Exam 4 Fact Sheet/Lecture Notes

Recombinant frequency

# of recombinants/total number of offspring x 100 Cannot be greater than 50% the proportion of offspring of a genetic cross that have phenotypes different from the parental phenotypes due to crossing over between linked genes during gamete formation

What do chromosomes contain?

-long DNA molecule + accessory proteins -the long DNA molecule contains "instructions" --instructions come in discrete units that we call genes (each chromosome has MANY genes) --each gene is located at a SPECIFIC location on a SPECIFIC chromosome

Two major problems to solve in cell division:

1. The actual feat of cell division: a) take one cell b) make two out of it c) both new cells need to have EVERYTHING that the original cell had 2. Only getting cell division WHEN and WHERE it is beneficial to the organism -- REGULATION

Match the specifics of Mendel's work with corresponding general steps in the scientific method. What are the steps of the scientific method? Define each. Give an example of each from Mendel's work.

1. The work of Gregor Mendel a) the scientific method b) Mendel's explanatory framework Good experimental design: 1. characters with discrete variants (e.g., purple vs. white flowers; "either-or") 2. started with "true breeding" varieties What is "true-breeding"? Offspring produced from two "true-breeding" flowers of the same color would always have the same color flowers as their two parents. P Generation (true breeding parents) Breed true breeding purple flower with true breeding which flower --> all plants had purple flowers Making sense of the data/observed pattern Why were ALL the flowers in the F1 generation purple? Why were some flowers in the F2 generation white? Why was the ratio of purple:white in the F2 generation approximately 3:1?

Homozygous genotype

A genotype in which both alleles are identical PP or pp Individuals with homozygous genotypes are homozygotes

Heterozygous genotype

A genotype with two different alleles Pp or pP Genotype carried by heterozygotes

Meiosis I -- Anaphase and Telophase/cytokinesis

Anaphase 1 -- - homologous chromosomes are seperated from each other Telephase 1 -- - cells divide from one another - nuclear membrane reforms, two new cells are in the process of forming

Yeast

Arguably has taught us more about eukaryotic cell cycle regulation than any other organism we have ever studied 2001 Nobel Prize in medicine (http://jnci.oxfordjournals.org/content/93/23/1766.full) Its byproducts have likely messed up more humans than any other organism in history

Process of meiosis for chromosomes

Before meisos -- 2n chromosomes per cell End of meiosis -- n chromosomes per cell

Define biological inheritance; compare and contrast the hypotheses of "blending inheritance" and "particulate inheritance". Write these definitions in your own words. When do the two different hypotheses predict the same outcomes? When do they predict different outcomes?

Blending inheritance: Traits of offspring will be an average of the traits of the parents. Problem: Loss of variation predicts a population uniform in its traits -- but this isn't what we see! Particulate inheritance: Alternative versions of heritable "particles" (i.e., different alleles of the same gene) account for variations in inherited characters

Describe how cancer relates to checkpoints, mutations, and loss of proper regulation of the cell cycle. Write a paragraph defining each term (checkpoints, mutations, regulation) and then relating them in the cell cycle:

Both checkpoints and cyclin degradation act to prevent division -- cancerous or unhealthy cells from crossing the checkpoint between G2 and the Mitotic phase Cancers result from a loss of cycle control --> chemotherapy halts the cell cycle Proper regulation in healthy cells Anchorage dependence: cells require a surface for division Density dependent inhibition: cells form a single layer Density dependent inhibition: cells divide to fill a gap then stop Cancer cells: No longer exhibit anchorage dependence -- continue to divide even if they are not in contact with the ptitri dish and over fill a gap "Multi-hit" or "multi-step" hypothesis: mutations in several cell cycle regulators build up -Mutations in genes which,w hen functional, maintain checkpoints -Because it takes multiple steps, exposure to anything mutation causing increases cancer risk but does not always give you cancer -- uv radiation, cigarette smoke, radioactivity

Organization of genetic material in cells

Cell --> Nucleus in cell --> Multiple chromosomes in nucleus --> Each chromosome one very long DNA molecule + accessory proteins

