Dia- MCB181R Exam 4

Gene

A sequence of DNA that encodes a protein

Trait

The physical manifestation of a gene or set of genes. Also called a phenotype

Genotype

gives rise to the Phenotype. The particular combination of alleles present in a given organism

Alleles

gene’s several different variations. Slight variation in its specific nucleotide sequence from one organism to the next.

Homozygous

An organism that can inherit 2 of the same allele for a particular gene.

Heterozygous

Organism can inherit 2 different alleles for a gene. What the associated trait ends up looking like depends on which allele is dominant.

Basis of Inheritance

IN meiosis 1, which homolog ends up in each daughter cells is independent for each chromosome- based on random orientation of homologs during metaphase. We can predict the chances of offspring inheriting particular combinations of alleles using the mathematical rules of propbability.

2 key principles:

• The segregation of alleles of each gene in genome. Individuals inherit 2 alleles of each gene. WHen that individual forms its own gametes, those 2 alleles separate equally into each gamete.

• The two alleles of one genes on one chromosome segregate into gametes independently. The independent assortment of different genes on different chromosomes
  

The law of Segregation

• This reflects the separation of homologogous chromosomes during anaphase 1 of meiosis.

• When heterozygous F1’s form their own gametes, A allele and a allele will get separated. When meiosis 2 is comple, ½ the gametes will contain A and the other ½ a.

• the two alleles of each gene separate during gamete formation (meiosis)

• each gamete receives only one allele for each gene.

Independent Assortment of genes

Reflects the fact that random alignment of homologs during metaphase 1

• During crossover in Prophase 1, alleles of 2 genes on a chromosome can get “recombines if crossing over occurs between where they are located (their loci) along the chromosome

• The allele combinations that were originally together in each chromosome (A with B and a with b) have recombined (A with b and a with B) in 2 of the 4 chromatids.

• Each daughter cell (haploid gamete) at the end of the meiosis 2 receives one chromatid which one of the following genotypes: AB, Ab, aB, or ab

• Most homologous chromosomes have one or more crossover. All of which are independent events

3:1

Ratio of recessive phenotype in F2. probabilities of each phenotype in next gen. Expected ratio of dominant:recessive phenotypes

Punnett Square

The probabilities of different allelic combos from this union can be determined in this.

1 (AA): 2 (Aa) : 1 (aa)

Probability of each genotype in next generation.

Dihybrid crosses

A genetic cross that examines the inheritance of two traits at once. This is how Mend established the 2nd principle of inheritance. This is when he tracked two traits on 2 different chromosomes over successive generations.

F2 Generation

The generation resulting from a cross breed from F1 individuals.

9:3:3:1

When you cross heterozygotes for 2 genes to each other, you get this phenotypic ratio..

There are 9 possible genotypes and 4 possible phenotypes.

• Results from independent assortment of 2 genes when 1 allele of each gene is dominant and when the two genes affect different traits.

Non-Recombinant

Independent assortment of A and B did not occur.

Frequency of Recombination between Genes

on a single chromosome, it depends on their physical distance from each other on the chromosome.

• Scientist can use this across generation to map the relative locations of genes on a chromosome

Genes close to each other

• the less likely crossing over will occur between them

• rarely get recombined, and are said to be linked to one another

Law of Independent Assortment

genes on different chromosomes segregate independently of one another.

Locus

a particular position, point or location on a chromosome

NonHomologous Chromosome

chromosomes that contain different sets of genes

Hybridization

The interbreeding between two different varieties or species of an organism.

True Breeding

The physical appearance of the offspring in each successive generation is identical to the previous one

P1 Generation

The parental generation in a series of crosses

F1 Generation

The first offspring or filial, generation

Reciprocal Crosses

Crosses like these, in which the expression of the trait in the female and male parents are interchanged.

Diploid Organisms

In this, The molecular basis oof dominance in this case is the fact that only one copy of a gene is needed to carry out its proper function

1:2:1

Expected Ratio of AA:Aa:aa genotypes.

The Principle of Segregation

The alleles in heterozygous individuals become sparated in the gametes and appear in 1:1 ratio

The segregation of alleles reflects the separation of chromosomes in meiosis. Homologous chromosomes separate during anaphase 1 of meiosis 1, leading to the segregation of the alleles. Chromosomes display independent assortment during meiosis when they are sorted into daughter cells randomly.

