatids

o II. Polar Microtubules Lengthen (polymerizes)

▪ This pushes the cell poles

∙ The pulling/tugging

o This separates the Sisters

▪ If not, nondisjunction occurs

o Each pair of Sister Chromatids becomes single Chromosomes ∙ Cytokinesis is initiated by these steps (when the chromosomes are on  either end)

6. Telophase

∙ Quick Overview

“Reverse Prophase”

∙ Everything in prophase is reversed now:

o I. Chromosomes – begin to decondense

o II. Nuclear Membrane – begins to reform

o III. Nucleolus – begins to become evident again

o IV. Microtubules Disappear – spindle apparatus breaks down ∙ At this point, the cell is binucleate (two nuclei)

7. Cytokinesis

∙ Plant Cells

o Occur on the Cell Plate

o Cell plate is formed from Golgi Vesicles carrying plate proteins ▪ The vesicles merge and extend to the side

▪ Once they reach the side Plasma Membrane, maturation of  the Cell Wall occurs

o Contains very large polysaccharides

Cell Division

∙ Animal Cells

o Occurs through Actin movement (done through Myosin)

▪ Actin is already present at the Cell Membrane

o Cleavage furrow forms from actin overlapping

▪ Ring diameter shrinks

Mitosis + Cytokinesis gives you a Genetically Consistent Cell,  Mitosis on its own merely gives a Binucleate Cell

Sexual Reproduction 

∙ Cellular Overview

o Gametes

▪ Types

Cell Division

∙ I. Isogamy – identical gametes

∙ II. Heterogamy – male and female are different and  


▪ Reduction Division Occurs – division that reduces to haploid ∙ Occurs before fertilization

∙ They are not daughter cells – genetically inconsistent

o Meiosis precedes by Syngamy (germ cell fusion, fertilization) ▪ This:

∙ 1. Keeps Consistent Chromosome Number

∙ 2. Brings About Variation to Increase Survival

A. Spermatogenesis

∙ Testes have Spermatagonial Cells, which are self-renewing cells o This is a Diploid Cell (Spermatagonia)

o These cells divide (through Mitosis) to produce two new cells, one  that remains a Spermatagonial Cell and one that becomes the  Primary Spermatocyte

∙ The Primary Spermatocyte goes through Meiosis to produce Gametes o After Meiosis I the Primary Spermatocyte has been split into two  Secondary Spermatocytes

o The final phase (Meiosis II) results in four Spermatids

o The spermatids go on to differentiate into the Sperm Cells ∙ The main goal of Spermatogensis is to produce haploid nuclei ∙ What does Sperm Differentiation add?

o I. Motility

▪ The develop a flagella, helps motility

o II. Enzyme Capsule

▪ This is known as the Acrosome (enzyme capsule that breaks  down egg membrane)

B. Oogenesis

∙ Very important because the cell must initiate and sustain embryonic  development

∙ Accumulation (this is a much more complex process) for Embryo o I. Cytoplasm and Enzymes

o II. mRNA

o III. Proteins

o IV. Organelles

∙ Creation Process

o Special diploid cells in the Ovary are called Oogonia

▪ Mitosis is the first step again

▪ But this isn’t Self-Renewing (constant division)

o Oogonia develop into Primary Oocytes and an additional Oogonia

Cell Division

▪ This one will go through Meiosis I, but in an Asymmetrical  manner

▪ Spindle Apparatus forms to one side, and organelles follow,  forming Secondary Oocyte and a Polar Body (which divides  again)

o By month seven, however, the addition Oogonia degenerate and  leave the Primary Oocytes

o Through a long activation process, the Primary Oocytes go on to  become Three Polar Bodies and A Functional Egg

∙ Activation Process

o I. Early Development

▪ Through Mitotic Proliferation of early ovary cells, about 7  Million Oogonia form

▪ As development continues, this number declines to roughly  1 Million Functional Oogonia (undergo Meiosis)

o II. Selection Process (7 Months)

▪ At Seven Months, a selection process occurs to the  

1,000,000 that results in 400-500 Primary Oocytes

o III. Diplotene Arrest (Primary Signal, 7 Months, Before Birth) ▪ At the same time as selection occurs, Primary Oocytes begin  to undergo Meiosis

▪ They are halted at Diplotene, however, in Prophase I

▪ It’s important to note that Prophase has begun, so the  

spindle apparatus has formed

∙ That’s why age creates problems

o IV. Second Signal (12 Years, Puberty)

▪ Hormonal shifts result in Meiosis progressing through to  Metaphase II

∙ Occurs in monthly cyclic process

▪ So the first division has occurred, giving rise to a Polar Body o V. Final Signal (Sperm Cell)

▪ Sperm cells arrive and attack the membrane of the Egg in  order to fuse

▪ This signal induces completion of Meiosis and creation of egg  cell and ultimately embryo

C. Plant Gametogenesis (Double Fertilization)

∙ Methodology of Alternation

o Gametophytes are the Haploid Phase, Sporophyte the Haploid  Phase

o Large visible structures are generally Gametophytes

∙ Creation



Anther, Stamen (producer) = Male

Stigma, Ovary (Producer) = Female

Cell Division

Diploid Parts

Diploid Parts

I. Microsporocyte (Meiosis) ???? Microspores

II. Microspores ???? Pollen Grain This division occurs without  


III. Pollen Grain is made of Tube Cell (Pollen Tube) and Generative Cell (Active Sperm Cells)

I. Megasporocyte ???? Megaspores (4) II. Three Megaspores Degenerate

III.Three Rounds of Mitotic Division  and Unequal Cytokinesis

ultimately result in Seven Cells  (Embryo Sac) (one is Binucleate)

Egg, Central Cell (Binucleate),  Synergids (2), Antipodals (3)

∙ Fertilization

o I. Stigma (Female Part)

▪ Nectar and lipids present on tip

▪ Lipids and nectar initiate germination, maturation of pollen  grain

o II. Pollen Grain (Male) (Pollen Tube and Sperm Cell Nuclei) ▪ Tube Cell – develops into the pollen tube

▪ Generative Cell – splits into two germ cells (mitosis) to become  active sperm (sperm nuclei)

o III. Newly Created Sperm Cells Fertilize (Endosperm and Embryo,  this is the Double Fertilization)

▪ Central Cell (Female) – this Binucleate cells now becomes a  large trinucleate, known as the Endosperm

▪ Egg Cell (Female) – fertilization of the Egg results in the  

growing Embryo

o IV. Fleshy fruit forms from the rest of the Ovary and Ovule ∙ Plant vs. Animal

o Plants Start with Meiosis, Animals End with Meiosis

Sex Determination 

∙ Different species have different cellular sex mechanisms

o Homogametic – XX, same sex chromosome

o Heterogametic – XY, different sex chromosomes

∙ Determination

o 1) Human

o 2) Insect

▪ Number of X Chromosomes to Autosomal Sets

▪ Ratio 1.0 = Females

▪ Ratio 0.5 = Males

Cell Division

o 3) Bird

▪ ZZ = Males

▪ ZY = Females

o 4) Alligators

▪ 33O = 100% Male

▪ < 33O = 100% Female

▪ > 33O = 95% Female

o 5) Bonilla Worm

▪ Hits the ocean floor? Becomes Female

▪ Hits the Female? Become sperm producing machine

o 6) Parthenogenesis

▪ Bees, Wasps, all males are Haploid Organisms

▪ Female are all diploid

∙ Morgan’s Work on Chromosomes

o Morgan wanted to experiment with Phenotypes, specifically hoping  to induce some sort of mutation in his breeding flies

▪ Inducing through Radiation

o White eye mutation occurred and he found 44:1 ratio, with females  being more red

o Test Cross

▪ Heterozygous Female with White Eyed normally gives 1:1,  but white eyes males die before birth

Extensions of Mendelian Genetics

Chapter 4: Extensions of Mendelian Genetics

A Broad Overview of The Extensions 

Limitations of Mendel’s Work

∙ Only looks at purely dominant and recessive from a narrow point of view o Dominant: present, wild type – the right cell, right protein, right time ▪ But what if the wild type (beneficial type) is recessive?

o Recessive: generally mutant variety, a loss of function

▪ So what if this occurs as the dominant fashion?

∙ Balding is an example

∙ Mendel Looked at only 7 Pea Traits

o Pea Color, Pea Shape, Pod Color, Pod Shape, Flower Position,  

Height, Flower Color

o But his finding and explorations didn’t go beyond that

∙ So Consider Genetic Disorders and Diseases

o They are generally recessive, but as considered above, they can be  dangerous as dominant

o So how do these developments occur?

Modern Genetics Begins to Ask Why?