Diploid vs. haploid

Cells having 2 copies of each chromosomes (two chromatids) vs cells with only 1 copy (half the DNA, one chromatid)

Construct pictures or tactile representations of what is happening to cells and chromosomes during the major steps involved in accomplishing mitosis. Draw a cell with 4 chromosomes going through all stages of mitosis. Repeat for some different number of chromosomes of your own choosing. Answer the following: What is the smallest number of chromosomes you can use for this exercise? Why? The major events happening to chromosomes during interphase and the mitotic phase

During S phase of interphase all the genetic material is duplicated -- one DNA molecule synthesizes into two DNA molecules Chromosomes go through S phase --> end up with two DNA molecules that are attached to one another --> still considered 1 chromosome Chrosomes go through mitosis --> get split into seperate chromatid Chromosomes --> The structure of the DNA molecules -- the number of free-floating things in the nucleus/cell, one free-floating genetic object Chromatid --> when two copies are still together before breaking up, they are 1 chromosome, but each copy is a chromatid -- corresponds to DNA molecule, sometimes on chromosome is formed from multiple chromatids -- number of chromatids is the same as the number of DNA molecules

Meiosis I -- Prophase and Metaphase

Early in Meiosis I -- Prophase 1 •Homologous chromosomes loosely pair up, aligned gene by gene •In crossing over, nonsister chromatids exchange homologous DNA segments (à IMPORTANCE will become apparent soon...) -- exchanging pieces -Nuclear envelope has broken down -Chromosomes became condensed Middle of Meiosis I -- Metaphase 1 •Pairs of homologous chromosomes line up in the middle of the cell, with one chromosome facing each pole •Spindle attaches to chromosomes

Explain what a chromosome is to someone who is not a biologist; describe where chromosomes are in the cell and what they are made of. Write a short paragraph here in your own words:

Examples: Dog diploid cells have 78 chromosomes, so for dogs 2n = 78, and thus n = 78/2 = 39 dog gametes (dog sperm and dog eggs; haploid) thus have 39 chromosomes each Cat diploid cells have 38 chromosomes, so for cats 2n = 38, and thus n = 38/2 = 19 cat gametes thus have 19 chromosomes each

Explanatory framework/theories

Explanatory framework = multiple internally consistent hypotheses that together explain general phenomena of interest. In science this is also called a theory.

Describe four main processes that create genetic variation in the offspring produced from sexual reproduction Build upon your paragraph from the previous learning goal. List and define all four if you didn't already: 1. 2. 3. 4. Explain each of these in your own words if you haven't already. Note when in the process of the cell cycle, meiosis, and/or life cycle each can occur (for example: What is a mutation, and when do mutations commonly occur?).

Four mechanisms contribute to genetic variation in the offspring of sexual reproduction: a) Mutations = change in DNA sequence -Mutations create different versions of genes called alleles b) Independent assortment of chromosomes -behavior of chromosomes during Meiosis 1 -Homologous pairs of chromosomes orient randomly during Meiosis I -maternal and paternal homologs assort into daughter cells independently of the other pairs --How one chromosome lines up is independent from how any others line up --Assortment - might have chromosomes lined up as blue blue red on one side, red red blue on the other Ex. --There are two ways for a cell with 4 chromosomes to line up --- there are 4 possible assortments of chromosomes in the gametes depending on what the cell looks like to start with -- c) Crossing over •During crossing over, homologous chromosomes pair up gene by gene and exchange homologous segments •This combines alleles that originated from two parents into a single chromosome! d) Random fertilization

Phases of Mitosis/getting ready for mitosis Construct pictures or tactile representations of what is happening to cells and chromosomes during the major steps involved in accomplishing mitosis. Draw a cell with 4 chromosomes going through all stages of mitosis. Repeat for some different number of chromosomes of your own choosing. Answer the following: What is the smallest number of chromosomes you can use for this exercise? Why? The major events happening to chromosomes during interphase and the mitotic phase

