GENETICS F13

Biology 2030

Rene Dawson, Ph.D. dawson@biology.utah.edu JTB335 T H 12:30-1:50 pm by appointment or after class

Tuesday Tuesday Tuesday Tuesday

8:35 - 9:25 am 9:40-10:30 am

LS107 2030-004 LS107 2030-002

John McCormick John McCormick Miles Christensen * Ani Schjelderup *

10:45-11:35 am LS107 2030-003 11:50am-12:40pm LS107 2030-005

Wednesday Wednesday Wednesday Wednesday

8:35 - 9:25 am 9:40-10:30 am

LS111 2030-006 LS111 2030-008

Michael Guernsey Michael Guernsey Daniel Ence Daniel Ence

10:45-11:35 am LS111 2030-009 11:50am-12:40pm LS111 2030-007

* Contact Miles and Ani to arrange office hours

Biol 2030 F13 2-3:20pm T&H Genetic Analysis: An integrated Approach

$130 ($275)

Turning Point clicker optional but recommended: $60 new $45 used Register Clicker on Canvas before the next class
Device ID

-see Canvas for syllabus, slides Exam Practice, etc.

Biol 2030 is a problem-based class and the concepts build. The key to your success is doing many, many problems.
Be aware of your thought patterns. Make of list of places you get stuck

1 Mastering Genetics (required) 2 End of chapter questions (even # answers in back) 3 Additional Problems Sets on Canvas

Blooms Hierarchy of Thought

listed from the lowest to highest levels of thought!

1. Knowledge - memorize, define, recall 2. Comprehension - summarize, describe, discuss 3. Application - use ideas in different situations, solve problems 4. Analysis - compare and contrast, ask questions, separate concepts into parts, understand relationships 5. Synthesis - combine known facts with new idea, creative solutions, hypothesize 6. Evaluation - relevance, significance, identify new frontiers, personal judgments.

For THIS lecture

TEXT Basic Mendel (Chapter 2: 25-43)

For NEXT lecture

TEXT Probabilities (Chapter 2: 44-50)

First discussion review problems APS #1 (Mendel) Mastering due this Sunday
Introduction to MG Ch 2 Mendel pt 1

GENETICS
Biology 2030

Lecture 1 Chapter 2 MENDELs LAWS

Alternative forms of a gene lead to different traits

We are diploid meaning each person inherits 2 homologs 1 from mom and 1 from dad Chromosome contain a DNA molecule A gene can be thought of as: the portion of DNA that encodes a protein (or functional RNA) Homologous chromosomes have genes at same loci (place)

Can have alternative forms of a gene (alleles)

Phenotype the appearance of an individual ABd Genotype the genetic composition of an individual AABbdd Homozygous carry the same alleles AA or dd Heterozygous carry different alleles Bb Dominant trait is the one that shows in the heterozygote Recessive trait does not show in heterozygote Bb is a carrier of recessive t bb is homozygous recessive not called a carrier even though it carries two copies of b

In the garden of Mendel

Modern genetics began with Gregor Mendels quantitative experiments with pea plants 1854-1863

Without knowledge of DNA, chromosomes or meiosis described the units of inheritance and how they pass from generation to generation

PEAS good choice of model system

White

-lots of variation, easy to detect -easy to grow -short generation time -can do out crosses -self fertilizing, keel closed

Removed stamens from purple flower

PARENTS (P) Carpel

Stamens

2 Transferred
Purple

Mendel followed the Scientific Method

- Make initial observations about a phenomenon or process - Formulate a testable hypothesis - Design a controlled experiment to test the hypothesis - Collect data from the experiment - Interpret the experimental results, comparing them to those expected under the hypothesis - Draw a conclusion and reformulate the hypothesis if necessary
OFFSPRING (F1)

pollen from stamens of white flower to carpel of purple flower

3 Pollinated carpel
matured into pod

Planted seeds from pod

see Figure 2.3

Figure 2.4
parental

Monohybrid Cross
AA aa
Mendel started with true breeding plants, self-fertilization produces same traits generations after generation (homozygous) F1 showed only one of two parental traits Trait not seen in F1 reappeared in 25% of F2 (recessive) One gene with two alleles Purple (A) is dominant to white (a)

First Filial

Aa Aa x Aa

Second Filial offspring of F1 X F1

A_

aa
Phenotypic ratio 3:1 3A:1a Genotypic ratio 1:2:1 1 AA : 2 Aa : 1 aa This tells you that one gene is involved!

see Figure 2.4

see Figure 2.6

MENDELS FIRST LAW:SEGREGATION

From his experimental data, Mendel concluded that: An organism has two distinct elements or units (alleles) for each inherited characteristic (diploid).

Two alleles of a trait will separate or segregate from each other into (haploid) gametes Gametes combine randomly to form offspring

Mendel's Inferences (Abstractions):

Idea that a discrete particle of information (gene) transmits information governing each trait. Two copies of this information are present in the adult (diploid). One copy is transmitted to the progeny from each parent via the gametes There are different forms or versions of each bit of information (alleles). Dominant and recessive types of alternative versions.

Phenotype vs genotype. Because of dominance the effect of recessive alleles are masked in the heterozygote (skip a generation)

Mendelian Traits
Mendel started with 34 different varieties and found 7 traits that behaved the same way. We call these Mendelian traits. They all have a trait that is encoded by a single gene with 2 alleles, and simple dominant/recessive

Figure 2.1

Quantification Replication

Reciprocal Crosses

Figure 2.5
All crosses were the same; it did not matter if pollen came from purple or white plant (autosomal, not on sex chromosome)

Figure 2.5

Phenotype

dominant

recessive If Rr, then only half are round

If RR, then all are round

R R

r Rr
Rr

r Rr
Rr

R r

r Rr
rr

r Rr
rr

 Mendel was not an isolated genius

lots of botanist were working on plant hybridizations not as lucky with choice of model systems, or traits (height)

cultural difference observed didn't use math

mendelweb.org original paper and discussion

publish 1866 and went virtually unnoticed not an obscure journal widely distributed in England, US and Russia Darwin saw, took notes on next article in journal, no marks on Mendel, didn't read?, wasn't wondering about source of variability

Independent Assortment of Two Traits

Dihybrid Crosses
Seed shape gene with two alleles: Round and wrinkled Seed color gene with two alleles: yellow and green

By looking at two characteristics at once (dihybrid), Mendel found 9:3:3:1 ratio, each trait 3:1 so not affecting each other

3:1 Round:wrinkled 3:1 Yellow: green

See Figure 2.11 Round and yellow are independent

MENDELS SECOND LAW: INDEPENDENT ASSORTMENT

During gamete production, two (unlinked) genes segregate their alleles independently. The inheritance of one does not influence the chance of inheriting the other.

Figure 3.4 9 3 3 1 3:1 Round:wrinkled 3:1 Yellow: green

Round and yellow are independent

Do ONE 16 square dihybrid cross so that you can SEE the results. After that do two independent monohybrid crosses and multiply.

P F1

AABB x aabb AaBb

A AA Aa a Aa aa

B BB Bb b Bb bb

F1 self cross AaBb x AaBb 9/16 A_B_ 3/16 A_bb 3/16 aaB_ 1/16 aabb

A 9:3:3:1 ratio tells you that two independent (non-interacting, unlinked) genes are involved!

The forked-line diagram is used to determine gamete genotypes and frequencies

See Figure 2.10

GENETICS
Biology 2030

Lecture 2 Chapter 2 PROBABILITIES

Probability
The likelihood that an event will occur The probability that a coin will land heads up is The probability that a heterozygous individual (Bb) will produce a gamete with the B allele is

Inheritance follows the rules of probability multiplication and addition can be used to determine the probability of certain events occurring

1/2 x 1/2 = 1/4 BB READ 2.4 and When to add 1/2 x 1/2 = 1/4 bb and when to multiple 3 methods 1/4 Bb + 1/4 bB = 2/4 = 1/2 Bb document on Canvas

Product Rule
The probability of independent events = the product of the probability of each event If both parents are heterozygous (RrYy) what is the probability that they will produce a rryy child?

Probability of a sperm with r allele = Probability of a ova with r allele = Probability of a rr child is X =

rr

yy

rr 1/4 x yy 1/4 = rryy 1/16

rryy

see page 44

Sum Rule
The probability of dependent events = the sum of probability of each event Parents are heterozygous for a trait, R. What is the chance that their child carries at least one dominant R allele? Probability of child carrying RR = Probability of child carrying Rr = Probability of child carrying R_ = + =
see page 45

p probability of a boy ; q probability of a girl Binomial expansion: (p + q)3 p3 3p2q 3pq2 q3 p3 1/8 (3 boys); 3p2q 3/8 (2 boys, 1 girl); 3pq2 3/8 (1 boy, 2 girls); q3 1/8 (3 girls)

Binomial Probability pages 45-47

Pascals Triangle A shortcut to the binomial expansion.

In a self-fertilized Gg pea plant, give the proportion of yellow and green peas in pods with six peas each p probability of yellow peas 3/4; q probability of green peas

see Figure 2.15

Chi-Square (2) Analysis Tests the Fit Between Observed and Expected Outcomes

= (O

2 E) /E;

0 = observed values E expected values

Probability (P) value is the probability that the results of an experiment will deviate from the expected results by chance degrees of freedom (df) is the number of independent variables = number of outcome classes, n, minus 1

Statistical Significance
A statistically significant result from 2 analysis has a P value less than 0.05 P<0.05 means that the experimental result has less than 5% probability (1/20) of happening by random chance, thus the null hypothesis (random chance) is rejected P values above 5% indicate a nonsignificant deviation between observed and expected results. failure to reject the null hypothesis (random chance)

The Chi Squared method allows you to determine if the observed and expected numbers are significantly different. GgLl x ggll (if unlinked)
Observed O Expect (if unlinked) E O-E d

Phenotype

Genotype

d2(dxd)

d2/E

GL gl Gl gL

G_L_ ggll G_ll ggL_

965 944 206 185

1/4 (575) 1/4 (575) 1/4 (575) 1/4 (575)

390 369 -369 -390

152,100 136,161 136,161 152,100

264.5 236.8 236.8 264.5

2= = 1002.6
The formula for chi squared is 2 = d2/E means the sum of E is expected d(difference)=O(observed)-E(expected) d=O-E df (degrees of freedom)=# phenotypes -1= (1 in this case) fix this for 1 df a 2 >110.83 gives you a P value of < 0.001 which is extremely significant. The "null hypothesis" is always that the "Observed values are NOT different than the Expected values".