BIO 30: LECTURE 4 – 6

LECTURE 4: LINKAGE AND RECOMBINATION Linkage in Drosophila

Linkage - Studied by Thomas Hunt Morgan

- X-linked traits in Drosophila (1910)
 Linear arrangement of non-allelic genes on
the same chromosome Phenomenon of CO (crossing over)
 Genes located on one chromosome coding
- Alfred Sturtevant, Hermann Muller, Calvin
for diff. traits
Bridges
 Genes do not assort independently
- Used to construct chromosome maps
 Genes can be separated by crossing over at
- Higher % of recombination = genes are far
pachytene
from each other
 Crossing over is the source of recombinants
 Number of gene per species exceed its
X-linked mutants
number of chromosome pairs
- Percent of recombination is used as a
Linkage in Sweet Peas measurement of distance
- One map unit (1cM) = distance of 1%
 Discovered by William Bateson, ER Saunders,
recombination
RC Punnett
 Exception to the principle of independent GENE / LINKAGE MAPPING IN DIPLOIDS
assortment
1) Do 3-point test cross
2 TYPES OF LINKAGE Genes:
C – colored endosperm
1. Complete Linkage
Sh – shrunken
- Genes are very close to each other, thus
wx – waxy
transmitted together
- Only parental types are obtained in the
Parentals: ShshCcWxwx x shshccwxwx
testcross
(double heterozygous x double recessive)
2) Observe test cross data (get the gametes’
- Mas mappair sa kalink na trait
genotypes and its frequency)
- To determine gene order and compute
2. Incomplete Linkage
distance
- Genes are far from each other
- Recombination types are obtained genotypes frequency
through crossing over 4
Sh C Wx
- There is a non-sister chromatid exchange
sh C Wx 2358
- Farther, so the more they recombine w/
Sh c wx 2708
each other
Sh C wx 116
3. No Linkage sh c Wx 113
- Genes are ind. segregating, ind. assorted sh c wx 2
Sh c Wx 626
Linkage Group sh C wx 601

 Physical association of genes on a

chromosome 3) Find parental types (most frequent)
 Number of linkage group = haploid
sh C Wx 2358
chromosome number (n)
e.g. Humans: 2n = 46 / n = 23 Sh c wx 2708
Fruit flies: 2n = 8 / n = 4
4) Find DCO types (less frequent)
Genetic / Linkage Map
Sh C Wx 4
 Linear arrangement of non-allelic genes on
sh c wx 2
the chromosome
 Distance between genes is based on % of
recombination
 5) Establish the gene order Strength of Linkage

- Get the 2 genes that are always together  Measured by Coefficient of Coincidence
in the parental and DCO types (CC)
- Proper gene order (following the parental - Will only range to 0-1
types): *if 0 = genes are close to each other /
complete interference
I II *if 1 = genes are far from each other / no
C sh Wx interference

c Sh wx ADCO (actual DCO)

CC =
EDCO (expected DCO)
ADCO (actual DCO)
ADCO =
total progeny
6) Find SCO I.
(C Sh wx – 116) (c sh Wx – 113)
EDCO = CO I x CO II (decimal form)
I II
C sh Wx

c Sh wx Interference
- Will only range to 0-1
*if 0 = genes are far from each other / no
7) Find SCO II. interference
(C sh wx – 601) (c Sh Wx – 626) *if 1 = genes are close to each other /
I II there is complete interference
C sh Wx

c Sh wx I = 1 – CC

8) Establish gene distance by % recombination >>>>>

Computing for the frequencies of DCO, SCO I, SCO II,

CO at Region 1 = (SCO I + DCO / total) x 100 and Parentals
= (116 + 113 + 2 + 4)/6708 X 100
= 3.5% Given:
parental DCO CC = 0.6
CO at Region 2 = (SCO II
abc ABc Total = 1000
+ DCO / total) x 100
ABC abC A B C
= (601 +
20% 30%
626 +2 + 4)/ 6708 x 100
= 18.5 %
1) Computing for DCO frequency
Linkage Map - There will always be 2 DCOs in the test
cross data
parental DCO - Use the
DNA DnA top parental type = CC x CO I x CO II x Total
dna dNa = 0.6 x 0.2 x 0.3 x 1000
C sh = 36
Wx = 18 and 18
3.5% 18.5%