∙ Why would the Dominant Gene be Enough?

o 1. 50% of the protein being transcribed is enough to have the  


o 2. Cellular recognition mechanisms to upregulate a particular  


∙ So how do other mutations manifest themselves other than the simple  above potential mechanisms?

o 1. Gain of Function

▪ A mutation gives a gene a new function and ability

∙ But this ability ends up being bad for the cell and is  

then upregulated because of the new ability

∙ So a loss of function does not occur – the normal allele  

is still fine

∙ It is merely being down regulated for the novelty allele

▪ Ex: p53

∙ P53 is a tumor suppressant

∙ It generally functions in a dominant, wild type manner

∙ But when a mutation giving a new ability occurs, it  

becomes upregulated

o This upregulation (so dominant form now) of the  

new ability is actually harmful because the new  

ability is to proliferate cancer cell metastasis

Extensions of Mendelian Genetics

o 2. Dominant Negative

▪ Antagonistic Mechanisms occur

∙ The mutation occurs that inhibits the ability of the  

other (proper) gene to function properly

o No loss of function occurs – the gene is still  

perfectly fine, it’s simply “drowned out” by the  

mutated allele

▪ Ex: ras Gene

∙ Works with GDP to activate a kinase (conversion to  


∙ The mutated allele ends up creating a protein that  

binds to ras and stops it from working

o It can no longer move

o Can no longer switch to GTP to activate

o 3. Haploinsufficiency

▪ Generally genes are transcribed and proteins created by a  combination of each allele on the chromosomes

∙ So both contribute to the functioning

▪ Ex: Consider a deletion

▪ In essence, one is not enough (the Haplo is not enough to  express)

▪ Thinks of it this way:

∙ A gene will be expressed with 50 Units of protein X  


∙ You have two alleles that are both wild type, one is  

just highly expressive (varies per person)

Extensions of Mendelian Genetics

∙ In the highly expressive, each allele codes for 50 units,  

so it is Haplo sufficient

∙ But in the low expressive, each is only 30 –


Types of Dominance Patterns 

1. Simple Dominance (3:1)

∙ Straightforward Mendelian Expectations with the 3:1 Raito

2. Incomplete Dominance (1:2:1)

One copy of the dominant allele is not enough to express the gene

∙ Ex 1: 4 O’clock Flower

o A mix occurs

o Punnett Square View (Diagram)

∙ Ex 2: A Molecular Look at the Pea Shape

o Take a look at protein composition and it becomes clear that the  Homozygous Dominant varies from the Heterozygous

Looking at the EET1 Gene Expression

o But must be done molecularly speaking

∙ Ex 3: PKU (Phenylketonuria) Molecular Perspective  

o Same idea here  

o PKU patients lack the functioning protein “Phenylalanine  


▪ This breaks down Phenylalanine

▪ Without it, Phenylalanine releases damaging ketones

o So blood samples can be taken and checked for Phenylalanine  composition, reflective of its proper breakdown

▪ Healthy (Homozygous) – 1mg/dL

▪ Carrier (Heterozygous) – 2-3mg/dL

▪ Infected (Homozygous Recessive) – 6-8mg/dL

3. Incomplete Penetrance (Varies by Generation)

∙ Normally, the genotype penetrates the phenotype in order to express the  present gene

o The dominant trait is said to have the ability to “penetrate” the  phenotype

o But when the dominant trait is present but somehow unexpressed,  it is known as incomplete penetrance

∙ Important to note the different between Penetrance and Expressivity o Penetrance – viewed in the population, the capacity to be expressed  in Heterozygous individuals

Extensions of Mendelian Genetics

▪ Only consider Heterozygotes because the other two are easy  to identify and explain already

▪ So within a population, the gene has 66% penetrance

o Expressivity – deals with an individual, how is the gene expressed? o In the example below, the consistent lack of expression of the  dominant allele is penetrance while one person having 12 and  

another having 11 is expressivity

∙ Ex: Polydactism

o Being a heterozygote with the Dominant Polydactyl  

o This allows for the trait to skip generations with relative ease ∙ Possible Explanations?

o 1. Environmental – environmental factors influence the gene  


▪ I. Light

∙ Snapdragon present different colors depending on  

what temperature it is in which they grow

▪ II. Temperature

∙ Drosophilia facets are more present when growing in  

cold weather and less so in warm weather.

▪ III. Diet

∙ PKU patients cannot have Phenylalanine in their diet,  

but strict regulations allow them to live perfectly fine.

∙ Can they be reversed?

o A question may be, however, if they don’t catch  

it early can it be reversed?

o PKU doesn’t present such a prospect, but the  

conditioned allele on Shibiar alleles can be

o Flies grown at given temperatures can have the  

effects reversed

o 2. Modifier Genes

o 3. Combination of the First Two

4. Overdominance (1:2:1) – (But Heterozygotes are Selected for)

∙ Overdominance deals with Heterozygous individuals – only looking at the  carriers and only looking at one gene 

o These Carriers have an advantage

∙ Why does Overdominance Occur?

o 1) Cellular Morphology

▪ Antigen is present because of the slight expression (Sickle  

Cell example)

o 2) Dimerization of the Protein

▪ Dimerization occurs to form the final protein (Quartneary  


∙ 2 units come together

▪ With another type of allele, three possible dimerization  

possibilities arise

Extensions of Mendelian Genetics

∙ With two of the same allele, only one permutation  


∙ Results in the creation of different Monodimers and  


▪ New capacities are created

o 3) Protein Reactivity

▪ Say one allele reacts at a given temp (low) and another at a  different temp (high)

∙ With both present, the organism can respond to low  

and high temperatures

▪ So a range of enzyme activity is created

∙ That range creates a survival advantage

∙ Ex: Sickle Cell

o Hemoglobin overview

▪ Made up of four subunits, Two Alpha, Two Beta

▪ A small point mutation occurs on the Alpha

∙ GAG goes to GTG on the DNA

∙ Goes from Glycine (charged) AA to Valine (Neutral) AA

▪ Pressure then results in cytoskeletal transformation due to  the neutral Valine connection

∙ 1. Stiffness occurs because the cytoskeleton is  

inefficient, leads to clotting

∙ 2. They morphed form leads to inefficient Oxygen  


o Cells of Sickle Cell Lifespan

▪ Each cell normally lives 90-120, but sickle cell cells only  

survive 10-20

▪ So the body can’t keep up

o But Carriers have an advantage:

▪ HbA and HbS are the alleles

▪ Their cells are mostly fine and properly functioning, but a  few of them present some sickle traits

▪ When their cells are attacked by Malaria plasmodium,  

propagation cannot occur

∙ 1. They burst because of the shape

∙ 2. They have a particular antigen from the trait  


▪ But non-malarial environments don’t have high heterozygote  populations

∙ Ex: Tay-Sachs

o A mutation occurs in a lipid storage and synthesis protein o Allow them to fight TB

∙ Ex: PKU Females

o In certain areas, the likelihood to ingest the Ochratoxin A is much  higher

Extensions of Mendelian Genetics

▪ Normally even a small ingestion is enough to cause a likely  

miscarriage but is not fatal to the mother

o But PKU females do not experience such miscarriages

5. Heterosis

∙ This example begins to look at multiple genes 

o Multiple genes are introduced – so the genetic benefits are not from  an allelic mixture of a given gene, they are from a conglomeration of  genetic effects from multiple genes

∙ Ex: Crops

o Genes are introduced to optimize crop life

∙ The phrase here is “Hybrid Vigor”

o Merely referring to the mix of alleles

Considering Multiple Alleles 


∙ Overview

o Several mutations exist for a given gene, each showing a slightly  different and altered phenotype

o Morphologies:

▪ 1. Monomorphic – one wild type exists

▪ 2. Polymorphic – multiple wild types exist

▪ 3. Multiple Alleles

∙ Examples of Multiple Alleles

o A. Mouse Fur Color (True Monomorphism)

▪ Mentioned above, the distribution is not equal

o B. Rabbit Fur Color (Like Monomorphism, but still all present) ▪ Detailed above

o C. Lintels (Like Monomorphism, but still all present)

▪ Some predominate more than others, but all alleles are still  


Marbled 1 > Marbled II > Spotted, Dotted (They are equivalent) > Clear Dominant Form 1 Dominant Form II Strong Recessive Completely Recessive

o D. Blood Types (True Polymorphism)

▪ Different types of blood exist that are all equally as present

Extensions of Mendelian Genetics

A. Polymorphism – (Only deals with One Gene)

∙ Hair and Eye Color may be a common consideration, but consider how  those manifest themselves:

o They are a mix of genetic influences, influenced by Polyploidy  genes

∙ A true example is blood type:

o They are all the same gene and are not phenotypically affected by  other genes

o But there are three different forms of the gene

o And if not force chooses for a particular phenotype, it is  


o But if the wild type is chosen, it is Monomorphic 

B. Monomorphism

∙ The mutation distribution is not equal

o Other alleles can exist, but one wild type predominates, so the  phenotype is monomorphic

o The mouse coat color is a good example:

▪ Agouti is dominant (A)

▪ But the Black/Yellow Body is possible (at)

▪ And Black is also possible (a)

o So in essence, polymorphic alleles can be monomorphically  expressed

∙ Mouse Fur Example – (This deals with pigmentation protein)

o Tyrosinase is responsible for pigmentation

▪ Different Melanins can be acted upon

▪ EuMelanin is a Dark Brown/Black color

▪ PheoMelanin is a Yellow Color

o The gene for properly functioning Tyrosinase is C

▪ So CC is complete Tyrosinase, which Gives a lot of  


▪ Cc is a mix of Eumelanin and Pheomelanin, which gives a  

grayish Agouti color

▪ Then other recessive alleles exist

o But there are Recesive alleles as well, mutations that occurred on  the tyrosine gene