Getting ready for mitosis -- G2 of interphase Chromosomes are in diffuse form floating around the nucleus First stage of mitosis -- Prophase: Chromosomes condense --> they become supercoiled -- distinct objects -- for efficient movement during subsequent processes Preparation of the mitotic spindle -- a molecular scaffold that will help guide chromosomes Each chromosome is made of two sister chromatids Prometaphase: 1) Nuclear membrane breaks down 2) Spindle attaches to chromosomes 3) Chromosomes become fully condensed Metaphase: Chromosomes line up in the middle of the cell Anaphase: Sister chromatids separate, they are pulled apart by the spindle As soon as the chromatids are separated, each one by definition is a full-fledged chromosome Telophase: Nuclear membranes reform around groups of chromosomes -- need to make a new nucleus for each of the new cells -- chromosomes decondense Cytokinesis can begin at the same time -- division of everything else

Describe what happens to chromosomes during meiosis. For the drawings you made for the learning goal above, write a narration to go along with them, or annotate those drawings with full sentence explanations of each stage.

Have to start diploid to do meiosis -- chromosomes must be in pairs Interphase -- pair of homologous chromosomes in diploid pant cell --> Chromosomes duplicate Pair of duplicated homologous chromosomes with sister chromatids -- diploid cell with duplicated chromosomes We now have 2n chromosomes with 4n chromatids --> 2 rounds of cell division will give us 4 cells each with n chromosomes We have only 1n of haploid cells --> Meiosis 1 Homologous chromosomes split -- haploid cells with duplicated chromosomes --> Meiosis 2 Sister chromatids separate --> now have 2 haploid cells with unduplicated chromosomes

Cellular questions

How you get 2 cells from one How you make a cell from two gametes

Predict patterns of heredity and trait expression for crosses involving genotypes that have various combinations of dominant and recessive alleles (also, do the reverse: predict genotypes from observations of patterns of heredity and trait expression).

If something is homozygous for two genes that we are studying, there is only one type of gamete that they can make, and we will have a one by one pundit square

independent assortment

Independent assortment = all possible combinations of inherited alleles of different genes are equally likely in an individual's gametes

Construct a diagram or flow chart of the order of the major processes and steps involved in the cell cycle. Draw a picture on your own. Then check it against the pictures in the book. What did you leave out? Did you get everything and in the right order?

Interphase: G0 --> this is where cells go to take a break (could be permanent, but mostly there for important reasons) but is technically part of interphase, hanging out waiting in the wings in the event of an injury when they can go back into the cycle to provide new cells that are needed G1 --> Growth one/gap 1 -- cell gets bigger, new organelles are made Synthesis --> new copies of genetic material -- duplication G2 --> Growth two/gap 2 -- cell is preparing to go into mitotic phase Mitosis and Cytokinesis

homologous chromosomes

Members of a pair of chromosomes that are the same size, same appearance and same genes. Homologous chromosomes have the same genes in the same locations -- members of a pair each have the same genes in the same locations not necessarily identical in the content of their recipes -- book is the same, same recipe on the same page, but different versions of the reciped

Compare and contrast the similarities and differences between mitosis and meiosis. Construct and fill in your own compare-and-contrast table, similar to what we did in lecture. Try to do it without looking at that table, of course!

Majorly different in Prophase 1 and Metaphase 1 in Meiosis vs. Mitosis Meiosis -- chromosomes are paired up Majorly different in Anaphase 1 and Telophase 1 Meiosis -- sister chromatids stay together, bits of chromatids are mixed up and exchanged

Construct pictures or tactile representations of what is happening to cells and chromosomes during the major steps involved in accomplishing meiosis. Draw a cell with 4 chromosomes going through all stages of mitosis. Repeat for some different number of chromosomes of your own choosing. In your drawings, find some way to denote some chromosomes red and some blue. How many of each color are there? Why? What is the smallest number of chromosomes you can use for this exercise? Why?

