Genetics Introduction

Inheritance Patterns

Mendel was the first scientist to develop a method for predicting the outcome of inheritance patterns. He performed his work with pea plants, studying seven traits: plant height, pod shape, pod color, seed shape, seed color, flower color, and flower location. Pea plants pollinate themselves. Therefore, over many generations, pea plants develop individuals that are homozygous for particular characteristics. These populations are known as pure lines.

In his work, Mendel took pure-line pea plants and cross-pollinated them with other pure-line pea plants. He called these plants the parent generation. When Mendel crossed pure-line tall plants with pure-line short plants, he discovered that all the plants resulting from this cross were tall. He called this generation the F1 generation (first filial generation). Next, Mendel crossed the offspring of the F1 generation tall plants among themselves to produce a new generation called the F2 generation (second filial generation). Among the plants in this generation, Mendel observed that three-fourths of the plants were tall and one-fourth of the plants were short.

Mendel's laws of genetics

Mendel conducted similar experiments with the other pea plant traits. Over many years, he formulated several principles that are known today as Mendel's laws of genetics. His laws include the following:

1. Mendel's law of dominance: When an organism has two different alleles for a trait, one allele dominates. 2. Mendel's law of segregation: During gamete formation by a diploid organism, the pair of alleles for a particular trait separate, or segregate, during the formation of gametes (as in meiosis). 3. Mendel's law of independent assortment: The members of a gene pair separate from one another independent of the members of other gene pairs. (These separations occur in the formation of gametes during meiosis.)

Genetics Part - I

DNA replication, transcription and translation. In very general terms, what does a chromosome contain?

• Information, genetic information to carry out the characteristics of life -- precise self replication, ability to exchange energy with the environment, etc.

In very general terms, what are the two related functions of DNA?

• Information storage

• DNA replication

• Information transfer

• DNA transcribed into RNA

• DNA's function in information transfer

What is the Central Dogma associated with information storage and retrieval?

• Central Dogma: DNA-->RNA-->unfolded protein-->native, folded protein

What are the three processes of the central dogma? How does DNA function as an information molecule? • replication, DNA --> DNA

• transcription, DNA --> RNA

• translation, RNA --> unfolded protein --> folded protein

In terms of molecular conformation, what occurs through the central dogma?

• Translation of linear information, a sequence of nucleotides, into 3-D information, the structure of a protein.

What are the differences between DNA and RNA?

• base composition: RNA = AGCU, DNA = AGCT

• carbohydrate: RNA = ribose, DNA = deoxyribose

• structure: RNA = single stranded, DNA = double helix

RNA

• usually single stranded

• linear polymer of ribonucleotides.

• Some secondary and tertiary structure but often ill-defined.

What are the different types of RNA? What are the functions of the different types of RNA?

• messenger RNA = mRNA, information transfer

• transfer RNA = tRNA, information transfer

• ribosomal RNA = rRNA, structural

• small nuclear RNA = snRNA, ribozymes, RNA processing. What is replication?

Transfer of genetic information from one generation to the next.

DNA-directed DNA synthesis: replication of the genome.

What is the structural basis for the precise duplication of the genome?

• The Watson-Crick structure of DNA: the strands are complementary, the nucleotide sequence in one automatically specifies the other.

• The enzyme, DNA polymerase III, is very accurate: it has proof reading capabilities.

Is replication conservative or semi-conservative? What does that mean?

• Is the parental genome of double stranded DNA fully conserved in the parental cell or is it split equally (semi- conserved) between two daughter cells?

• Replication is semi-conservative. Genetics Part - II

What is the evidence for semi-conservative replication?

Classical experiments of Meselson and Stahl. Label DNA with *heavy isotope* N15 and allow replication in light N14: distinguish heavy, light and hybrid DNA by centrifugation.

Results: after 1 generation, each genome contains a hybrid N15-N14 DNA; after 2 generations, there are 2 hybrid and 2 light (N14-N14) genomes.

• Each strand of DNA serves as a template for the synthesis of its complement.