▪ cCh – Chinchilla

▪ ch – Himalayan

▪ c – Albino

o So Phenotypic expressions Can include:  

▪ cchcch – Chinchilla

▪ cchch – Incomplete Dominance

▪ cch/chc – Paler Version of the other

o As a side note, these have interesting Thermolable properties,  specifically with the Himalayan variety

Extensions of Mendelian Genetics

▪ Body temperature influences gene expression

▪ The cold causes and increased expression when the  

Himalayan allele is present (ch)

▪ This causes a darkening of the extremities

C. Conditional Alleles

∙ Definition: particular environmental conditions cause the gene expression o These alleles were mentioned in regards to the PKU discussion in  Incomplete Penetrance

o But unlike with penetrance (reversal is much more difficult and/or  impossible), purely environmental factors can often be reversed ∙ Examples

o Rabbits

▪ Himalayan gene in rabbits

▪ Tyrosine activation in the recessive Himalayan gene are  

influenced by temperature (upregulated in the cold)

o Siamese Cats

▪ Same Tyrosine effects in the cold

o Cattle

▪ Cold now down regulated Tyrosine action for Cattle color

o Drosophilia

▪ Shibire genes (regulating cytoskeletal development) occurs  

normally at 210 or lower

D. Codominance

∙ Definition

o Multiple alleles present themselves as wild type dominate equal in  phenotypic expression

∙ Blood Types is a great View

o The Blood Gene codes for Particular Antigens (used for self


▪ i = isoglutanogen (mutant form lacks enzyme binding spot on  the blood cell)

▪ A = UDP (Uridine DiPhosphate) N-Acetyl Galactosamine  

(NAG) binding site

▪ B = UDP Galactose (G) Binding Site

o Glycosyltransferase (Transfers sugars) moves the sugar to the  blood cell binding site

o When exposed to the given blood types with sugar markers,  

antibodies are generated because the host cell has no binding site  for the foreign sugar (eg., O blood cell has no sites for A or B  


o Blood Genotype Options:

▪ A – IAIA or IAi

▪ B – IBIB or IBi


Extensions of Mendelian Genetics

▪ O – ii

o Rhesus factor is the Rh factors for plasmid antigens

o And M/N blood types are for blood protein antigens

o H-Factor (Bombay Blood Disorder)

▪ The H-Factor generates the H-Antigen, which is the precursor to A and B antigens

▪ So a mutation in the H-Factor gene is detrimental to blood  

type because no A or B antigens exist

▪ So no matter what, the blood type is O (no antigens)

∙ Cattle Color

o Spots become present when Red/Brown is crossed with White E. Sex Linked Genes

∙ Linked – they are present on a Sex Chromosomes

o Y: Holandric Genes (only about 83 present)

o X: About 500 present

o This phrase is generally used considering inheritance

∙ Hemizygous

o This term refers to the Y Chromosome

o One type of allele is present (the idea behind homozygous) but only  one chromosome will carry that given allele (whether on X or Y)

o So the phrase is Hemizygous – there’s only one “slot” to fill

∙ Examples:  

o Duchenne Dystrophy

▪ Dystropin is a cytoskeletal protein that attached the  

cytoskeleton to the plasma membrane  

∙ So dysfunctional dystropin leads to inefficient muscle  

cell development

∙ So the person has not development

▪ The disease affects men much more, demonstrated by the  

reciprocal cross (shows and X-Linked Inheritance)

















Extensions of Mendelian Genetics

o Teeth Color

▪ The enamel and coloration gene is located on the X  


F. Sex Related Traits

∙ Important Differences

o Sex Influenced

▪ Refers to hormonal influences on gene expression

▪ This is usually with Autosomal genes

▪ When it is Allosomal, it’s generally known as  

Pseudoautosomal (because it displays autosomal tendencies  

on a sex gene, so it must be present on both)

∙ MIC (Development) is present on both Sex  


o Sex Limited

▪ Refers to genes only present on a given Sex Chromosome

▪ SRY is only present on the Y Chromosome to induce male  


∙ Types:

o 1. Sex Influenced – Pattern Baldness

▪ Mutation on Chromosome 3

▪ Looking at Heterozygotes (that’s where the influence is noted)




Male Phenotype










▪ Why does this happen?

∙ 5α Reductase is present in all people

∙ It works on Testosterone to produce  


o This acts on the hair follicles

∙ A case study looking at an adrenal gland tumor in a  

woman displayed an upregulation of Testosterone in  

her system, resulting in all parts increasing

o 2. Sex Limited – Breast Development

▪ Limited is an Either/Or sort of thing

▪ This only occurs in Females

Extensions of Mendelian Genetics

o 3. Sexual Dimorphism – Hen/Rooster Color

▪ This is an offshoot of limited genes that specifically separates  phenotypes into male or female

▪ Roosters are most colorful and elaborate

▪ Ovary hormones repress color expression

G. Lethal Alleles (1:2)

∙ Definition – very important alleles, critical to proper functioning and  survival

∙ Genotypic Expressions

o With a Homozygous Lethal allele, the organism dies, so the ratio  becomes 1:2

∙ Examples

o Manx Cat

▪ They lack a tail, which has to do with a skeletal spine  

formation gene

▪ But if they have the Homozygous Dominant Genotype  

(because having it all produces defects it is dominant), it dies  

before birth

∙ The two mutant alleles messes up spinal development  

too much

o Mice Coat

▪ Yellow or Non Yellow coat

▪ Scenarios:

∙ Homozygous Recessive – normal

∙ Heterozygous – pleiopatry causes negative growth  


∙ Homozygous Dominant – death

∙ Differentiating Between Codominant, Incomplete Penetrance, and  SemiLethal

o Looking at Heterozygous Individuals

o Codominant?

▪ It’s tempting to say the allele is Codominant because an in  

between form is expressed

▪ But the allele cannot be “partially lethal,” and it occurs  

before birth

▪ So it’s considered a recessive wild-type allele behaving in a  

recessive manner, even though it’s a dominant allele

o Incomplete Penetrance?

▪ Incomplete penetrance deals with a gene that is actually  


∙ Lethal alleles result in the 2:1 ratio because they occur  

before birth

▪ Huntington’s is a good example

∙ Not semilethal, which are often sex specific and affect  

given ratios

Extensions of Mendelian Genetics

∙ And not lethal either, since they act after birth

H. Variants on Lethal (or more accurately, Genes that appear Lethal)

∙ 1. Semilethal Alleles

o Kill about half the population in a lethal, before birth manner  (hence the applicability of the ‘lethal’ nomenclature)

o The dominant/recessive “lethal” allele is present in Homozygous  manner (Genotypically Speaking), but only half the organisms die o Ex) Drosophilia Eyes

▪ The recessive eye color for drosophila is white

▪ But if 100 males are predicted to have the recessive genotype  for white eyes, only 50 will even be born

∙ Side note: presence only in males suggests hemizygous  


∙ 2. Incomplete Penetrance

o Different than Lethal or Semi-Lethal, the gene just happens to  result in death

▪ So this isn’t even considered lethal because it occurs after  


o Ex) Huntington’s Disease

▪ Tripeptide Repeats

∙ The Tripeptide ‘CAD’ repeats, but depending on the  

number functionality can differ

o Below 26 – Normal

o 27-30 – Slight Changes (Intermediate)

o 31-35 – Moderate Changes (Incomplete)

o 36-39 – Notable Changes (Incomplete)

o Above 40 – Drastic Changes (Disease)

∙ Males vs. Females

o Female Oogenesis is a much more concentrated,  

fail prove process that results in minimal coding  


o Spermogenesis has more errors, resulting in  

more repeats of the CAD sequence

▪ Creates various Possible Combinations in Parents

∙ Normal + Normal = Small Chance of Disease

∙ Incomplete + Incomplete = Decent Chance for Late  


∙ Incomplete + High = Strong Chance for Early Onset

▪ Looking at those trends, CAD repeats only determines and  

influence penetrance but not lethality

▪ Anticipation is a notable side effect

∙ Each generation shows early and early onset of the  

disease (trinucleotide repeats)

∙ They are incompletely dominant, not purely so

Extensions of Mendelian Genetics

∙ 3. Codominant?

o It’s tempting to say the allele is Codominant because an in between  form is expressed

o But the allele cannot be “partially lethal,” and it occurs before birth o So it’s considered a recessive wild-type allele behaving in a  

recessive manner, even though it’s a dominant allele

What Affects the Phenotype? 