Meiosis = the division of a diploid cell leading to the eventual production of haploid cells Meiosis makes haploid cells out of diploid cells --Begin with a cellt hat is initially diploid in the ovary or testis, then through the process of meisos we wine up with eggs or sperm

Relate Mendel's "law of segregation" to the behavior of genes and chromosomes during meiosis. If you have not done so already for a previous goal, write a definition of the "law of segregation" in your own words. For pictures you drew of chromosomes going through meiosis (for previous learning goals), how could you use those to demonstrate the "law of segregation"? What do you need to add to those pictures to show it? Make new drawings showing the "law of segregation" or make the appropriate additions to your drawings from the previous learning goals. Explain your drawing and the reasoning in your own words

Mendel did not know about genes or chromosomes per se. However, in modern terms, Mendel's "law of segregation" can be phrased as stating that the TWO alleles an individual possesses for a given gene SEPARATE during gamete formation. If the two alleles an individual possesses for a given gene "segregate" (i.e., separate) during gamete formation, at the chromosomal level: haploid cells are arising from diploid ones

List several biological functions or processes in which cell division plays a key role. Make a list here of as many as possible:

Mitotic cell division: 1) Renewal 2)Replacement after injury. 3) Development 4) For single-celled organisms: reproduction

Mitotic phase: Construct a diagram or flow chart of the order of the major processes and steps involved in the cell cycle. Draw a picture on your own. Then check it against the pictures in the book. What did you leave out? Did you get everything and in the right order?

Mitotic phase -- when the cell divides Mitosis -- division of nucleus and nuclear material Cytokinesis -- division of the rest of the cell

Understand the concept of "checkpoints" as applied to the cell cycle; explain how checkpointing can be accomplished with molecules. Write a paragraph in your own words in which you define "checkpoint" and then explain how they work:

Multiple checkpoints on the cell cycle in healthy cells -- control of monitoring cells is localized, don't involve any computing Mitotic checkpoints: move on to the next phase only if conditions are right. • Prevents sick or precancerous cells from dividing and maintains proper cell number. • Checkpoint sensing mechanisms monitor: -Progression of the current phase -DNA integrity -Cell density -Cell anchorage G1 checkpoint M checkpoint: Cell monitors if the chromosomes are attached to the spindle, until it has detected that the chromosomes are attached to the spindle, it will not leave prometaphase With full chromosome attachment, go ahead signal is received G2 checkpoint The cell cycle is regulated by concentrations of proteins molecules in the cytoplasm -- dynamic process, build up when they're needed, decrease when they're no longer needed to signal mitosis One example: Cyclin accumulation: Causes binding and signals mitosis Cyclin degradation: Binding of cyclin to CDK in reversible Whether you have a lot of mitosis promoting factor is dependent on whether you have a lot of cyclin

Mutations

Mutations (changes in an organism's DNA) are the original source of all genetic variation Mutations create different versions of genes called alleles

Naked mole rat

Naked mole rat is cancer proof Key mechanism that arrests cell division when there is a high density of cells

Describe alternative hypotheses that Mendel formulated and tested about inheritance; describe what each hypothesis predicted Mendel should have observed; relate his actual findings to the falsification of some hypotheses and support for others. List each hypothesis here and then explain what it means in your own words. Hint: there are 5 explicit hypotheses we covered in lecture related to Mendel's work:

P Generation: True breeding parents F1 generation: hybrids F2 generation: hybrid purple flowered plants mixed with true breeding white flower plants 1) Law of independent assortment???: Alternative versions of heritable "particles" (i.e., different alleles of the same gene) account for variations in inherited characters 2) For each character (gene) an organism inherits two alleles, one from each parent 3) If the two alleles at a locus differ, then one (the dominant allele) determines the organism's appearance, and the other (the recessive allele) has no noticeable effect on appearance 4) "Law of segregation" = the two alleles an individual possesses for a heritable character separate (segregate) during gamete formation and end up in different gametes

Three possible genotypes with two alleles (P)

PP Pp pp

The scientific method

Scientific inquiry often begins with simple curiosity about the natural world. From there, systematic observations document patterns. Those patterns, informed by existing scientific theory, help us generate plausible, testable hypotheses about the causes of the patterns we have documented. Generating general hypotheses from specific observations involves inductive logic. Scientific hypotheses generate testable predictions, which are tested with experiments and/or further observational work. Comparisons of predictions with actual data lead to re-evaluation of hypotheses, and refinements of theory. The scientific method is NOT a recipe with each step done once and always in the same order. Rather, we continuously move back and forth between its components to refine, rarefy, and expand our knowledge in so doing.

Combinations of inherited characters

Seed color: Possible phenotypes = Yellow OR green Yellow is dominant to green 2. Seed shape: Possible phenotypes = Round OR wrinkled Round is dominant to wrinkled

Meiosis II

Starting with the two cells produced by Meiosis I, at the end of meiosis II we have a total of 4 daughter cells, all haploid, all genetically different Prophase II - nuclear membrane dissolves Metaphase -- chromosomes line up int he middle of the cell Anaphase II -- sister chromatids seperate Telephase II and cytokinesis -- haploid daughter cells forming

Chemotherapy/chemotherapetuic drugs

Stops the cell cycle -- stops cell division Side effects (after all, cancer cells are not the ONLY dividing cells in a person's body) The most affected tissues have the most cell division. • hair, nails • skin • bone marrow • gut Many chemotherapeutic drugs were first isolated from plants: Vinca alkaloids from the Madagascar periwinkle bind to spindle building blocks, prevent the assembly of spindles by binding to the building blocks -- interrupts attachment of spindle to chromosomes Podophyllotoxin from American and Himalayan mayapples prevents DNA replication -- interrupts s phase

strict dependent assortment

Strict dependent assortment = inherited allele combinations are ALWAYS preserved in the gametes an individual produces

Good vs. bad things of cell division

The Good • growth • repair • replacement • renewal • development The bad • cancer

Describe what happens to chromosomes during the cell cycle and mitosis. For the drawings you made for the relevant learning goal above, write a narration to go along with them, or annotate those drawings with full sentence explanations of each stage.

They are copied and split

Explain reasons why the cell cycle must be regulated in order for any human to be healthy during growth, development, and maintenance of the body. Explain why in your own words here. Write a short paragraph:

What happens when cell division goes wrong? 1) Cancer = uncontrolled cell division 2) Developmental malformations

diploid cells

cells that contain 2 sets of homologous chromosomes are called diploid (example: all human cells OTHER than our gametes) most of the cells we can see are diploid, only cells that are haploid are gametes Chromosome number in diploid state = 2n

haploid cells

cells that have only one of each kind of chromosome are haploid (example: our gametes) most of the cells we can see are diploid, only cells that are haploid are gametes -- sperm and egg Chromosome number in haploid state = n

Recombinant gametes

combinations of alleles that are non-parental

Variety of sexual life cycles in the biological world

common theme: alternation of haploid/diploid, meiosis/fertilization Animals -- diploid multicellular organism Plants and some algae -- haploid multicellular organism and diploid multicellular organism, sporophyte Most fungi and some protists -- haploid unicellular or multicellular organism

Alleles

different versions of a specific gene

Cell cycle

from the time a cell is formed (from the division of its parent cell), to the time it undergoes its own division into two cells Interphase: growth, synthesis, growth Mitotic phase: Mitosis, cytokinesis

Ploidy

number of sets of chromosomes in a cell

Interphase

period of the cell cycle between cell divisions (G1, S, G2) Cell spends most of it's time here

random fertilization

source of genetic variation caused by the unlimited number of possible sperm & egg combinations, which gamete makes it to fertilization from the father is independent of which gamete makes it to fertilization from the mother

Test cross

the crossing of an individual of unknown genotype with a homozygous recessive individual to determine the unknown genotype

Explain how and why the chromosomal makeup of an offspring produced by sexual reproduction differs from that of its parents Write a paragraph in your own words in which you list each of the explicit processes that makes offspring chromosomally different from either parent. Define each technical term you use in your own words. Describe HOW each process contributes to making offspring different from their parents.

•"2^n rule": the number of possible chromosome sorting combinations = 2n For humans (n = 23), there are 2^23 = 8,388,608 possible combinations of chromosomes! The behavior of chromosomes during meiosis and fertilization reshuffles alleles and chromosomes every generation

Crossing over

•During crossing over, homologous chromosomes (non-sister chromatids) pair up gene by gene and exchange homologous segments •This combines alleles that originated from two parents into a single chromosome! Parental type chromosomes -- no crossing over, exactly the same as parents Recombinant chromosomes -- chromosomes that have been changed in some way from their parent chromosomes