Lecture outline

Lecture 1
Introduction
Lecture 2
Study of genes and everything related to it.
Three divisions:
i. Transmission or classical genetics
Study of hereditary, arrangement of genes on the chromosomes and gene mapping
ii. Molecular genetics
Chemical nature of the gene: replication, transcription, translation and gene regulation
iii. Population genetics
Study of gene composition of populations
Computational Genetics
Use of computational methods to study all the above

DNA as genetic material

Condensed into a nucleus of few microns

Identification of DNA as genetic material

1. Federick Griffith experiment: Streptococcus pneumonia
2. Avery, MacLeod and McCarty: extension of Griffith experiment
3. Hershey and chase experiment: E.coli bacteriophage 32P, 35S

Lecture 3
Cells: fundamental units of life
Chromosomes: packaged form of DNA (DNA+proteins)
The chromosome packaging is flexible to allow on-demand access for DNA replication, repair and gene
expression
DNA+histones = nucleosomes -> chromatin fiber
Histones have high positively charged amino acids – lysine and arginine
Heterochromatin: highly condensed chromatin
Euchromatin: less condensed chromatin in the interphase
Non-histone proteins help in further looping and condensation of chromatin to form visible fibers during mitosis
Histone modifications further enhance or suppress access to DNA during gene expression
Heterochromatin helps in regulation or silencing of gene expression
Eg. X-chromosome inactivation in females
X-inactivation is random and passed on to the descendants of the cell

Lecture 4

DNA+histone = nucleosome(s) = chromatin+non-histone-condensation = chromatid+centromere =

chromosome

Cell division
DNA is inherited
During cell division from mother to daughter cells
Reproduction: parent to offspring
Replication of DNA is required for transferring the genetic material during cell division
Cell undergo limited number of divisions and then enters senescence
Cell cycle: series of stages through which a cell passes during cell division
At the end of cell cycle, two cells are produced from a single cell
Progression is regulated by check points
G0-resting stage
G1-Cell prepares for cell division, signal is received at this stage, proteins for cell division are synthesized –
several hours (10 hours)
G1/S checkpoint: enzymes and proteins required for cell division
S phase: DNA replication, sister chromatid formation (9 hours)
G2 phase: organelle duplication (*4 hours)
G2/M check point: DNA is completely replicated and undamaged
M stage: mitosis:
Cytokinesis

Lecture 5
Interphase:
DNA synthesis, protein and RNA synthesis
G1, S, G2 stages are included in interphase
How many DNA molecules at each stage of cell cycle?
Mitosis
Prophase:
chromosomes condense & visible under microscope
condensins bind and bring chromosome condensation
Cohesins – bind sister chromatids
Spindle fibers –microtubules arise from the centrosomes (centrioles) in the cell poles
Centromere: a genetic locus- site of kinetochore assembly (sister kinetochores)
Kinetochore is a group of proteins assemble at 5-10mb of DNA region
Kinetochore attaches to the microtubule: as a interface between the DNA and microtubule

Prometaphase:
Disintegration of nuclear membrane
Spindle microtubules enter the nucleus
Attach to kinetochore of sister chromatids
Leads to chromosome biorientation
Metaphase
Chromosomes arranged in the middle of the metaphase plate
spindle assembly Checkpoint: ensures microtubule attachment and assembly of chromosomes at the
metaphase plate
Tension due to attachment of sister chromatids to opposite centrosomes is created – passes through
checkpoint
Anaphase:
Connection between sister chromatids break separated by separase
Cohesins are released and the sister chromatids separate
Chromatids pulled to opposite poles due to the rearrangement of microtubules
Telophase:
Chromosomes arrive at the opposite ends
Nuclear membrane forms around each set of chromosomes
Chromosomes relax
Cytokinesis
Cytoplasm division
Cytoplasmic content varies between the daughter cells
Senescence:
Due to telomere shortening
End replication problem
Breakage-fusion-bridge cycle due to telomere shortening

Lecture 6
Meiosis
Mitosis produces genetically identical progeny
Mutation can create variation, but frequency is limited
Meiosis introduces genetic variation in the offspring
Reduces the genetic information into half
Occurs in germ cells
Meiosis I and Meiosis II
Prophase I divided into five sub stages
Leptotene: chromosomes condense
Zygotene: homologous chromosomes pair and begin synapsis (a close pairing association), tetrad formation
Pachytene: further condensation of chromosomes, chromosomes and non-sister chromatids are visible, crossing
over between non-sister chromatids occurs
Diplotene: chiasmata (connection between the crossed non-sister chromatids) formation is visible,
chromosomes separate
Diakinesis: The chromosomes are pulled apart, the nuclear membrane breaks down and the spindle is formed