1) Pleiopatry

∙ Definition – one gene influences many phenotypic traits

o 1) The gene can make a given protein a different stages of cell life o 2) The gene protein can affect numerous cell types

∙ Example Population: Maori Tribe in New Zealand (Chromosome 7) o Respiratory Issues and Sterile

o What is the common thread? Similar Microtubule Proteins

▪ Sperm Flagella

▪ Respiratory Cilia

∙ Additional Example: Mice Coats

o Tumor Susceptibility, Diabetes Development, and Coat Color are  all affected by the same gene

2) Gene Interactions

∙ Definition – two or more different genes influence a given trait ∙ Two Types

o Discrete Multiple Gene (Discrete meaning discontinuous)

▪ There is an Either/Or effect present

▪ No gradient occurs

▪ Ex: Purple and White flowers only

o Quantitative Multiple Genes (Quantitative Meaning Continuous) ▪ A range occurs, variation

∙ Results from polygenic nature (several contributing  


▪ Most traits fall into this category

▪ Ex: Height, Skin Color

3) Gene Dosage Effect

∙ Definition – inheritance of single gene depends on particular allele of the  gene

o So having more alleles present could contribute

∙ Example: Drosophilia Eye Color

o Females have a Dark Eoisin (Homozygous Recessive)

o Males have a light Eosin (Hemizygous)

Extensions of Mendelian Genetics

Important Multiple Gene Interactions 

1. Two Gene Interactions (9:3:3:1)

∙ How is it Different Than Mendel’s Studies?  

o Presence of Parental Alleles

▪ Mendel’s parent pea generations phenotypes always showed  up in the filial generations

▪ They could have various combinations, but nothing in and of  itself was novelty

o Formation of New Dominant Alleles

▪ Here, however, completely new phenotypes are produced

∙ Examples

o Ex) Hen Combs

▪ Roosters have different types of Combs

∙ Rose

∙ Pea

∙ Walnut

∙ Single

▪ Have various Genotypes

∙ (R) Rose is Dominant to (r)

∙ (P) Pea is Dominant to (p)

∙ R and P are Codominant to form  

the Walnut

∙ All recessive produces the Single  


▪ Punnet Square (Rose (RRpp) and Pea  

(rrPP) are the Original Parents)

o Ex) Fur Color

▪ The same thing occurs:

∙ AAbb = Tan

∙ aaBB = Gray

∙ A_B_ = Brown

∙ aabb = White

Extensions of Mendelian Genetics

2. Epistasis (9:7) – one gene masks another

∙ I. Complementation Epistasis

o The genes affect one another (recessive  


o Two White Flowers are Bred

CCpp (White) X ccPP (White)

o It becomes clear that they are  

somehow epigenetically related (A large  

number of Purple Show Up – 9:7)

o How?

▪ There’s a molecular pathway needed to have the protein be  


∙ 1) Precursor

∙ 2) Intermediate

∙ 3) Functioning Pigment

▪ Each has an intermediate enzyme that functions on the  


∙ If one enzyme is messed up, the pigment cannot be  


o Complementation is often a factor with Recessive  

Epistasis, too.

▪ In that case, two recessive phenotypes are  

being considered (hence,  


o Deafness is another strong example  

▪ In this manner, some deaf parents have children who can  

hear while others don’t – because the parents are  

homozygous recessive for the same gene, which is one of two  

complementation and epistatic options

▪ Two options for parents exist (assuming both are deaf)

Intergenic Mutation (Occurring on  different genes) can result in  complementation.  

AAbb (Deaf) x aaBB (Deaf)


AaBb (Normal)

Intragenic Mutation (Occurring on  the same gene) cannot result in  Complementation.  

AAbb (Deaf) x AAbb (Deaf)


AAbb (Abnormal)

Extensions of Mendelian Genetics

∙ II. Simple Recessive Epistasis (9:3:4) – The Labrador Retriever o Two genes are being considered that are part of a different  process:  

▪ 1. Coat Color

▪ 2. Pigment Depositing onto Shaft

o Some terms for these genes:

▪ Hypostatic Gene – the gene cannot express itself

▪ Epistatic Gene – the gene affects the expression of another  without affecting the code  


o Considerations:

▪ Color Genotypes:

∙ BB, Bb – Black

∙ bb – brown

▪ Depositing Genotypes (the  

epistatic gene):

∙ E – functioning

∙ e – mutated

▪ How is this different than  

complementation (two recessive  

lead to dominant)?

∙ Complementation is dealing  

with one process, one  

function towards phenotypic  

expression (both flower  

genes were with color)

∙ Simple Recessive Epistasis is two genes and two  

functions (the lab genes have different functions)

▪ The “default” color for a pigment-less lab is yellow due to  

pheomelanin presence

o Punnett Square (9:3:4)

∙ III. Dominant Epistasis  

o What’s the difference between Recessive Epistasis?

▪ Recessive: homozygous recessive for a gene masks the  

dominant gene of another

▪ Dominant: heterozygous or homozygous dominant genes  

mask the gene of another

Extensions of Mendelian Genetics

Dominant Epistasis 

Type I Type II 

epistatic allele affects both dominant and  recessive of another gene

∙ Let’s say  

o AA/Aa = Yellow, aa = Green

o BB/Bb = No Color, bb = Color ∙ Both colors can be drowned out by the  dominant “No Color”

epistatic allele affects only dominant allele of  another gene

∙ Let’s say

o AA/Aa = Yellow, aa = no color  pigment

o BB/Bb = No Color, bb = Color

∙ In this case, it’s only possible for the  Dominant allele of the “Color” gene to be  drowned out

∙ The other does not express itself

3. Complementation

∙ Consider Deafness Example

4. Modifier Genes (8:4:3:1)

∙ Definition – genes on separate chromosomes influence each other o They are in different loci within the genome (generally separate  Chromosomes)

∙ Drosophila Eye Color is an Extremely Potent Example

o What Happened?

▪ It is knows that eye color follows the trends for Drosophila  from the X-Chromosome

∙ Dominant = Red

∙ Recessive = White

∙ Eosin = Orange (mutant red)

▪ What they found was a random Cream colored fly in a true  breeding Eosin culture

o What Could Explain It?

▪ There were really only two possibilities:

∙ 1. A Completely New Mutations had Occurred

Extensions of Mendelian Genetics

∙ 2. A Mutation on another Gene Modified the Eosin  


▪ They also knew it wasn’t epistatic, because more flies would  have been affected (recall the purple plant had a (9:7 Ratio)

o What Did They Find?

▪ Decided to run an experiment

∙ Bred Wild Type Female with Cream Colored Male

∙ Then crossed that generation (because they knew the  

Cream Had been passed on somewhere)

▪ Found the following gene categories:

∙ Eye Color:

o Xw+ = Red (Dominant)

o Xw-e = Eosin Color

∙ Modifier Gene:  

o C =  


o ca =  




o Numbers Results:

▪ 8 Red Eyed Females

▪ 4 Red Eyed Males

▪ 3 Light Eosin (C  

Slightly Affects)

▪ 1 Cream Color  

(Dysfunctional C)

5. Gene Redundancy (15:1)

∙ Definition – one functional copy is  

enough to exhibit the gene

∙ These studies are run through knockout individuals

o Normal Traits are discontinuous

▪ So they are an accumulation of proteins and gene expression ▪ So losing one doesn’t often do much

o But sometimes a trait is affected and determined by two genes ▪ This makes the defective phenotype rare, but more possible

▪ In these instances, we can knock out both genes to see the  


∙ Consider: Seed Shape

o If Gene “T” and Gene “V” can give normal shape on their own,  abnormal shape only comes from both being dysfunctional

o So “ttvv” is needed for abnormal shape

∙ So how does Redundancy develop anyway? The Creation of Paralogs o Occurs through the Gene Duplication process

Extensions of Mendelian Genetics

▪ Genes are accidentally inserted into additional spots on  


▪ At this point, the Duplicate Genes are still exact copies

▪ Over time, however, mutations accumulate and the genes  

remain similar, but have small differences, now known as  


o Definition: different forms on a gene that reinserted in a new  location and retain old function, but not the same gene sequence

o Gene Duplication does not make Paralogs, but it leads to them 6. Intergenic Suppressors

∙ Definition – the phenotypic effects of one gene are reversed due to a  suppressor mutation another gene

o It’s an Extragenic/Intergenic Suppressor

∙ Consider a phenotype that needs two proteins to function conjointly for  expression

o Bristles on insects are an example

▪ Functioning Bristles = Normal Function

Protein A (100% Capacity) + Protein B (100% Capacity)

o Say One is mutated = Abnormal Function

Protein A (50% Capacity) + Protein B (100% Capacity)

o Balance Response – Normal Function

Protein A (50% Capacity) + Protein B (50% Capacity)

∙ Difference between “Extra/Inter” and “Intra”

o Suppressor Genes are Intergenic

7. Duplicate Interactions (9:6:1)

∙ In this case, duplicate alleles (affect same  

trait) can produce a newfound phenotype

∙ Let’s take the following example of squash  


o Spherical (Dominant) =  


o Elongated (recessive) = aabb

o But Newfound Phenotype Exists When  

the Dominant Alleles of the two genes  


▪ Disk = AaBb/AABb/AaBB

o The two dominant expression for a new Phenotype

Non-Mendelian Genetics

Chapter 5: Non-Mendelian Inheritance


∙ What Exactly is Mendelian Inheritance?

o 1) Defined By Independent Assortment and Law of Segregation

o 2) The Presence of Gene and the Expression of the Phenotype are  Directly Connected

∙ What is Non-Mendelian Genetics?

o Broad Topics:

▪ 1. Nuclear Genes – genes in the nucleus of the cells

▪ 2. Epigenetic Inheritance

▪ 3. Extranuclear Genes – mitochondria and chloroplasts

o These are essentially factors that change gene expression without  changing the gene sequence

∙ The Three Categories of Non-Mendelian Inheritance

o 1) Nuclear Genes

o 2) Epigenetic Inheritance

o 3) Extranuclear Genes

1) Nuclear Genes 

A. Maternal Effect

∙ Definition – the mother’s genotype determine the offspring’s phenotype o The Father’s and Offspring’s genotypes have nothing to do with the  Phenotype

o How is this any different than Maternal Inheritance?