*NOTES ON ESTABLISHING GENE ORDER 2) Computing for SCO I frequency

parental DCO
Proper Gene Order: a c b
sh C Wx Sh C Wx
ACB Sh c wx sh c wx
Proper Gene Order:
- There will always be 2 SCO I in the test
Already in proper gene order because walang same cross data
genes sa parentals at DCO.
= (CO I x Total) – Total DCO
= (0.2 x 1000) – 36
= 164
= 82 and 82
 3) Computing for SCO II frequency 2) Y-linked
- There will always be 2 SCO II in the test - Genes on Y chromosome
cross data - Transition is from father to son
- (Shows holandric transmission)
= (CO II x Total) – Total DCO
- Webbing of toes, hypertrichosis (hairy
= (0.3 x 1000) – 36
ears)
= 264
= 132 and 132

Sex Determination
4) Computing for Parentals frequency
- There will always be 2 Parentals in the test 1) Genetic sex determination
cross data - A genetically regulated process
a) Specific genotypes
- = Total – (DCO + SCO I + SCO II)  Neurospora, chlamydomonas
- = 1000 – (36+164+264) b) Presence of Multiple Alleles
- = 536  Hymenoptrans (9 alleles)
- = 268 and 268 F – heterozygous
M – homozygous
GENE / LINKAGE MAPPING IN HAPLOIDS
c) Presence of Multiple genes
1) First division segregation  Boniellia
al al al+ al + = 129 4 sex gene loci
(no crossing over) F – 7 to 8 alleles
M – 7 to 8 alleles
Second division segregation Hermaphrodite – equal
al al+ al al+ = 141 number of male and female
alleles
2) Consider % recombination
3) Establish distance between centromere 2) Environmental sex determination
and the gene - Marine worms
If free swimming at larval stage, F
2nd division
=½(
2nd division+1st division
) =% If larval attaches to F, it becomes M due
to masculinity hormones secreted by the
= ½ (141/ (129+141))
females
= 26%
- Coral reef fish (labroides dimidiatus)
One male in several females
When male dies, the most dominant F will
Sex Linkage take over
 Sex chromosomes carry other genes aside If successful, there will be sex reversal in 2
from genes responsible for sex determination weeks

2 TYPES OF SEX LINKAGE 3) Chromosomal sex determination

- McClung
1) X-linked
- Association of sex chromosomes with a
- Due to sex-linked recessive genes
particular chromosome
- A female becomes a carrier of the
- For XX – XY system,
recessive allele when she is heterozygous
 Females of human, cats, and
- Colorblindness, hemophilia, absence of
mice
central incisors, congenital deafness,
 w/ Barr body at interphase
congenital cataract
 Discovered by Murray Barr
 Barr body = no. of X
𝑋𝐻𝑋ℎ 𝑥 𝑋𝐻𝑌
chromosome - 1
X^H Y  If 1 barr body, F (inactive x
X^HX^H chromosome)
X^H X^HY(normal)  If 0 barr body, M
(normal)
X^HX^h X^hY - Inactive X
X^h  For dosage compensation
(carrier) (hemophilia)
(Lyonization)
 Discovered by Mary Lyon
 LECTURE 5: CHEMICAL BASIS OF HEREDITY FEATURES/MOLECULAR STRUCTURE OF THE DNA

Gene (a part of) DNA (DNA condensed form is) 1) Composed of 2 polynucleotide strands
chromosome (which is found in the) nucleus 2) 2 strands are anti-parallel
3) Specific pairing of nitrogen bases (A=T and
 Nucleosome
C=G)
- DNA + proteins
4) Forms a helical coil
Concept of a Gene 5) Sugar is 2-deoxy-D ribose