How do the mechanics of meiosis and the movement of homologous chromosomes underlie Menndel’s principles or segregation and independent assortment?

If you know the genotypes of the parents, you can determine the alleles that occur in each gamete by applying Mendel’s principles of segregation and independent assortment. One systematic approach makes use of a Punnett Square, which predicts the probability of every possible combination of one maternal allele with one paternal allele for a particular cross. F

How can you predict the genotypes and phenotypes of offspring if you know the genotypes of the parents?

Principle of independent assortment

States that segregation of one set of alleles of a gene pair is independent of the segregation of another set of alleles of a different gene pair. It is obsesrved when genes segregate independently of one another. Also reflect the random alignment of chromosomes in meiosis.

Linked genes

Not all genes undergo independent assortment. Gene near one another in the same chromosome do not assort independently of one another. This is the genes in the same chromosomes that fail to show independent assortment. They also tend to move together into gametes

Epistasis

The gene products can interact to affect the phenotypic expression of the genotupes, resulting in a modification of the expected ratio. interaction between genes that modifies the phenotypic expression of genotypes.

• Types of these leading to different modification of the 9:3:3:1 ratio. Among the more common modified ratios are 12:3:1, 9:3:4 and 13:3

recombinant

Only two of the 4 products of meiosis are recombinant because crossing over takes place at the four-strand stage of meiosis. With 2 strands that are recombinant and 2 that are nonrecombinant, the frequency of recombination is 2/4= 50% and so this is the maximum

Why is the upper limit of recombination 50% rather than 100%?

Independent assortment means that a doubly heterozygous genotype such as A B/a b produced gametes in the ratio 1/3; A B ; 1/4 ; A b : 1/3 ; aB : 1/4; ab. The first and last are nonrecombinant gametes, and the second and 3rd are recombinant gametes. The frequency of recombination is therefore 1/4+ 1/4 = ½ or 50%. This means that independent assortment is observed for genes that are far apart in the same chromosom as well as for genes in different chromosomes

For 2 genes that show independent assortment, what is the frequency of recombination?

The closer, or more tightly linked, that two genes are to each other, the smaller the frequency of recombination because it is less likely that a crossover event would take place in the interval between them. The farther two genes are from each other, the greater the frequency of recombination becusae there would be a greater chance that a crossover event will happen in the interval between the genes. The frequency of recombination can be used as a measure of distance between the genes.

How can recombination frequency be used to build a genetic map?

Inheritance Patterns for a Trait

These can be due to

• Different degrees of dominance

• Genes carried in the sex chromosomes are transmitted fdifferently in and in female (X- linked and Y-linked genes)

• Genes that are close together on the same chromosome do not undergo independent assortment (linkage)

• Mitochondria and chloroplast DNA follow their own inheritance pattern

• Sex chromosomes segregate into separate gametes during meiosis like any other chromosomes.

Sex Chromosomes

Similar to autosome (non-sex chromosomes 1-22) in many ways, but also some key differences. chromosomes that determine the biological sex of an individual

• Which are designation as the X-chromosomes and the Y chromosome.

Similarities of Sex Chromosomes and Autosomes

• Sex chromosomes are paired, just like any other chromosomes (either two X’s or X+Y)

• Sex chromosomes go through meiosis , along with all other chromosomes

Differences of Sex Chromosomes and Autosomes

The sex chromosomes for one of the two biological sexes are non-homologous. In humans, males have one X and one Y chromsoomes. Females have homologous sex chromosomes

• Almost none of the genes in the X chromosomes have counterparts in the Y chromosomes.

• The tips of the arms of the X and Y chromosomes share a small region of homology (red) so they can pair up during synapsis

Why do males have very little crossing over X and Y during prophase 1?

Random Fertilization

During sex results in an expected ratio of ½ XX (female) ½ XY (male) progeny

Sex Bias

reasons why genes on the sex chromosomes show non-Mendelian patterns of inheritance.

• For example, the gene for red-green color vision is carried on the X-chromosomes and using a punnett square, we can figure out why males are more likely red-green colorblindness.