▪ Inheritance has to do with things being passed on by the  

mother (some X-Traits, Mitochondrial DNA)

▪ Effect merely means some aspect of the mother has an effect  

on the Genotype

∙ Why does this happen?

o Some sort of protein accumulation occurs on an Oocyte of Embryo ▪ This accumulation occurs because of Diploid surrounding  


o This occurs through the action of Nurse Cells

o So, the genes do not affect the Oocyte, but the gene products do

∙ Examples:  

o 1. Shell Style in Water Snail

▪ Genotypes (have to do with the cleavage pattern of body  


∙ Dextral (D) is Dominant (to the Right)

∙ Sinistral (d) is Recessive (to the Left)

▪ Diagram of the Cross

Non-Mendelian Genetics

▪ How do Nurse Cells Work? (Diagram)

∙ This is an example of Oocyte  

development with the snails

o 2. Drosophila Anterior Structures

▪ Genotypes – Bicoid genes arrange posterior/anterior axes

▪ In this instance, the Nurse Cells affect the embryo’s 

development (as opposed to egg like above)

∙ What types of development genes do Nurse Cells affect?

o 1. Early Stages of Cell Cleavage

o 2. Body Plan Curvature

o 3. Anterior/Posterior and Ventral/Dorsal Axes

Non-Mendelian Genetics

2) Epigenetic Inheritance – refers to patterns of inheritance in which a  modification on a nuclear gene of a chromosome occurs that alters gene  expression without changing the base pair sequence

A. Dosage Compensation

∙ Definition – phenomena that occurs to ensure equal gene expression  between male and female with different X chromosome members o Most often refers to X Chromosome Genes, not the semi autosomal  genes

∙ Animals’ Mechanisms:

o I. Marsupial Mammals – paternal X is deactivated in females

o II. Placental Mammals – random inactivation of one of the extra X’s  occurs

o III. Drosophila – X is doubled in the male

o IV. Nematodes (Hermaphrodites) – female Sex Chromosome is  downregulated

o V. Birds – (males are ZZ) Some genes are upregulated in females,  some are downregulated in males

∙ Examples: Drosophila Apricot Eye Color

o We already saw that Eosin eyes are not equal in males and females  (cream can occur in males)

▪ In this case, Apricot is equal in males and females

o So how is the Apricot color equal?

▪ 1. Mutated allele has Protein Leakage

∙ This allows protein to leak in the Male

∙ So to compensate, they produce more

▪ 2. Gene modifier effect occurs

∙ Sort of the opposite of the cream color effect

∙ Enhanced in males

Barr Bodies

∙ Overview – What Are They?

o Scientists began noticing a highly condensed structure in the  nuclei of women

o Only seen in women, so a suspicion of X-Chromosome connection ▪ Phenotypically speaking, they also noticed variegated coat  

patterns in females

▪ Also noted that these compactions occurred at varying  

points, but always at least before the blastula forms

o But it’s important to note:

▪ Barr Bodies have sections that are less compact and are  

sometimes transcribed, so they’re known as Faculative  


Non-Mendelian Genetics

▪ Constitutive/Telomeric Heterochromatin are completely  inaccessible

∙ The Lyon Hypothesis – How Did We Figure it Out?

o Lyon observed the expression of an X-Linked Gene, Glucose 6  Phosphate Dehydrogenase (G6PD), which is involved in Sugar  Metabolism

o This particular gene has two types, the fast acting and the slow  acting

o This difference allows them to be sorted in gel electrophoresis o Minced cells and spread then thinly to be cultivated as single cell  types

▪ Found the gel created distinct bands in the individual  


∙ Mechanism – How Do They Form?

o The X-Chromosome has a cell inactivation center (Xic)

▪ Having an extra Xic (Extra X Chromosome) causes one to be  activated

▪ This is done randomly

o On this activation center are two genes

▪ Xist (X Inactive Specific Transcript) – transcribes RNA coating  around the Chromosome all the way to the telomere (it’s not  

considered mRNA because there is no possibility of it being  


▪ Tsix – counteracts the Xist

o Xist coats the Chromosomes in RNA and recruited compaction  proteins

▪ Similar to histone compaction process

▪ The chromosome is coated, and the coating recruits protein  that induces compaction

▪ This is in response to the Xic marking

o Tsix is the reversal of Xist

▪ This prevents Chromosome compaction

▪ Creates a complementary RNA strand to Xist (essentially an  RNAi actor)

▪ The created resulting double strand is degraded very quickly,  removing Xist transcript

o Interesting finds have occurred, however, with the Xce Region (this  is downstream of the Xic region)

▪ This is the X-Chromosome Controlling Element

∙ Has an impact on which chromosome becomes Barr  


▪ When a gain of function mutation occurs on the Xce  

location, the result is a Tsix expression (which counteracts  

Xist and leaves the Chromosome open)

∙ Gain of function on Xce in a a Chromosome causes  

Tsix expression

▪ Xce causes Tsix expression

Non-Mendelian Genetics

∙ So the one that lacks Xce activation (from mutation)  

leads to the preferential creation of Barr body

∙ So it can keep activated (and by doing so inactivate the  

other) a given maternal/paternal chromosome

▪ But the normal Xce has no effect

∙ Phenotypes – Why Do Patches Form?

o This has to do with regional replication, which starts with Blastula  formation

▪ Each cell randomly turns off one of the X’s

▪ After, they continue to replicate, in essence forming large  

patches of the original cell

o Diagram

∙ Barr Body Process

o 1. Initiation

▪ Occurs in early stages, up to the Blastula stage

▪ Very early on

o 2. Spreading

▪ Mechanism of the Chosen X Chromosome (The Barr Body)  

being coated by RNA

▪ This is done by the Xist RNA and proteins

o 3. Maintenance

▪ Every cell that arises afterward shows the same X

Chromosome compaction

Non-Mendelian Genetics

∙ So Why Barr Bodies?

o Amazon Women considerations (Triple X females)

▪ There is a masculinization effect because of the slight  

increase in proteins and hormones during early development

▪ So the presence of the Chromosome still makes a difference  even though to will be Barr Bodies

o They are compacted in very specialized manner to allow some gene  transcription

▪ 1. Facultative – can switch between heterochromatic and  

Euchromatic regions

▪ 2. Psuedoautosomal

∙ Genes that are present on X and Y Chromosomes need  

to be expressed

∙ Otherwise, the Barr Body would defeat the purpose of  

balancing out protein presence

∙ So Dosage Compensation would be reversed

∙ Mic2 is a gene present in both

∙ So Barr Body regions with Pseudoautosomal can  

switch between Hetero and Euchomatin

▪ 3. Xist

∙ Xist has to unwind to make an RNA to coat the  


∙ Has to be allowed to be transcribed so Maintenance of  

Barr Body can occur

2. Genomic Imprinting

∙ Also known as monoallelic imprinting

o Phenomena in which expression of a gene depends on whether it’s  inherited from the male or female parent  

o The inheritance is dependent entirely on how the genes are marked o So only one gene is leading to expression (monoallelic)

▪ But Haploinsufficiency is dealing with defects

∙ Early in process

o Occurs in Spermogenesis or Oogensis

o Marking memory (chick knowing its mother)

∙ Example of IGF2 (Insulin Growth Factor 2)

o What were the findings?

Non-Mendelian Genetics

▪ Normal Father + Mutant Female = NORMAL

▪ Mutant Father + Normal Female = ALL MUTANT

o The General Rule of Imprinting:  

▪ Imprinting is silencing

o So it is seen with Igf-2 that it is paternal expression

∙ Process of Imprinting

o Overall

▪ 1. Establishment

∙ During gametogenesis

∙ Which is going to be silenced?