• The strands separate and each is used as a template for the synthesis of a daughter strand.

• The two new double helices each contain half the parental DNA.

• This process produces a replication fork

Is replication uni-directional or bi-directional?

• Bi-directional

• Two replication forks proceeding from the origin.

DNA replication, transcription and translation. What is the major replication enzyme?

DNA polymerase III, a DNA-directed DNA polymerase

• Synthesis is 5'-->3'

• Substrates are deoxynucleoside triphosphates (to make deoxyribonucleic acid)

• Proof reading , errors removed by 3'--5' exonuclease

• Processivity is very high (the ability of the enzyme to replicate a large tract of DNA before *falling* off)

• Replication requires DNA unwinding by enzymes termed helicases: these enzymes unwind the DNA helix before the replication fork and wind it up again afterwards.

There are large numbers of different enzymes and proteins involved at the replication fork in the replisome.

DNA damage by UV radiation or chemicals is repaired by other DNA polymerases. UV-damage results in adjacent T residues in one strand becoming covaletly linked to each other, producing a thymine dimer. This causes the double helix to become distorted -- kinky. Xeroderma pigmentosa is a genetic disorder in which patients cannot carry out UV-radiation repair. They are very prone to skin cancer from an early age.

What is Transcription?

• Copying a gene as RNA

• DNA-directed RNA synthesis from a gene

What is a gene?

• There is no good definition of a gene! • A sequence of DNA that is transcribed from specific start to specific stop base sequences.

• Beadle and Tatum, working with the eukaryote mold Neurospora crassa, concluded that one gene codes for one protein.

• But what about genes that code for RNA's like rRNA and tRNA?

• A gene is a sequence of DNA that is transcribed into a single RNA as defined by specific start and stop sequences of bases.

• Note the circularity of the argument!

• But the single RNA may be polycistronic!

What does that mean?

• A cistron is synonymous with a gene.

• A polycistronic RNA results from the transcription of an operon. DNA replication, transcription and translation. What's an operon?

• A genetic unit containing several genes with related functions: the bacterial operon for lactose (milk sugar) metabolism contains 3 genes coding for 3 different proteins.

• An operon is transcribed as a single unit, a polycistronic messenger RNA (mRNA) that codes for more than one gene product.

Name 4 types of RNA. What are their functions?

• mRNA, messenger RNA that is translated into protein

• rRNA, ribosomal RNA that, together with ribosomal proteins, forms a structural scaffold for the translation of mRNA, the ribosome

• tRNA, transfer RNA, a specific carrier of amino acids

• snRNA, small nuclear RNA involved in processing of mRNA in the nucleus

What is the major transcription enzyme?

RNA polymerase, a DNA-directed RNA polymerase

• RNA synthesis is 5'-->3'

• substrates are ribonucleoside triphosphates ( to make ribonucleic acid)

• begins at the promoter, 5' end of the gene

• processivity is very high, proceeds to 3' end of gene without stopping or falling off the gene

• proof reading by precise Watson-Crick base pairing, A=U and G=C

Regulation of transcription of a gene is at the 5'-end of the gene at region(s) termed operators

• Transcription of some genes is constitutive = housekeeping genes • Transcription of other genes is in response to a stimulus = inducible genes

Genetics Part - III

What are exons and introns?

• exons are coding regions, and

• introns are non-coding regions of the mRNA transcript

• exons and introns are found in most, but not all, eukaryote genes

• introns have to be spliced out before the mRNA is translated

• splicing is by snRNA's acting as enzymes, or ribozymes, an example of the catalytic function of RNA DNA replication, transcription and translation: Translation:

• Synthesis of a linear polymer of amino acids from a linear polymer of nucleotides

Where does it occur?

On the ribosome, a rRNA-protein complex that provides:

• a scaffold for mRNA

• sites for the docking of tRNA charged with a specific amino acid

• an enzyme for peptide bond synthesis between amino acids

• an enzyme for translocation of the mRNA through the ribosome

What is the function of tRNA?