Metaphase I
Homologous pairs of chromosomes arrange at the metaphase plate
Spindle fiber from one end is attached to one of the chromosomes and the other spindle fiber to the other
homologous chromosome
Anaphase I
Separation of homologous chromosomes
But the sister chromatids are attached to each other
Telophase I
Chromosomes arrive at the poles and cytoplasm divides
Cytokinesis
Cytoplasmic division
Meiosis II
Period between meiosis I and II is interkinesis where the nuclear membrane reforms around the chromosomes at
the poles
Spindles break down
Chromosomes relax
No DNA synthesis takes place
Prophase II
Chromosomes recondenses, spindle reforms and nuclear envelope breaks down
Or cells can directly enter metaphase I from cytokinesis
Metaphase II
The chromosomes align on the metaphase plate like in mitosis
Sister chromatids are attached to spindle fibers from opposite poles
Anaphase II
Sister chromatids are pulled to opposite poles
Telophase II
Chromosomes arrive at the poles and nuclear membrane reforms
Cytokinesis
Cytoplasm divides, chromosomes relaxes
Result of meiosis
Four cells from one cells
Chromosome number is halved to produce haploid cells
Chromosomes/cells are genetically different from one another and form the parent cell
Crossing over happens for genetic variation, results in intrachromosomal recombination: new combination of
alleles
Thus, crossing over shuffles alleles on the same chromosomes into new combinations
Random segregation: random distribution of maternal and paternal chromosomes

Meiosis in animals
Multicellular organisms reproduce through meiosis
Gametes in male and female are formed through meiosis
Spermatogenesis: male gamete formation
Oogenesis: female gamete formation
Spermatogonium -> primary spermatocyte->2 secondary spermatocyte->4 spermatids->4 Sperms
(Primordial germ cells) (Meiosis I) (Meiosis II) (Mature)
(Divide by Mitosis)
(Enters prophase I)

Takes place continuously in adult reproductive life

Oogonia -> primary oocyte -> 2ndary oocyte+1st polar body -> Ovum+2nd polar body
(Primordial germ cells) (Meiosis I) (Meiosis II)
(Divide by mitosis)
(Enters prophase I) (arrested in prophase I at birth)
Polar body disintegrates

Oogenesis begins before birth and female is born with primary oocytes
Hormonal change leads to Meiosis I
Secondary oocyte is released from ovary in a process called oogenesis
In humans and many species, Meiosis II starts after sperm penetrates outer layer of secondary oocyte
Nuclei of sperm and ovum fuse to form zygote
Lecture 7

Plants:
Meiosis produces pollen grain: male part, contains two haploid nuclei
During fertilization, pollen lands on the stigma, germinates and one nuclei, pollen nuclei gorws the pollen tube
into the ovary
Other haploid nuclei divides mitotically to produce two sperm cells enter through the pollen tube and one of the
sperm cells fertilizes the egg cell

Female part of the flower produces one egg present inside the flower’s stigma, which is then fertilized by the
sperm cell
Two haploid polar nuclei present in the plant formed during egg formation fuses with another sperm cells to
form 3n endosperm which stores nutrient that can be used by the embryonic plant.

Chromosome mutations
1. Rearrangements :A part of chromosome is duplicated, deleted or inverted
2. Aneuploidy: Number of chromosomes is altered, individual chromosomes are added or deleted
3. Polyploidy: One or more complete sets of chromosomes are added
Rearrangements:
Due to double stranded breaks and wrong rejoining, rearrangements happen
Due to error in crossing over or when crossing over occurs between repeated DNA sequences

Duplication
Tandem duplication: duplicated segment is immediately adjacent to original segment
Displaced duplication: duplicated segment is at some distance on the same or different chromosome
Reverse duplication: duplicated segment is inverted
Segmental duplication: Numerous duplicated segments

Duplication/deletion arise due to unequal crossing over

Eg: color blindness in humans
Green and red opsin genes help in color perception, present in x chromosomes
DNA sequence of both genes are 98% identical
Due to improper alignment and unequal crossing over, one X chromosome has extra opsin gene and one is
missing an opsin gene
When male inherits the X chromosome with missing opsin gene, color blindness occurs
Effect of duplication
Duplication can be homozygous or heterozygous
Heterozygous - Lead to problems in chromosome pairing during prophase I of meiosis, chromosomes twist
and loop for correct pairing
Leads to phenotypic effects
Eg. Color blindness
MECP2 duplication syndrome
Due to extra copy of the gene in X chromosome
Seizures and intellectual disability
MECP2 required for brain development and regulation of other brain related genes
Males: manifest the disease
Females: heterozygous, no disease due to skewed inactivation of affected X-chromosomes
but behavioral and psychiatric symptoms might be due to different inactivation pattern in brain?