 Mendelian Concept STRUCTURE OF NUCLEOTIDE AND

- Mendelian factor “elementen”/bivalent POLYNUCLEOTIDES
factor 1) Nucleotide components
 Ronald A. Fisher a) Phosphate group
- A qualitative geneticist - backbone of the DNA;
- 2 view points about genes - phospoester, phospodiester bond)
1) Hypothetical entity b) Pentose sugar
2) Gene is a chemical compound - 2-deoxy D-ribose (DNA)
- D-ribose (RNA)
CHEMICAL COMPOSITION OF THE CHROMOSOME
c) Nitrogenous bases
1) Lipids - will be linked to the sugar through N-
2) Proteins glycosidic bond)
- Histones/protamine (basic proteins) - 2 types of nitrogenous bases:
- Non-histones chromosomal proteins (acid  Purines: GA (2-ring)
proteins)  Pyrimidine: CUT (1-ring)
3) Nucleic Acid
DNA – AGCT
- DNA ((-) charged)
- RNA RNA - AGCU
CHARACTERISTICS OF A GENETIC MATERIAL 2) Nucleotides
3) Polynucleotides
 Points by Hermann Muller
EVIDENCES TO SHOW THAT DNA IS A GENETIC
1) DNA can duplicate itself with extra fidelity MATERIAL
(replication).
- Can occur 1/1M copies 1) Relative constancy of DNA in all diploid tissues
2) It is a stable molecular structure - Starvation, DNA unchanged
- Very low frequency of mutation 2) Haploid all has half the amount of DNA in
3) Mutation is duplicated diploid cell
- Another source of genetic variation - Diploid = 2n
- Inheritance of mutation - Haploid = n
4) Can carry all necessary biological information 3) Doubling of DNA content at S-phase
5) Can transmit information from generation to - There will be 2 identical strands of the DNA
generation (replication at S-phase occurs) after S-phase called sister chromatids
6) Stored information must be decoded and 4) Cells with extra sets of chromosomes have a
translated into action proportional increase in DNA
- Involves 2 processes: - Polyploidy
 Transcription - Polyteny (characterized by continuous
 Translation replication without separation of the sister
chromatids)
COMPONENTS OF THE DNA 5) Parallelism of UV absorption with mutation
rates
 DNA is a polymer composed of repeating
- Higher UV absorption = higher mutation
nucleotides (building blocks of nucleic acid)
rates
 Is larger than the nucleus, needs to be
6) Transformation and transduction in bacteria
packaged to fit inside nucleus
(See HO)
 DNA Packaging
-
- with the help of histone proteins: H2A, H2B,
7) Production of new viral particles in bacterial
H2, H4 (octamere)
cells
- histones wrap around the DNA forming
8) RNA content of TMV (tobacco mosaic virus)
beads on a string called “solenoid”
caused infection and not the protein coat
 RNA STRUCTURE Primer
- provides 3’ OHN needed by DNA Gyrase
 Composed of 1 polynucleotide strand
III
 D-ribose sugar
- length: 11+1 nucleotides (prokaryotic) and
 Nitrogenous bases are: A, G, C and U
10 to 60 nucleotides (eukaryotic)

3 MODELS OF DNA REPLICATION b) Lagging (5 to 3)

 Primase (provides RNA Primer)
1) Conservative  DNA polymerase 3 (5’ to 3’ dir)
2) Semi-conservative (uses the old strand as  DNA polymerase 1 (3’ to 5’,
template strand; the mode of replication) removes DNA primers, check
3) Dispersive pairing/ proofreading for excision
and filling in of gaps left by the
Matthew Meselson & Franklin Stahl
primers)
- Proved that DNA is semi-conservative  Ligase (joins the phosphodiester
- They grew E. coli in 15N and 14N bonds, prevent breaks)
- They isolated DNA and performed cesium
Primer
chloride centrifugation
- can be several primers
- Will provide Okazaki Fragments (DNA
REPLICATION
islands/ discontinuous segments of
 Faithfully copying a DNA to produce 2 DNA
complementary DNA)
molecules
- Length of OF: 1000-2000 nucleotides (P)
 2 DNA strands will be identical to each other
and 100-200 nucleotides (E)
and would be identical to the parent
molecule
3) Termination
 Transmission of biological information from a
- Resulting to 2 identical DNA molecules
parent cell to its daughter cell / generation to
(identical due to specific base pairing)
generation
- There is simultaneous synthesis of leading
 “DNA Synthesis”
and lagging strands
 Occurs at S-phase
- No enzyme needed
 Occurs due to specific pairing/complement
bases (A to T; C to G)
Products: 2 DNA molecules
 Unwinds to produce template