• Carrier of a specific amino acid during translation

What is the structure of tRNA?

• secondary structure has some base-pairing --> cloverleaf

• information transfer at the anti-codon loop, complementary to the codon

• note the importance of H-bonds in the genetic code

• tertiary structure is L-shaped which places the amino acid far from the codon-anticodon site

• degeneracy of the code produces wobble

What is the genetic code?

A sequence of 3 nucleotides forms a codon

• unambiguous, each codon specifies an amino acid, or start, or stop

• degenerate, some amino acids have multiple codons • 2-letters often sufficient, specifiy hydrophobic and hydrophillic amino acids

What is the enzyme that charges tRNA with an amino acid?

An aminoacyl-tRNA synthetase

• it has proof reading capabilities through the precise fit of amino acid and tRNA

• energy provided by ATP: energy for the formation of aminoacyl-tRNA and for proof reading

• there are at least 20 synthetases, isoaccepting for the tRNA's coding for a single amino acid What is the mechanism of translation?

• mRNA forms a large complex with the ribosome and protein factors

• together they guide in the correct aminoacyl-tRNA

• correct amino acid specified by codon-anticodon base pairing (H-bonds)

• protein factors have proof reading capability--energy provided by GTP

• an enzyme catalyzes polymerization of two amino acids, peptide (amide)bond formation between two amino acids

• an enzyme catalyzes movement of mRNA through the polymerization site: energy provided by GTP

• mRNA translated from 5'--> 3', same direction as it is synthesized

Reprise:

• Flow of information: central dogma

• DNA--> RNA-->linear amino acid sequence --> 3D-conformation of protein

But some viruses have only RNA as their genome: no DNA.

How do they carry out information transfer? How do they get around the unidirectional flow of information in the central dogma?

• Use an enzyme called reverse transcriptase to transcribe RNA into DNA.

• Example: HIV, a retrovirus

• Then, use central dogma.

• For HIV:

RNA-->DNA--> mRNA --> linear amino acid sequence --> 3D-conformation of protein. BOTONY

Introduction

Botany is the scientific study of plant life. As a branch of biology, it is also called plant science(s), phytology, or plant biology. Botany covers a wide range of scientific disciplines that study plants, algae, and fungi including: structure, growth, reproduction, metabolism, development, diseases, and chemical properties and evolutionary relationships between the different groups.

The study of plants and botany began with tribal lore, used to identify edible, medicinal and poisonous plants, making botany one of the oldest sciences. From this ancient interest in plants, the scope of botany has increased to include the study of over 550,000 kinds or species of living organisms.

Scope and importance of botany

As with other life forms in biology, plant life can be studied from different perspectives, from the molecular, genetic and biochemical level through organelles, cells, tissues, organs, individuals, plant populations, and communities of plants. At each of these levels a botanist might be concerned with the classification (taxonomy), structure (anatomy and morphology), or function (physiology) of plant life.

Historically, botany covers all organisms that were not considered to be animals. Some of these "plant-like" organisms include fungi (studied in mycology), bacteria and viruses (studied in microbiology), and algae (studied in phycology). Most algae, fungi, and microbes are no longer considered to be in the plant kingdom. However, attention is still given to them by botanists, and bacteria, fungi, and algae are usually covered in introductory botany courses.

The study of plants has importance for a number of reasons. Plants are a fundamental part of life on Earth. They generate the oxygen, food, fibres, fuel and medicine that allow higher life forms to exist. Plants also absorb carbon dioxide through photosynthesis, a minor greenhouse gas that in large amounts can affect global climate. It is believed that the evolution of plants has changed the global atmosphere of the earth early in the earth's history and paleobotanists study ancient plants in the fossil record. A good understanding of plants is crucial to the future of human societies as it allows us to:

• Produce food to feed an expanding population • Understand fundamental life processes • Produce medicine and materials to treat diseases and other ailments • Understand environmental changes more clearly

Human nutrition

All foods eaten come from plants, either directly from staple foods and other fruit and vegetables, or indirectly through livestock or other animals, which rely on plants for their nutrition. Plants are the fundamental base of nearly all food chains because they use the energy from the sun and nutrients from the soil and atmosphere and convert them into a form that can be consumed and utilized by animals; this is what ecologists call the first trophic level.