X-linked inheritance

traits differ from Medelian inheritance patterns because inheritancce of recessive phenotypes is sex-specific. Refers to the transmission of genes that are found on the X-chromosomes across generations

Recesive phenotyppes are expressed more often in males because males have one one X chromosomes (and thus only need one recessive allele to express phenotype)

Human Genetics

More difficult to study because

• fewer offspring

• keeping track of generation is difficult (long generation times_

• Cant force amtings between people with genotype/phenotypes of interest

Pedigrees

Useful tools to study human genetics. Allow us to track patterns of inheritance based on phenotype (from which we can infer genotype). It is a diagram of family hisotry that summarizes the record of the ancestor/descendant relationships among individuals

Anatomy of Pedigrees

includes symbols representing individuals and relationships, with circles for females and squares for males, and lines indicating mating and offspring connections. They help visualize inheritance patterns across generations.

Affected Individuals

• Mostly males because they only need one copy of mutant gene to be affected and its a typical pedigree of an X-linked recessive trait.

• Can have unaffected sons because males transmited their affected X only to their daughters if the son is unaffected

• The heterozygous daughters of affected males carry the mutant X and can thus have affected sons

• Appear in each generation

• From matings in which one parent is affected, about ½ the offspring are affected

Autosomal Dominant Trait

Can use pedigrees to track other types of traits. These are the traits associated with a gene on autosomal chromosomes that’s expressed when an individual is heterozygous or homozygous for the affected allele. They appear in every generation.

1. Affected individuals are equally likely to be females or males

2. Most matings that produce affected offspring have only one affected parent. When a trait is rare, mating between two affected individuals are extremely unlikely. if so, then affected individuals will laways be heterozygous (Aa)

3. Among Mating in which 1 parent is affected, approximately half the offspring are affected

   • In a mating in which 1 parent is hetero dominant (Aa) and the other is homo(aa), half the offspring are expected to be hetero (Aa) and the other half will be homo recessive (aa)

One copy of a mutant allele is enough to express the trait

Autosomal Recessive Trait

can use pedigrees to tract this traits that are associate with a gene on autosomal chromosome that is expressed only when individual is homozygous for the affected allele.

The typical pedigree of an autosoal recessive trait.

• Males and females are equally likely to becom affected.

• Typically skips one or more generations.

• Unaffected parents can have affected kids because carriers dont manifest the affected phenotype.

• Affected individual may have unaffected parents

• For this trait that is rare, almost all affected individuals have unaffected parents .

• Affected individuals often result from mating between relatives, typically first cousins (because of the familial prevalence of carriers)

Has these characterisit because these alleles can be transmitted from generation to generation without manifesting the phenotype.

• If both parents are unaffected carriers of the allele, they both have the genotype Aa, and ¼ of their oddspring are expected to be homozyggous aa and affected

Autosomal Gene

Refers to a gene that is not found on a sex chromosome. These genes follow standard Mendelian inheritance patterns, they are inherited in pairs and can be dominant or recessive.

Requirement of the Cell

• A membrane separating the inside of the cell from the outside

• A way to encode and transmit infromation on how to build and maintain a cell

• Energy

Cellular Life

A biochemical reaction

Biochemical Reactions

Require Energy.

• Cell signaling, Transcription, mRNA splicing, translation, epigenetic, DNA replication, mitosis, meiosis are all drive that follow cellular processes.

The law of Thermodynamics

Determine whether a chemical reaction requires or release free enegy

Gibbs Free Energy (G)

Free energy (availabile to do work)

Net Change

Whether a chemical’s reaction will require energy or release it depends on this in Gibbs Free energy between the reactants and the products (deltaG)

• also The total gain or loss after adding and subtracting everything.

Endergonic

Nonspontaneous, Reactions with a positive deltaG requires an input of energy

• Ex: Chemical energy increases (positive deltaH) and the degree of disorder decreases (Negative deltaS).

Exergonic

They will occur spontaneousy and these reactions have a negative deltaG release energy.

• Even thhese spontaneous reactions don’t always proceed quickly on their own because of activation energy.