▪ 2. Maintenance

∙ Development of embryos as well as all somatic cells  


∙ Somatic cells of adult

▪ 3. Erasure

∙ The imprint is removed

∙ Occur only in germ cells during Meiosis

∙ Then reimprinted as well

o Makes it so the presence of imprinting markers only exists during  life

▪ So imprinting is only present in lifespan

▪ Reestablishment is gender specific and occurs during  


∙ Examples

Non-Mendelian Genetics

o House Fly Methodology

▪ Male has three X-Chromosomes (2 paternal, 1 maternal)

▪ And always the 2 Paternal Chromosomes are silenced

∙ They are imprinted (so maternal X is functioning)

∙ Father’s are marked for silencing

▪ 2X/2Somatic = 1 (Female), 1X/2 Somatic = .5 (Male)

o Marsupial Mammals

▪ The paternal X is chosen for inactivation

∙ Imprinting is a process of silencing

o Differential methlylation

▪ Methylation occurs on the Chromosome to differentiate  


o Involves the presence of an ICR (Imprinting Control Region)

▪ A portion is called the Differentially Methylated Domain  


∙ In the specific region with [Cytosine – Thymine – 

Cytosine] rich region (added to Cytosine)

∙ Done either in sperm or oocyte, not both  

▪ So methylation occurs on Cytosine

▪ Addition of Methyl Group causing silencing

▪ ICR has 2 sites for binding:

∙ 1. Proteins that can enhance transcription (inducing  


∙ 2. Proteins that can inhibit transcription (preventing  


▪ So when you Methylate the region, those binding sites  

(specifically the enhancement sites) cannot be accessed

∙ 1. Causes bending in the Chromosome

∙ 2. Sterically hiders access

o Methylation prevents enhancer protein binding through:  

▪ 1. Genomic bending

▪ 2. Stereochemical Hindrance

o Let’s go back to IGF2 – why is it encoded?

Non-Mendelian Genetics

▪ The ICR region is large and inclusive of a few genes, three of  particular interest:

∙ Igf-2

∙ H19


o So a review:

▪ Methylation (Imprinting) does not occur in gametogenesis –

erasure occurs

∙ Adding methylation does not occur during germ  


∙ Only later does the imprinting occur based on the  

given sex

o It is erased and then reestablished based on the  


▪ So, if a maternal gene is Expressed, the Paternal gene is  


∙ In this instance the paternal gene is imprinted  


∙ So, on the same idea, Maternally Imprinted = Paternal  


∙ So, in A Paternally Imprinted Chromosome, a maternal  

mutation results in the disease of interest

o Prader Willie is Maternally Imprinted (so  

mutation in paternal gene results in disease)

o Angelman is Paternally Imprinted (so Maternal  

Deletion results in Disease)

Non-Mendelian Genetics

▪ So in the table, Expression is the Opposite of Imprinting


Allele Expressed




Wilms tumor-suppresor  gene; controls excessive  growth



Insulin production; cell  

growth hormone



Produces Insulin-Like  

Growth Factor II; cell growth



Receptor for Igf-2






Splicing Factor on genes



Neurotransmitter Receptor

∙ Examples: Angelman Syndrome and Prader-Willie

o Angelman – hyperactivity and unusual seizures

▪ Paternally Imprinted (so a functional maternal chromosome  

is adequate)

o Prader Willie – reduced motor function, obesity

▪ Maternally Imprinted (needs proper Pternal DNA)

o The concept of Isodisomy is Important

▪ Meiosis provides copies of each (paternal and maternal)

▪ Isodisomy results in unequal distribution (so two copies of a  chromosome exist from one parent)

o A Look at Chromosome 15

▪ PW an AS genes are very close

▪ SNRPN (Small Nuclear Ribonucleoprotein)

∙ Lack of proper SNRPN expression from the Paternal  

Chromosome results in Prader-Willie

∙ Involved in the removal of introns and splicing exons;  

creates splicesomes (so issues lead to problems  


▪ UBE3A (Ubiquitin Protein Ligase 3A)

∙ Lack of proper UBE3A expression from the Maternal  

Chromosome results in Angelman Syndrome

∙ Ubiquitin tagging of malfunctioning proteins in  


Non-Mendelian Genetics

3) Extranuclear Inheritance 

Overview – involves DNA and inheritance patterns outside of the nucleus (also  known as cytoplasmic inheritance)

∙ Extranuclear DNA is congregated and found inside a region called the  Nucleoid

o A single, circular chromosome of DNA

o A Nucleoid can have more than one copy of a chromosome and a  chromosome can code for more than one gene

o But they also have ORF’s (Open Reading Frames) which encode for  polypeptides with unknown functions

∙ Mitochondrial DNA (mtDNA)

o Have only about 1-5 nucleoids

o Chromosomes are about 17,000 base pairs

o 13 Genes

▪ Most of the genes code for ETC proteins (oxidative  

phosphorylation proteins)

▪ Most genes used in Mitochondria are shipped in

∙ Chloroplast DNA (cpDNA)

o 150,000-160,000 base pairs (nucleotides)

o 110-120 Genes

▪ Many still shipped in from outside

Non-Mendelian Genetics

o 15-20 Nucleoids


∙ 1. Maternal Inheritance (seen in the 4 O’clock Flower)

o The pigmentation depends solely on the maternal plant

▪ And this pigments is present in an Extranuclear location  

(plant chloroplasts)

▪ These are passed through the Eggs’ Cytoplasm

▪ A mix of the two is known as heteroplasmy

o 4 Test Crosses (all looking at THE LEAF)

▪ 1. White Female with Green Male

∙ White Offspring

▪ 2. Green Female with White Male

∙ Green Offspring

▪ 3. Variegated Female with Green  


∙ Any of the Three Offspring

▪ 4. Green Female with Variegated  


∙ Green Offspring

o Leaf Color

▪ Similar to the Blastula question  

with Mouse Coat Color, the somatic cell can contain all  

mutant chloroplasts, which case it becomes white

▪ But if both are present, Green dominates

o Heteroplasmy and its Phenotypic Effect

∙ 2. Petite Trait (Seen in Yeast)

o Mitochondrial Determination of Growth Patterns

▪ More mitochondria leads to more growth

▪ So with the mutants, the mitochondria don’t promote growth  as they should

o Yeast gametes are Isogamous

▪ This means there is no real difference between the male and  female

▪ They’re simply

Non-Mendelian Genetics

o Two Types of Genetic Inheritance Seen

A. Segregational Mutations 

This is the normal  

Mendelian expectation for  the inheritance patterns 

B. Vegetative Mutations

In Vegetative Mutations, one form completely dominates  the other, so the two extremes occur

– I. Neutral

The mutant has no effect 

II. Suppressive

The mutant form dominates 

∙ In this case, two and two ∙ So all wild type show up ∙ They reproduce rapidly and  outpace the wild types 

∙ 3. Organelles

o The effect on inheritance varies among species

▪ Gamete production plays a huge role but can be very  


▪ But let’s consider most studied species

o Heterogamous Organisms (the two produced gametes are different) ▪ Female Gamete – the egg is large and full of all the nutrients  

and machinery to sustain life for a period of time

∙ Provides cytoplasm and organelle machinery

▪ Male Gamete – much smaller and motile, not constructed to  

survive for long on its own

∙ Has a small package of proteins it uses to fertilize, so  

no real contribution other than DNA

▪ Process considered Oogamous – the female gamete (oocyte) is  

highly specialized and developed

∙ So the offspring inherit all of their organelles from the  

mother, male or female

∙ A rare exception is called paternal leakage, when the  

sperm contain a few mitochondria

o But even with a sever case, 1-5 paternal exist for  

every 100,000 maternal

o Mitochondrial diseases can arise

▪ So because the mother provides all the mitochondria,  

mitochondrial related disease can be spread more easily

Non-Mendelian Genetics

▪ Some examples:

∙ 1. Liver, Kidney, Brain tissue (higher concentration of  


∙ 2. Leber’s Heredity Optic Neuropathy (affects retinal  

ganglion cells)

Endosymbiotic Theory 

∙ Primordial Eukaryotic cell engulfed smaller Bacterial cells

o Purple Bacteria – Mitochondria

o Cyanobacteria – Chloroplasts

∙ There are two aspects to this theory

o Endocytosis – the cell wall is broken down and the membranes of  the two move together

▪ Hence the development of the double membraned nature of  

Chloroplasts and Mitochondria

o Symbiosis

▪ There was some sort of mutual benefit present

▪ While it’s not entirely clear, it is thought the Eukaryote  

gained the ability to Photosynthesize and Produce ATP while  

the bacteria where now in a nutrient rich environment

∙ This theory is supported by further research:

o 1. Organelles have circular chromosomes

o 2. Organelle genes have striking similarities to bacterial genes  rather than nuclear genes

Genetic Linkage

Chapter 6: Genetic Linkage

Important Concepts of Linkage 

Genetic Mapping Overview

∙ Displays

o 1. What Genes are Present

o 2. What Physical Order They’re In

∙ Vocab to Know

o 1. Synteny – two or more genes are present on the same  


o 2. Genetic Linkage – genes are being linked

o 3. Linkage Groups – a chromosome

∙ Bateson and Punnet’s Work

o Two Factor Heterogeneous Cross

o So they question is – why was it so far off?

Crossing Over

∙ Pachytene Phase

∙ Crossing Over increased the variability

o Nonrecombinant is the Pure Linkage Group

∙ So Watson decided to look at three traits

o He assumed that linkage would be consistent and ubiquitous

o But he found that some were “linked” to varying degrees

o Additionally, he found a large variety of potential options as well

∙ How Could They Prove Crossing Over is Occurring?

o Took a look at corn

o Corn has 10 Chromosome, and various Chromosome 9’s have  

some abnormalities

▪ I. Translocated Piece of 8

▪ II. Knob on the End

o Both ends were also known to have specific gene loci

o So they decided to run a cross (Test Cross): Heterozygote with  


o Proved?

▪ I. Were able to view the Crossed Over portions under the  


▪ II. The crossing Over created new phenotypic combinations

Genetic Linkage

∙ Mitotic Recombination

o This occurrence is much less likely

▪ This process is always Nuclear, so not like variegated leaves

o Two Periods of Occurrence:

▪ I. It Can Happen Very Early on in Development – different  

body tissues

▪ II. Or It Can Happen After Development – mosaicism, patches

o Ex) Drosophila Body Types

▪ Body Color and Bristle Type is found on the X Chromosome

▪ So females have 2 X-Chromosomes in their cells

▪ When they replicate, the homologues on the two can match  

up and cross over

∙ So think about it: couldn’t occur in males in this  


▪ Also consider what would happen at either of the locations of  


∙ I. Early Stages – divided body tissues

∙ II. Somatic Cells – can form a path of phenotypically  

altered appearance

Genetic Linkage

Dr. V’s Questions for Clarity 

∙ Linkage Groups vs. Linked

o Linkage Groups –

o Linked –

∙ Chi-Squared Analysis

o The possibilities in this case are “Recombinant” and  

“Nonrecombinant,” so the DF = 1

∙ Crossing Over Occurs in Pachytene Phase of Prophase I between Non Homologues

∙ Genetic Mapping

o It is done with a Test Cross

o So there needs to be a recessive individual

o To Lay it Out:

∙ Keep in mind that whole segments of Chromosomes are being moved, not  simply alleles

Genetic Linkage

o To prove this, a Heteromorphic Allele was utilized (Chromosome  9 in corn)

∙ Mitotic Recombination

o This is incredibly rare

o But it should not be confused with the effects of Maternal  

Inheritance in the form of Variegation

o This effect is Mosaicism, a Nuclear Phenomenon  

Genetic Mapping 

Key Concepts

∙ Overview

o Also known as Chromosome Mapping

o Definition – the arrangement of genes along the Chromosome

o Distance is being measured and is the key consideration

o Loci are being defined

∙ Uses:

o Eugenics and Disease Analyses

o Evolutionary Comparisons

∙ The Process

o Recombination Frequency is measured

▪ This is the capacity to Cross Over

o They are measured in Map Units (mu) or CentiMorgan (CM) ▪ Comes out to be that 10% frequency related to 10mu

∙ Test Crossing  

o Always need a Heterodominant paired with a Recessive

▪ So with Sex Chromosomes an extra consideration must be  

made: Hemizygous Recessive Can Occur in Males

▪ Heterozygote + Homozygote

o See how, when following gamete formation, the pieces start to  really fit together

Genetic Linkage

Genetic Linkage

Some Profiles of Examples of Genetic Mapping

∙ I. Multiple Genes – Drosophila

o Have about 10 Identified Genes on the X-Chromosome

o To analyze, they need to be broken into pairs

o What becomes evident is that going with frequency higher than  30% and up to 50% leads to Underestimation

▪ Multiple Crossovers can occur at that point

▪ So the preferred method is start close and move outward

▪ The smaller numbers are more closely linked and are  

therefore more accurate overall

o So these are the genes we’re looking at (Five Total Loci)

Genetic Linkage

o So to determine the significance of crossing over, each needs to be  compared in pairs

∙ II. Trihybrid Cross – Drosophila  

o The same general idea will apply

o Three Groups of Offspring Now Become Evident

Genetic Linkage

▪ 1. Parental Combinations

▪ 2. Intermediate (Single Crosses)

▪ 3. Double Crosses

o These groups will be important in the ultimate analysis of gene  mapping

∙ III. General Goal

o Compare the frequencies between two alleles to begin mapping the  Chromosome

Calculating the Map Distance

∙ Formula

(������������������ ������������������ �������������� �������� �� ������ �� 

���������� ������������������) �� 100

This is equivalent to…

(���������������������� ������������������ 

���������� ������������������) �� 100

∙ You always have to compare two genes, but you can’t use a Dihybrid  cross – there’s nothing else with which to compare them

∙ If the genes are far apart, there’s a higher likelihood of recombination  occurring

∙ It’s also always best to start “close up,” so to say, and “zoom out” o So calculate the smaller numbers (more accurate) and add them o Instead of taking the big numbers first


∙ Example I: Simple, The Bristle Types (Dihybrid)

o Recall, the colored picture in the test cross, the numbers were  about 450 and 75 for Parental and Recombinant, respectively.

o So look at how to plug those numbers in:

Genetic Linkage

∙ Example II: More Complex, The Above Trihybrid Cross

o But when more genes are involved, more options become apparent o The next example will outline two manners in which you can  determine the mapping units in a Trihybrid Cross

o As a side note, Polyhybrid Crosses become too complicated to be  useful and efficient

Genetic Linkage


∙ One crossing over prevents another from occurring

∙ Calculating Interference

���������������� ������������ �������������� = �������� ������������������ = (���������� 1/2 ������������������)��(���������� 2/3 ������������������) �� = �������������������� ���������������������� =���������������� ������������ ��������������������

���������������� ������������ ��������������������

������������������������ = 1 − ��

∙ When Prevention Occurs, it is called Positive Interference

∙ Negative Interference Never Occurs

Chromosomal Structure and Number

Chapter 8: Chromosome Structure and Number Overall Concepts 

∙ Overview of Mutations

o Genetic Mutation – single gene, single protein; small sequence  

change; Allelic Mutation

o Chromosome Mutation – array of proteins and genes in large  


▪ 1. Structure – Aberration

▪ 2. Number – Genome Mutation

∙ Cytogenetics

o Definition – examination of the chromosomal compaction and  

composition of an organism

o Process for Examination

▪ 1. Addition of Division Inducing Agent (condenses and  

duplicates Chromosomes)

▪ 2. Allowance of Replication

▪ 3. Centrifuge to Stop Replication and Collect Sample (forms  

sample pellet)

▪ 4. Addition of Hypotonic Solution (swells up cells)

▪ 5. Drop Cells on a Slide and Fix Them (no more changes can  


▪ 6. Stain Cells With Geimsa (stains different components  


▪ 7. Addition of Trypsin (breaks down histones, reveals DNA  


▪ 8. Photo Imaging (computer or camera)

▪ 9. Karyotype Arrangement

o Karyotype Arrangement – the entire chromosome complement of an  organism arranged from tallest to shortest

▪ Homologue Identification

∙ 1. Size

o While size can help identify Homologues, it is no  

suggestive of overall genomic complexity of an  


∙ 2. Centromere Position

o 1. Meta-Centric – in the middle

o 2. Sub-Met-Centric – closer to the middle

o 3. Acro-Centric – closer to one end; ‘p’ is short, ‘q’  

is long

o 4. Telo-Centric – only one arm

Chromosomal Structure and Number

∙ 3. Banding Patterns

o Banding is induced by the addition of the  


o This can identify and differentiate based on Loci,  

not based on Alleles

∙ Mutations

o General Types

▪ 1. Loss of Genetic Material

▪ 2. No Loss of Genetic Material

o Material Loss is a Common Form

▪ Deletion/Deficiency vs. Duplication/Addition (Loss/Gain) ▪ Inversion (No Loss/Gain)

▪ Translocation (No Loss/Gain)

Chromosome Mutation Types 

1. Deletion (Break Occurs in the Chromosome)

∙ Terminal (end is lost) vs. Interstitial (section is lost)

∙ An overall expression imbalance occurs

∙ Can de expressed as:

o I. Haploinsufficiency

▪ A deletion occurs in the Dominant Allele Location

▪ So the expressing gene is lost

o II. Pseudo-Dominance

▪ Dominant Allele (Cystic Fibrosis) is present, giving normal  


▪ But if the normal phenotype is removed, only the recessive  

sick copy is left

▪ So the recessive allele is enough

o III. Recessive Parity

▪ Consider why imprinting makes a difference – one functioning  gene is already lost

Chromosomal Structure and Number

∙ Why does Deletion occur?

o One form is Chromosomal breaking

o But Paralogs can also lead to Improper Crossing Over and a  deletion

o The locations are misaligned because of the similarities

▪ So there is always a loss and always a gain (deletion or  


▪ But never both

▪ Homologue separation

o This means that even if this were to occur every time, only 50% of  the final gametes would have the problem

▪ The process only occurs between two of the homologues  

during Prophase I

▪ The remaining 50% will be split 50/50 (delete, add)

2. Duplication

∙ Imbalance is the Key Idea

o Differentiates it from Deletions – they still have the whole genome  present

o But now they have more of a given protein present

∙ How Does Duplication Occur?