Botanists also study how plants produce food we can eat and how to increase yields and therefore their work is important in mankind's ability to feed the world and provide food security for future generations, for example through plant breeding.

Botanists also study weeds, plants which are considered to be a nuisance in a particular location. Weeds are a considerable problem in agriculture, and botany provides some of the basic science used to understand how to minimize 'weed' impact in agriculture and native ecosystems. Ethnobotany is the study of the relationships between plants and people.

Fundamental life processes

Plants are convenient organisms in which fundamental life processes (like cell division and protein synthesis for example) can be studied, without the ethical dilemmas of studying animals or humans. The genetic laws of inheritance were discovered in this way by Gregor Mendel, who was studying the way pea shape is inherited.

What Mendel learned from studying plants has had far reaching benefits outside of botany. Additionally, Barbara McClintock discovered 'jumping genes' by studying maize. These are a few examples that demonstrate how botanical research has an ongoing relevance to the understanding of fundamental biological processes.

Medicine and materials Many medicinal and recreational drugs, like tetrahydrocannabinol, caffeine, and nicotine come directly from the plant kingdom. Others are simple derivatives of botanical natural products; for example aspirin is based on the pain killer salicylic acid which originally came from the bark of willow trees.[2] There may be many novel cures for diseases provided by plants, waiting to be discovered. Popular stimulants like coffee, chocolate, tobacco, and tea also come from plants. Most alcoholic beverages come from fermenting plants such as barley malt and grapes.

Plants also provide us with many natural materials, such as cotton, wood, paper, linen, vegetable oils, some types of rope, and rubber. The production of silk would not be possible without the cultivation of the mulberry plant. Sugarcane, rapeseed, soy and other plants with a highly-fermentable sugar or oil content have recently been put to use as sources of biofuels, which are important alternatives to fossil fuels, see biodiesel.

Environmental changes

Plants can also help us understand changes in on our environment in many ways. • Understanding habitat destruction and species extinction is dependent on an accurate and complete catalog of plant systematics and taxonomy. • Plant responses to ultraviolet radiation can help us monitor problems like the ozone depletion. • Analyzing pollen deposited by plants thousands or millions of years ago can help scientists to reconstruct past climates and predict future ones, an essential part of climate change research. • Recording and analyzing the timing of plant life cycles are important parts of phenology used in climate-change research. • Lichens, which are sensitive to atmospheric conditions, have been extensively used as pollution indicators. In many different ways, plants can act a little like the 'miners canary', an early warning system alerting us to important changes in our environment. In addition to these practical and scientific reasons, plants are extremely valuable as recreation for millions of people who enjoy gardening, horticultural and culinary uses of plants every day.

Evolution of Botany

History

Early examples of plant taxonomy occur in the Rigveda, that divides plants into Vrska (tree), Osadhi (herbs useful to humans) and Virudha (creepers). which are further subdivided. The Atharvaveda divides plants into eight classes, Visakha (spreading branches), Manjari (leaves with long clusters), Sthambini (bushy plants), Prastanavati (which expands); Ekasrnga (those with monopodial growth), Pratanavati (creeping plants), Amsumati (with many stalks), and Kandini (plants with knotty joints). The Taittiriya Samhita and classifies the plant kingdom into vrksa, vana and druma (trees), visakha (shrubs with spreading branches), sasa (herbs), amsumali (a spreading or deliquescent plant), vratati (climber), stambini (bushy plant), pratanavati (creeper), and alasala (those spreading on the ground).

Manusmriti proposed a classification of plants in eight major categories. Charaka SamhitÄ and Sushruta Samhita and the Vaisesikas also present an elaborate taxonomy.