Replication Process
 Replisome
1) Initiation - DNA polymerase 3 with 2 catalytic core
- Starts at ori-site (origin of replication)
 Primosome
- Formation of single-stranded DNA - (helicase + primase)
templates
- Needed enzymes: MECHANISMS OF HIGH PRECISION REPLICATION
 Helicase/helix unwinding proteins (cut 1) Specificity of base pairing
hydrogen bonds, unwind DNA) 2) Proofreading ability of DNA Polymerase 1
 SSBP/single-stranded binding proteins 3) Excision with pair mechanisms
(prevent re-annealing) a) Repair of thymine dimer
 DNA gyrase (to remove tension,  Endonuclease (excision and filling)
prevent breaking during unwinding) b) N-glycosidase activity
 Primase (provides/attaches primers - Linking sugar to the bond
which are segments of RNA) - Hydrolyzes bond between damaged base
and sugar
2) Elongation
a) Leading (3 to 5) Prokaryotic chromosome
- Needs 1 RNA primer  called as nucleoid
 Primase (provides RNA primer)  organized into about 10 independent
 DNA polymerase 3 domains
o needs OH group from primer to  each domain is composed of loop
enlongate complementary strand  a loop is composed of super coiled DNA
from 5’ to 3’ dir  each domain is held by DNA binding protein
o then synthesizes, adds nucleotides
Hu & H (40kb or 40000bp)
Consider E. coli with single chromosome: Normal Pathway Alkaptonuria
- contains double stranded DNA phenylalanine phenylalanine
- DNA is approx. 1000x the length of E. coli
tyrosine tyrosine
- DNA length: 11000µm(1.1mm) (1mm=1000cm)
- # of bases: 4 x 106 base pair (1kb = 1000bp) p-hydroxypyruvate p-hydroxypyruvate
homogentisic acid homogentisic acid
(HA oxidase) (Non-functional HA oxidase)
Eukaryotic cell Maley-acetoacetic
accumulate HA / alcapton
 with large amount of DNA acid
genetic block (absence of HA
CO2 + H2O
oxidase)
Consider diploid human cell:
>absence of gene
- DNA length: 6ft or 183 cm (6ft x12in/ft x
>absence of enzyme
2.54cm/inc)
- # of bases: 5.5 x 109 bp
- Nucleic diameter: 5 x 10-4 Other inborn errors
- Human chromosome 1 has the longest (missing gene, missing enzyme = change in
DNA (7.2cm and 0.01mm length) phenotype)
- Phenylketonuria (PKU)
LEVELS OF CHROMOSOME PACKAGING - Albinism