o Misaligned Crossover occurs again

o Places homologue gene onto the adjacent homologue

o But it is not always detrimental

Chromosomal Structure and Number

∙ To What Does Duplication Lead?

o I. Paralogs

▪ Peripheral Neuropathy is an example (Demyelination  

affecting motor function)

∙ Chromosome 17 duplication

∙ Big toe and muscle myelination degrades

o II. Gene Families

▪ Globin is an example

∙ Myoglobin (precursor) placed itself on 22

∙ Alpha Globin on 16

∙ Beta Globin on 11

▪ Various forms are active – has an evolutionary significance

▪ Globin Timeline

∙ Fetus – Zeta/Epsilon

∙ Developing Second & Third Trimester – Alpha/Gamma

∙ Adult – Alpha/Beta

o III. Copy Number Variation

▪ Segmental duplication occurs again

∙ It confuses the alignment process during replication

∙ So crossing over is supposed to occur between allelic  

locations, but instead it occurs between Homologues  

in different locations

▪ Variable Genes

Chromosomal Structure and Number

∙ Small Segment of DNA (1000bp) present multiple  


∙ Variation of variable gene in the population 

▪ Nonallelic Homologue recombination

∙ Transposable Elements are an Example

o Different chromosomes can align due to duplicated regions

o Small Chromosome (21) and Large Chromosome (22) could have  homologues that swap

o You have to have 1) Similar Centromere 2) Homologues

3. Inversion

Pericentric Paracentric

∙ Centromere is  

∙ Centromere is not involved


o Much more harmful –

o Centromere  

can result in multiple  

also flips


∙ Dicentric Bridges and  

Monocentric Fragments


∙ Total content remains consistent

o Often times they remain functional and no real changes occur o In 2% of cases you can detect it Cytogenetically

o And often defects occur as well

∙ But what if it affects the Phenotype? What if function is lost? o 1. Point Break Effect

▪ The break occurs in the middle of a gene, rendering it  


▪ Proper protein can no longer be created

o 2. Location Effect

▪ Regulatory sequences are relocated

∙ Promotor sequence can be moved

∙ Imprinting sequence can be moved

∙ Inversion Heterozygotes

o In these individuals, one chromosome has inversion and the other  doesn’t

o So, considering expression, the genes from the proper chromosome  can compensate

▪ As long as the break hasn’t occurred

o This only plays a role during gametogenesis

▪ In this context, 2 Gametes will inherit the inverted  


▪ And other mechanistic errors occur as well

∙ What are the differences? (Always occurs during Synapsis during  Prophase I)

Chromosomal Structure and Number

o Differences occur during the Loop Formation, Homologous pair up o And after this the Centromeres are connected to Kinotechore  microtubules

▪ So Acentric Fragments are simply lost

▪ And Dicetric Bridges are ripped apart

4. Translocation – no net loss or gain of gene content occurs; usually occurs  as an improper repair mechanism (so dysfunctional telomere)

∙ 1) Simple – one break occurs

o Normally, a small Break Occurs and the Telomere responds

▪ But in this case the Telomere is not properly functioning and  the broken portion gets moved

o Simple and balanced has no loss of gene function

o Dysfunction Comes as a Result of:

▪ A. Point Break Effect  

▪ B. Location Effect

Chromosomal Structure and Number

∙ 2) Reciprocal – two breaks occur

o Often times balanced translocation occurs with two breaks o Unbalanced can be very deleterious to the organism

▪ Genes are lost, severe effects can result

▪ 13/14 and 14/21 Translocations are good examples

▪ Caner, Infertility, XX Male Syndrome all occur

∙ SRY is cleaved and connected to female

∙ 3) Robertsonian – also known as Centric Fusion

o As per the name, the Centromere’s of two fuse together

o Most common in the 14/21 Chromosomes

▪ Known as Familial Down Syndrome (14 (long)-21(small)  


▪ Breaks happen in the Centromeres in Acrocentric  


▪ “p” arms are removed and a new chromosome is created with  the whole set of #21 genes (psuedotrisomy)

Chromosomal Structure and Number

o Forms one Metacentric Chromosome

o Occurs during Crossing Over, so Four Chromatids are present (and  then two become one)

Chromosomal Structure and Number

5. Translocation Mechanisms In Gametogenesis – Individuals with  Balanced Translocation Have a Greater Risk of Gamete Translocation

o Overview of the Concept

▪ It all depends on segregation  

patterns in Meiosis I

▪ Misaligned crossover occurs,  

nonhomologous crossovers

▪ This occurs because of  

previously translocated  

homologues now present on  

different Chromosomes:

∙ 1. Alternate Segregation (Balanced)

o Balanced Translocated Stay  


o Chromosomes on opposite sides segregate into the same cell

o Balanced-2 Segregates with Balanced-1

o All the gametes are fine (they are balanced, two normal and two  trans)

∙ 2. Adjacent 1 (Unbalanced)

o Centromere of Normal-2 goes with Translocated-1

o Adjacent non-homologous chromosomes segregate into same cell o Centromere of Two goes with One

o All four will have deletions and duplications

▪ No viable gametes

∙ 3. Adjacent 2 (Unbalanced)

o Centromere of 2 Pairs with Centromere of 2

o Adjacent Homologous Chromosomes Segregate into the same cell o Centromere of Two goes with centromere of Two and vice versa and  vice versa

Chromosomal Structure and Number

Chromosome Number Variation 

General Overview

∙ Terminology

o 1. Aneuploidy – a single additional chromosome is present/taken  away

o 2. Eupoidy – normal number is present

o 3. Polyploidy – a set of chromosomes is removed or added

∙ Differentiation

Polyploidy Anneuploidy 

∙ Sets of  

∙ Individual Chromosomes


∙ Genomic number changes, almost always deleterious  

∙ 2n (diploid),  


3n (triploid),  

o Because each gene will now have 150% production


∙ Ex: Jimson Weed

o Diploid Number is 2n

o No Sex Determining, so 12 Chromosomes present in  


oSo with 12 Autosomes, there are 12 possible  


∙ 2n+1, 2n-1

∙ Aneuploidy Diseases

Trisomy 21


Down Syndrome

Mental retardation, structural  developmental issues

Trisomy 18


Edward Syndrome

Mental and physical  

retardation, extreme muscle  tone

Trisomy 13


Patau Syndrome

Mental and physical  

retardation, organ defects,  early death (2-3 days)

Trisomy 1

Fetal Death

Fetal Death

XXY (Male)




Sexual immaturity, breast  swelling

XYY (Male)


Jacobs Syndrome


XXX (Female)


Triple X Syndrome

Tall and Thin, Menstrual  Irregularity

X0 (Female)


Turner Syndrome

Short stature, sexually  


Chromosomal Structure and Number


∙ Definition – simply having present a proper number of chromosomes o Usually this is a rigid number – variations are often lethal

o But plants can display a sort of “euploidy polyploidy” pretty  


o Parthenogenesis is another example

Euploidy Variations 

1. Haploid

o Parthenogenesis

2. Polyploidy

o Plants

o Amphibians

3. Endopolyploidy

o In essence, particular locations in the body can display a variation  in the proper chromosome number

o These are usually very specific for reginal function

▪ Liver cell, is an example (can be 8n)

▪ Heart Muscle cells also

▪ Insects have Polytene Chromosomes

o Polytene (extended and connected chromosomes) can be studies in  interphase

▪ Mostly in Salivary glands of Drosophila and other insects

▪ So many are present

▪ They’re uncondensed, which creates new opportunities



∙ G1 ???? S ???? G1 (And Repeat)

∙ Chromosome replication is  


∙ Overall increased functioning ∙ They arrange themselves close to  one another

∙ Normally, Cyclodependent  Kinases check for damages to  allow progression

o Here they don’t allow  


∙ They end up arranging themselves  close to one another in an  

uncondensed form

∙ “Reduplicaiton”

∙ This is our process

∙ The idea is related to Polytene  chromosomes, but splitting  

eventually occurs

Chromosomal Structure and Number

o Overexpression can occur

o But no spindle apparatus from  G2

o So they remain in a clump,  called a Chromocenter

∙ So a Polytene Chromosome  occurs

∙ With splitting occurring but no  Telophase or Cytokinesis, Nucleate  forms can vary from cell to cell o 1. Mononucleate

o 2. Sinnucleate

o 3. Polynucleate

∙ This variation in number depends  on the environmental demands of  the organism

4. Plants (Autopolyploidy)

∙ Plants can intentionally induce Polyploidy cells to alter gene expression o Banana and Potatoes are good examples

o 30-35% of flowering plants

∙ Often results in sterility because odd numbers can be mixed in the  chromosomes number (triploid plus diploid)





Can occur in Three  


1. Meiosis I

Homologues don’t separate

2. Meiosis II

Sister Chromatids don’t separate

1. Failure of Sister  

Chromatids to separate

2. Failure of Sister  

Chromatids to Release

This is rare because  

homologues don’t come  together

Important to consider  Hybrid Vigor and  


Unrelated species are  crossed

Sterility is a common side  effect (synapsis cannot  occur during Meiosis)

Mule (Donkey, n64+  

Horse, n62)

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