• Example: The hydrolysis of ATP

• Not all cells are spontaneous. Anabolic reactions are a good example.

Transition State

In order to get from reactant to product, the reacting atoms must go through this that has a higher free energy than the reactants. It is highly unstable and therefore has a large amount of free energy.

• This reaction is spontatnous because free energy of the reactant is higher than the free energy of the product and delta G is negative.

• Corresponds to the highest free energy

Activation Energy

Difference in free energy between reactants and transition states

Enzymes

This is how cells overcome this energy barrier. The “ase proteins” reduce activation energy so rx can proceed. Can reduce the activation energy, but they do not change the total deltaG of the reaction.

Will couple exergonic ATP hydrolisis w/ endergonic reactions so energy release from one can directly “fuel” the nergy required by other

• Increase reaction rate and decrease activation energy. Do not change other parametes

• Acts as substrates that bind to its active site.

• Can increase the rate of chemical reactions dramatically

• Redce EA of a chemical reactions

Lowering Activation Energy

Enzymes make reactions go faster

Because enzymes can stabilize the transition state

how does lowering activation energy make enzymes make reactions go faster?

An example of exergonic

The digestion of proteins from food into amino acids

Cell Metabolism

The sum of all chemical exs that occurs in a cell is referred to as this. It is driven by the building up and breaking down of carbon sources to harness or release energy.

• Sometimes the cell needs to build molecules

Anabolism

Cells in which synthesis of RNA strand in transcription build molecules, require free energy +deltaG, and in the form of ATP usually

• Ex: the synthesis of macromolecules such as carbohydrate and proteins

• Decrease entropy because they use individual building blocks to synthesize more ordered molecules such as protein or nucleic acids

Catabolism

The cells needing to break down molecules into smaller unit. Like to extract energy stored in its bonds. It releases free energy, negative deltaG in the process, produce ATP

• Results in an increase of entropy as a single ordered molecules is broken down into several smalles ones with more freedom to move around

ATP

always involved in both anabolism and ccatabolism . This can store the perfect little dose of energy driving chemical reactions. Through energetic coupling, this powers nearly all cell functions.

• A form of chemical energy

• A readily accesible form of cellular energy

The chemical energy in the bonds of this is used to drive many cellular processes such as muscle contraction, cell movement, and membrane pumps

• this is a molecule of adenosine covalently linked to 3 phosphte groups with high potential energy

• Made up of the base adenine and 5 carbon sugar ribose and is one of the 4 building blocks of DNA and RNA. To complete the molecule, ribose is attached to triphosphate or 3 phosphate groups

ATP; ADP

When ___(3P’s) is hydrolyzed into ___ (2Ps) it releases moderate amount (7.3 kcal/mol) of free energy (i.e, an exergonic reaction)

• This releases energy and can be used to do work.

Making ATP

A main priority for a ll cells. which bring us to cellular respiration

Cellular Respiration

A series of chemical reactions collectively. ATP package this energy into a chemical form that is readily accessible to the cell.

• The goal of this is to break down the food eat and make ATP out of it..

• The process of this extracts and package that energy in a readily available format (i.e, ATP) for fueling rxs.

• Also a series of catabolic reactions

Cellular Respiration Stage 1

Glycosis: Fuel molecules are partially broken down producing ATP ANd electron carriers.

• The reaction are taking place in Cytoplasm

• The inputs are: Glucose, 2 ATP, 2NAD+

• Outputs are 4ATP, 2 NADH, 2 pyruvate

• ATP’s payoff is 2 net ATP

  Potential energy stored in chemical bonds, ATP, electron carriers (NADH), electromechical graduent

Fermentation: allows glycosis to continue in the absence of oxygen

Cellular Respiration Stage 2

Pyruvate oxidation and citric acid cycle, where glucose derivatives are further broken down to generate more ATP and electron carriers.

Cellular Respiration Stage 3

Citric Acid Cycle: Fuel molecules are fully broken down, prdocuing ATP and electron carriers. Generated the most NADH which will be used oin oxidative phosphorylation to produce ATP. This is where original Glucose gets fully oxidized

Cellular Respiration Stage 4

Electron carriers then go to the electron transport chain, and oxidative phosphorylation occurs. Electron carriers donate electrons transport chain, leading to the synthesis of ATP.

because ATP Stores just the right ammount of energy to drive endergonic reactions—enough to power them without being wasteful—and this energy is readily accessible through its high energy phosphate bonds

Why is making ATP Important for cells?

Substrate-Level Phosphorylation of ADP and Oxidative Phosphorylation of ADP

ATP is produce in these ways in cellular respiration

Substrate-level phosphorylation

A phosphate is transferred from one molecule to another (occurs in first few steps of cellular respiration).

• an example of this is during the cell cycle, the cyclin/CDK complex phosphorylates target proteins that promote the cell cycle.

Oxidative Phosphorylation

Electron movement is coupled to ATP synthesis.

• this occurs through a series of couples oxidation and reduction or redox reactions that transfer electrons from one molecule to another

• A way more efficient process than 1:1 substrate-level phosphorylation

• Overall Process of coupling Electron Transport Chain and Chemiosmosis to make ATP

• The only time this occurs is when electron carriers will carry electrons to the final step of cellular respiration.

Inputs: 10 NADH, 2FADH₁

Outputs: 32-36 ATP

ATP’s “payoff” 32-36 ATP

The potential energy is stored throughout the electron carriers (NADH , and FADH2)

Redox Reaction

Involves transferring electrons from one molecule to another.

• Example: we are transferring electrons from molecule A to molecule B. When A has donated (gotten rid of) its electrons, we say it is oxidized. When B accepts (gains) those electrons from A, it becomes “reduced”

Happens at all stages of cell respiration

Electrons

Can contain a lot of potential energy. Come from the covalent bonds in glucose

During a redox rx

When an electron is transferred from a donor molecule to an acceptor molecule, some of that energy is released. That is why transferring electrons from one molecule to another such a great way to make ATP

Released Energy

Can be harnessed to perform work (in oxidative phosphorylation, it’s harnessed to power a super machine that pumps out of 2-4 ATP for every pair of e-!)

First Stages of Cellular Respiration

Dedicated to extracting electrons from covalent bonds in glucose (and its subsequent derviative) via oxidation, then transferring them to electron carriers via reduction

NADH and FADH₂

Electron Carriers. These are also the reduced forms because you add 2e- and H+

NAD+ and FAD

The oxidized form of electron carriers.

Reduced Molecule

How to determine if this happens is to follow the H+ (or gained Electron)

The X and Y chromosomes can pair during meiosis through regions of homology located near the tips of the chromosomal arms

How can the human X and Y chromosomes pair during meiosis even though they are of different lengths and most of their genes are different?

Meiosis in females results in X-bearing eggs only. In contrast, meiosisin males results in a 1:1 ratio of X-bearing and Y-bearing sperm. Random fertilization of the egg results in a 1:1 ratio of female: male offspring.

What is the biological basis for the 1:1 ratio of males and females at conception in mammals?

Homology

(the red part). The tips of the arms of the X and Y chromosomes share a small region of this. Very few of the genes in the X chromosome have counterparts in the Y chromosome.

1:1

The expected ratio of females:males refers to the sex ratio at the time of conception. This is also a patteriah that MOrgan observed in the F2 generation of his crosses

Secondary Sex Ratio

This sex ratio at birth can be observed, which differs among population but usually shows a slight excess of males.

the phenotype outcomes of females compared to males could be different

A cross involving an autosomal gene versus a sex linked gene would in that:

X-Linked Genes

Sometimes called Sex-linked genes. These are genes in the X-chromosomes.

• ALso provided the first experimental evidence that genes are in chromosomes

Wild Type

The most common allele, genotype, or phenotype present in a population; nonmutant

Genes in the X-Chromosomes

Exhibit a crisscross inheritance pattern

2 Important Principles governing the inheritance of X-Linked Genes

• The phenotypes of the XX offspring indicate that a male transmit his X chromosomes only to his female offspring. In this case, the X chromosomes transmitted by the male carries the white-eye mutation

• The phenotypes of the XY offspring indicate that a male inherits his X-Chromosomes from his mother. IN this case, the X chromsome transmitted by the mother carries the nonmutant allele of the gene

• Also called a crisscross inheritance