Parashara, the author of Vrksayurveda (the science of life of trees), classifies plants into Dvimatrka (Dicotyledons) and Ekamatrka (Monocotyledons). These are further classified into Samiganiya (Fabaceae), Puplikagalniya (Rutaceae), Svastikaganiya (Cruciferae), Tripuspaganiya (Cucurbitaceae), Mallikaganiya (Apocynaceae), and Kurcapuspaganiya (Asteraceae).

Among the earliest of botanical works in Europe, written around 300 B.C., are two large treatises by Theophrastus: On the History of Plants (Historia Plantarum) and On the Causes of Plants. Together these books constitute the most important contribution to botanical science during antiquity and on into the Middle Ages. The Roman medical writer Dioscorides provides important evidence on Greek and Roman knowledge of medicinal plants.

In ancient China, the recorded listing of different plants and herb concoctions for pharmaceutical purposes spans back to at least the Warring States (481 BC-221 BC). Many Chinese writers over the centuries contributed to the written knowledge of herbal pharmaceutics.

There was the Han Dynasty (202 BC-220 AD) written work of the Huangdi Neijing and the famous pharmacologist Zhang Zhongjing of the 2nd century. There was also the 11th century scientists and statesmen Su Song and Shen Kuo, who compiled treatises on herbal medicine and included the use of mineralogy.

Important medieval works of plant physiology include the Prthviniraparyam of Udayana, Nyayavindutika of Dharmottara, Saddarsana-samuccaya of Gunaratna, and Upaskara of Sankaramisra.

In 1665, using an early microscope, Robert Hooke discovered cells in cork, and a short time later in living plant tissue. The German Leonhart Fuchs, the Swiss Conrad von Gesner, and the British authors Nicholas Culpeper and John Gerard published herbals that gave information on the medicinal uses of plants.

Modern botany

Considerable amount of new knowledge today is being generated from studying model plants like Arabidopsis thaliana. This weedy species in the mustard family was one of the first plants to have its genome sequenced. The sequencing of the rice (Oryza sativa) genome and a large international research community have made rice the de facto cereal/grass/monocot model. Another grass species, Brachypodium distachyon is also emerging as an experimental model for understanding the genetic, cellular and molecular biology of temperate grasses.

Other commercially-important staple foods like wheat, maize, barley, rye, pearl millet and soybean are also having their genomes sequenced. Some of these are challenging to sequence because they have more than two haploid (n) sets of chromosomes, a condition known as polyploidy, common in the plant kingdom. Chlamydomonas reinhardtii (a single-celled, green alga) is another plant model organism that has been extensively studied and provided important insights into cell biology.

In 1998 the Angiosperm Phylogeny Group published a phylogeny of flowering plants based on an analysis of DNA sequences from most families of flowering plants. As a result of this work, major questions such as which families represent the earliest branches in the genealogy of angiosperms are now understood. Investigating how plant species are related to each other allows botanists to better understand the process of evolution in plants. Among the earliest of botanical works in Europe, written around 300 B.C., are two large treatises by Theophrastus: On the History of Plants (Historia Plantarum) and On the Causes of Plants. Together these books constitute the most important contribution to botanical science during antiquity and on into the Middle Ages. The Roman medical writer Dioscorides provides important evidence on Greek and Roman knowledge of medicinal plants.

Important medieval works of plant physiology include the Prthviniraparyam of Udayana, Nyayavindutika of Dharmottara, Saddarsana-samuccaya of Gunaratna, and Upaskara of Sankaramisra.

In 1754 Carl von Linné (Carl Linnaeus) devided the plant Kingdom into 25 classes. One, the Cryptogamia, included all the plants with concealed reproductive parts (algae, fungi, mosses and liverworts and ferns). A considerable amount of new knowledge today is being generated from studying model plants like Arabidopsis thaliana. This weedy species in the mustard family was one of the first plants to have its genome sequenced. The sequencing of the rice (Oryza sativa) genome and a large international research community have made rice the de facto cereal/grass/monocot model. Another grass species, Brachypodium distachyon is also emerging as an experimental model for understanding the genetic, cellular and molecular biology of temperate grasses.