 DNA double helix  George Beadle & Edward Tatum

 Nucleosomes (beads on a string) - Presented 1 gene – 1 enzyme hypothesis
 Histone H attaching  “A gene is responsible for an
 Chromatin fiber enzyme”
 Protein scaffold (looped dimers)  “An enzyme catalyzes a step in a
 Metaphase chromosome metabolic reaction
- 1 gene – 1 protein
CENTRAL DOGMA  “Proteins are gene products”
 “Not all proteins functions as
DNA (transc) RNA (transl) Proteins enzymes”
 Example: keratin (gene product,
structural protein of the hair)
- 1 gene – 1 polypeptide
LECTURE 6: GENE FUNCTIONS: PROTEINS AND ENZYMES  Hemoglobin – 2 α and 2 β chains
 Antibody – composed of 4
Genetic Control of Proteins
polypeptides: 2 heavy and 2 light
 Archibald Garrod
chains
- English physician
- 1st evidences of specific relationship
Proteins to Phenotypes
between gene and enzyme
 Structural proteins (e.g. keratin)
- He studied alkaptonuria
 Will become enzymes that catalyse metabolic
 Inborn error of metabolism
reaction
 Urine turns to black upon exposure
 Will result to trait/phenotypic expression
to air
 Applies if heterozygous recessive
 Genetically controlled and
determined
 Freq. is high in families with the
disease
 Common in 1st cousin mating but
not in unrelated partners
 TRANSCRIPTION PRODUCTS OF TRANSCRIBED RNA
TYPE/TRANSCRIPTION
 RNA from DNA sample 1) Messenger RNA (mRNA)
 When gene needs to be expressed - Carries the message
 No T (use U) - Message is expressed as codons
 Fork movement: R to L - Codon codes for amino acid
- 5’ to 3’ dir
Terminologies 2) Transfer RNA (tRNA)
- Anticodon to codon to amino acid
 Gene - Brings amino acid to the polypeptide (site
- contains information for making 1 RNA, of synthesis)
and in most cases, 1 polypeptide 3) Ribosomal RNA (rRNA)
 Promoter - Major components of ribosomes
- a DNA sequence to which the - Ribosomes: rRNA + proteins
transcription enzyme binds - To synthesize protein
 RNA polymerase - There is a small subunit and large subunit
- main enzyme for transcription
Prokaryotic Ribosome 70 S
- 30 S (Svedberg value)
Prokaryotic Transcription Process
 16 S rRNA
1) Initiation  21 proteins
- Uses promoter region/site - 50 S
- Conserved sequence in the promoter  23 S rRNA
- Promoter (start site)  5 S rRNA
 10 seq TATAAT (Pribnow Box)  31 proteins
 35 seq TTGACA
- Uses anticoding or antisense DNA Segments that can bind to mRNA (PA)
template strand A site – aminoacyl-tRNA (acceptor/san
- Enzymes needed: papasok ang amino acid)
 RNA polymerase (bind promoter P site – peptidyl-tRNA
site to transcribe a DNA Exit site
sequence)
 Sigma fa)ctor (helps RNA Eukaryotic Ribosome 80 S
polymerase - 40 S
 18 S rRNA
Prokaryotic Promoter:  30 – 35 r proteins
- 60 S
-35 -10 +1
 5.8 S rRNA
TTGACA TATAAT T  285 S rRNA
 5 S rRNA
AACTGT ATATTA A  40-45 r proteins
(-) upstream (+) downstream
Eukaryotic Transcription Process
2) Elongation
- 5’ to 3’ direction 1) Initiation
- Enzymes needed: - Uses promoter region
 RNA polymerase (opens the strand - Conserved sequence in the promoter
and complements 3’ to 5 ‘ with - Promoter (start site)
RNA bases) So that RNA polymerase can bind to
promoter with the help of TF II D (with help
3) Termination of sigma factor)
- Rho factor enzyme (attaches; signal for  -25 to -30 TATA box (Goldberg-
termination; helps the RNA polymerase) Hogness Box)
- Rho dependent termination  -75 to -80 (upstream) CAAT box
- Rho independent termination - Enzymes needed:
 RNA polymerase
 Several transcription factors
 TRANSLATION  RF 1 (facilitates stop codon UAA
Terminologies UAG)
 RF 2 (facilitates stop codon UGA)
 Codon  RF 3 (aids RF1 and RF2 for release
- 3-base sequence on mRNA that specifies factor)
an amino acid  IF 1 (disbands 30S and 50S
 Anti-codon
- 3-base sequence in tRNA that base pairs Product of Translation:
with a specific codon - Polypeptide chain
 Enzymes - Primary protein structure/amino acid
- Biological catalysts/makes metabolic structure
reactions leading to a phenotype - Ala-trp-his-cys-tyr…
 Genetic code - Then folding, and association with other
- Set of 64 codons and amino acids they polypeptides
stand for - Then functional proteins
 Polypeptide
- Single protein chain
- Product of translation but needs to
undergo post-translation process

DNA strand template 3' ACC 5'

Transcription
mRNA 5' UGG 3'
Translation
Protein trp

Template: mRNA
1st step: amino acid activation
- Amino acid attaches to tRNA
- With the help of Aminoacyl-tRNA
synthetase (enzyme)

Initiation:
- Separation of small (30S) and large subunit
(50S) of the ribosomes
- 5’ to 3’ dir
- Enzymes needed:
 IF 1 (stimulates disassociation of small
and large subunit of ribosomes)
 IF 3 (bring 30S to the start site/codon
AUG)
 IF 2 (bring amino-acyl to 30S)
Elongation:
- Enzymes needed:
 EFTu (facilitate entry in the A site)
 Peptidyl transferase (forms
peptide bonds)
 EFG (displacing amino acid from
A site to P site to decode mRNA)

Termination:
- Release factor recognizes stop codon
- Then disassociation
- Then mRNA will be destroyed
- Enzymes needed: