biol 105: genetics dr. needhi bhalla hartwell et. al. genetics: from genes to genomes fourth or...

BIOL 105: GeneticsDr. Needhi Bhalla

Hartwell et. al. Genetics: From Genes to GenomesFourth or Third Edition Text Book, Custom BookWe will not be using ConnectStudy Guide/ Solutions ManualPortrait Chapters (available on syllabus page of website)

TAs:Nicole PereiraCynthia CarrionRyan HoffmanKevin Hagy

Modified Supplemental Instruction (MSI):Chia-Ying Lee and Tram HuynhACE Learning Skills Counselor:Jessica Hernandez

eCommons: announcements, forum, access to website and grades Website: http://bio.classes.ucsc.edu/bio105/Fall2014

Enrollment

There is a sign-up sheet for students who were unable to enroll

Please print your name, UCSC email and reason you were unable to enroll

If you are eligible for the course (you have taken all the pre-requisites, etc), you will be notified and provided with a permission code

Permission codes will only be sent to UCSC emails

Syllabus

Weeks 1-5: Genes, alleles, crosses and progeny, genotypes andphenotypes, chromosomes, meiosis, mitosis, DNA, mutations, cloning genes, RFLPs

November 6: midterm

Weeks 6-10: mapping mutations (meiotic recombination), geneticmodel organisms and genetic research (cancer, signalingpathways, maternal effect mutations, mouse knockouts)

December 16: Final (cumulative)

Re: Exams and GradesMidterm #1: 80 pointsFinal: 120 pointsTotal: 200 points

There will be no opportunity to retake the exams, except in casesof proven medical emergency.

NO EXCUSES, NO EXCEPTIONS!

Regrade policy:To have an exam regraded, submit a one page written petition withreasons for requesting a regrade along with the original exam(midterm or final). The exam has to be submitted and will becompletely regarded. Single questions will not be regraded!!!This may result in scores increasing or decreasing.

Re: Exams and Grades, cont’d

DRC:If you qualify for classroom accommodations, please provide mewith an Accommodations Authorization from the DisabilityResource Center during the first two weeks of class in personoutside of class (e.g. office hours).Contact them at 459-2089 or get more info at http://drc.ucsc.edu.

The integrity of the exam process will be strictly enforced:http://www.ucsc.edu/academics/academic%5Fintegrity/index.html

During exams:no phonesno talking

If I see you with a phone or talking, I will assume you are cheatingYou will need a calculator for all exams

We will be using iClickers

We will be using iClickers, starting next week

You can purchase iClickers, used or new, from the bookstore

Register them online at http://www1.iclicker.com/register-an-iclicker/

Clicker questions will be used to gauge your understanding of atopic during lecture and for review questions

Answering clicker questions can help your final grade:If your final grade is borderline, I will take take into accountwhether you have answered 95% of the clicker questions

My teaching style

Slides will be available on the website after class on Thursday

Worksheets will be available on the website before class

download them before coming to class

The pre-requisites for this class are Biology 20A: Introduction to

Cell and Molecular Biology & Biology 20B: Development

and Physiology and the text book for those classes is

Life: the science of biology

I can talk fast

I take questions during class

Homework will help you prepareThe best way to do well in class is to understand the logic thatunderlies genetics:•Read the chapters that accompany the relevant lecture beforelecture to familiarize yourself with topics and terms (“lingo”)

•Attend lecture and do problems in class

•Do the homework that accompanies the lecture

•Seek out other genetics problems to practice

•Ask questions if something is unclear•In class•During Section•At office hours•MSI

Goals

Become familiar with genetics and its terminology:difference between gene and allele?difference between meiosis and mitosis?what’s the link between genotype and phenotype?understand & be able to explain terms like chromosome,mutation, cloning, etc.

Use and understanding of genetics in a professional capacity:doctorsresearchersnursesgenetic counselors

Goals, cont’d

Appreciate how the study of genetics and its technology affectour everyday lives:

discovery of new genes linked with disease or traitgenetic therapy of diseaseancestrygenetically modified foodscloning (of whole animals, I.e. Dolly)nature vs. nurture in development and behaviorstem cell technology

Further develop the ability to solve problems through logicalreasoning:

given a set of rules, can you draw reasonableconclusions?

GOALS for BIOL105

Understand the relationship between genes and alleles, mutant and wildtypealleles and genotypes and phenotypes

• Be able to symbolically represent a genotype given a phenotype or determine aphenotype given a genotype• Be able to predict the effect of a mutation on protein function and whether thatmutation will result in a mutant allele• Be able to predict if a mutant allele will be recessive or dominant based on itseffect on protein function

Understand that genes reside on chromosomes and chromosomes are made up ofhundreds if not thousands of genes. Understand how genes and alleles areinherited during sexual reproduction if they are on different chromosomes or onthe same chromosome.

• Be able to draw how chromosomes segregate during meiosis and mitosis• Be able to determine the probability that progeny will have a given phenotype orgenotype if provided with similar information about the parents or vice versa• Be able to calculate recombination frequency given the genetic distancebetween two genes on the same chromosome and vice versa• Be able to calculate the frequency of recombinant or parental progeny given thegenetic distance between two genes on the same chromosome and vice versa

GOALS for BIOL105 (cont’d)

Understand that multiple genes can affect a biological process and thereforegenetically interact.

• Be able to predict whether mutations are in the same complementation group orgene based on the results of a complementation test and vice versa• Be able to predict the phenotype of double mutants in a biochemical or signalingpathway if given the phenotypes of the single mutants and the order of gene action• Be able to order genes in a biochemical or signaling pathway given thephenotypes of double mutants and single mutants.

 Understand how to molecularly monitor DNA for the purposes of cloning or thesegregation of alleles

• Be able to predict where DNA will run on agarose gels• Be able to construct a plasmid map based on the pieces of DNA generatedby a restriction digest or predict the sizes of DNA pieces that result fromrestriction digest of a plasmid with a given map• Be able to predict what DNA will be visible using a probe on a Southern blot• Incorporate DNA molecular analysis with pedigree analysis and the inheritanceof genotypes and phenotypes

 Understand how to problem solve

• Given a set of rules, can you identify which rules are relevantand apply them to a new problem

Mendelian Genetics

Gregor Mendel

Pea plants

• Allow cross and self-pollination• Allow reciprocal crosses• Production of large amount ofprogeny to perform statistics

Two prevailing hypothesesto explain traits of progeny:•Blending•One parent contributes it all

• Pick traitsthat breedtrue(progenyalways looklike parent)• Pick traitsthat are antagonistic(dominantandrecessive)

When Mendel performs monohybrid cross:prediction if homunculus hypothesis correct?prediction if blending hypothesis correct?

When Mendel performs monohybrid cross:prediction if homunculus hypothesis correct?

all progeny will look like one (male) parentprediction if blending hypothesis correct?

When Mendel performs monohybrid cross:prediction if homunculus hypothesis correct?

all progeny will look like one (male) parentprediction if blending hypothesis correct?

polleneggs

When Mendel performs monohybrid cross:prediction if homunculus hypothesis correct?

all progeny will look like one (male) parentprediction if blending hypothesis correct?

polleneggs

When Mendel performs monohybrid cross:prediction if homunculus hypothesis correct?prediction if blending hypothesis correct?

all progeny will appear like mix of parentsrecessive parental trait will not re-appear in F2

P = parents

F1 = children

F2 = grandchildren

Law of segregation• each plant carries 2 copies of a unit of inheritance (genes) for each trait

•one from mom•one from dad

• different copies of these genes are called alleles• these two copies segregate away from each other duringreproduction to produce gametes (I.e. pollen and eggs, eggsand sperm, etc) with only one allele of each gene• fertilization = random uniting of two alleles to generatea zygote

gametes

products offertilization

Genes encode proteins that perform biochemical function

Alleles are variants of genes that can effect what the resulting protein does

Symbolically IndicatingGenotypes and Crosses

Symbolically IndicatingGenotypes and Crosses

new terms:homozygote (true or pure breeding)heterozygote

Symbolically IndicatingGenotypes and Crosses:

The Punnett Square

Genotypes and Phenotypes

P = Y/Y x y/y

F1 = Y/y

genotype phenotype

P = yellow x green

F1 = yellow

Different genotypes can result in the same phenotype

Genotypes and Phenotypes

P = Y/Y x y/y

F1 = Y/y

genotype phenotype

P = yellow x green

F1 = yellow

Different genotypes can result in the same phenotype

yellow

yellow yellow yellow

A Test Cross can determine thegenotype of a particular plant

What is the genotype of a plant that produces yellow peas?

A. Y/YB. Y/-C. Y/yD. y/y

A Test Cross can determine thegenotype of a particular plant

What is the genotype of a plant that produces yellow peas?

A. Y/YB. Y/-C. Y/yD. y/y

What genotype can you cross this plant with to help youdistinguish the correct genotype?

A. Y/YB. Y/yC. y/yD. Y/-

A Test Cross can determine thegenotype of a particular plant

What is the genotype of a plant that produces yellow peas?

A. Y/YB. Y/-C. Y/yD. y/y

What genotype can you cross this plant with to help youdistinguish the correct genotype?

A. Y/YB. Y/yC. y/yD. Y/-

Genotypic versus phenotypic ratios in a monohybrid cross

R/R x r/r R/rself

Genotypic versus phenotypic ratios in a monohybrid cross

R/R x r/r R/rself

R/R R/r

R/r r/r

R

r

R

r

Genotypic versus phenotypic ratios in a monohybrid cross

R/R x r/r R/rself

R/R R/r

R/r r/r

R

r

R

r

genotypic ratio: 1R/R : 2R/r : 1r/r phenotypic ratio: 3 round : 1 wrinkled

phenotypic ratiodoes not reflectgenotypic ratio

Terms we’ve covered:

“pure-breeding”genesallelesdominantrecessivegametesfertilizationsegregationgeneration, P, F1, F2, etc.mono-hybrid crossheterozygotehomozygotegenotypephenotypetest cross