Genetics Lecture Notes PDF

# Genetics ## Dr Ahmed Noby Amer ## ILO'S - History of Genetics - Structure of DNA - Difference between DNA & RNA - DNA Supercoiling - Flow of Genetic Information ## Genetics - The study of heredity or the study of how traits are passed from parents to offspring. This study is largely based on gen...

# Genetics ## Dr Ahmed Noby Amer ## ILO'S - History of Genetics - Structure of DNA - Difference between DNA & RNA - DNA Supercoiling - Flow of Genetic Information ## Genetics - The study of heredity or the study of how traits are passed from parents to offspring. This study is largely based on genes. - Genes are information about traits that an organism has or carries ## History of Genetics ### Mendel's Laws of Inheritance: - That one in four pea plants had pure bred recessive alleles, two out of four were hybrid, and one out of four was purebred dominant. - That the inheritance of each trait is determined by "units" or "factors" that are passed on to descendants unchanged (these units are now called genes. - That an individual inherits one such unit from each parent for each trait. - That a trait may not show up in an individual but can still be passed on to the next generation. ### Griffith transformation experiment - Pneumococcus bacterium occurs naturally in two forms. The virulent (s-strain) form has a smooth polysaccharide capsule that is essential for infection. The non-virulent (r-strain) lacks the polysaccharide capsule. - Griffith was surprised to find in his experiments that mice injected with a mixture of heat-killed s-strain and live but non-virulent r-strain produced lethal results. In fact, Griffith discovered living forms of the s-strain bacteria in the infected mice! - He hypothesizes that "transforming principle", had been transferred from the heat-killed s-strain, had enabled the r-strain to synthesize a smooth polysaccharide coat and become ### Oswald Avery - They isolated a cell-free extract from the s-strain bacteria and were able to transform living r-strain into a culture containing both s-strain and r-strain cells. The purified extract contained Griffith's "transforming principle". - Only on treatment of the extract with DNase broke down the "transforming principle" ### The Hershey-Chase Experiment: - A "phage" is a virus composed of DNA enclosed by a protective coat of protein. To reproduce, a virus must infect a cell and take over the cell's metabolic machinery. - The experiments are performed with separate bacteriophage (virus) cultures in which either the protein capsule is labeled with radioactive sulfur or the DNA core is labeled with radioactive phosphorus. - If bacteria carries radioactive Sulphur label this means that proteins that codes for the genetic information, if carries radioactive Nitrogen this means that DNA codes for the genetic information ### Rosalind Franklin x-ray crystallography - Crystallography can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds. - She identified two distinct configurations, called by her the a and b forms, in which DNA could exist. - Franklin proposed a double-helix structure with precise measurements for the diameter, the separation between each of the co-axial fibers along the fiber axis direction, and the pitch of the helix ### James Watson and Francis Crick - Deoxyribonucleic acid (DNA) is a double-stranded, helical molecule. It consists of two sugar-phosphate backbones on the outside, held together by hydrogen bonds between pairs of nitrogenous bases on the inside - The bases are of four types (A, C, G & T): pairing always occurs between A & T, and C & G. "Genetic code" ## Nucleic Acid Structure - A nucleotide is made up of three units - A five-carbon sugar: ribose moiety or 2-deoxyribose (or ribose in RNA) - Phosphate groups - A nitrogen-containing base - There are five common bases: - Two of these bases are derivatives of purine. These are adenine and guanine. - Three of the bases are pyrimidine derivatives. These are cytosine, thymine, and uracil. - **Double helix structure**: - DNA has a double-helix structure, with sugar and phosphate on the outside of the helix, forming the sugar-phosphate backbone of the DNA where the nucleotides connected by "covalent bond between 5' phosphate group and 3' hydroxyl group - The nitrogenous bases are stacked in the interior in pairs, like the steps of a staircase; the pairs are bound to each other by hydrogen bonds. (A & T WITH TWO HYDROGEN BONDS, C & G WITH THREE HYDROGEN BONDS) - The two strands of the helix run in opposite directions, so that the 5' carbon end of one strand faces the 3' carbon end of its matching strand. This antiparallel orientation is important to DNA replication and in many nucleic acid interactions ## Differences between DNA and RNA | Structure | DNA | RNA | |---------|---------------------------------------------------------------------------------|---------------------------------------------------------------------------------------------| | Sugar | The sugar in DNA is **deoxyribose**, which contains one less hydroxyl group than RNA's ribose.| RNA contains **ribose sugar molecules,** . | | Bases | The bases in DNA are Adenine ('A'), Thymine ('T'), Guanine ('G') and Cytosine ('C'). | RNA shares Adenine ('A'), Guanine ('G') and Cytosine ('C') with DNA, but contains Uracil (‘U’) rather than Thymine. | | Pairing | Adenine and Thymine pair (A-T) (two hydrogen bonds) | Adenine and Uracil pair (A-U) (two hydrogen bonds) | | | Cytosine and Guanine pair (C-G) (Three hydrogen bonds) | Cytosine and Guanine pair (C-G) (Three hydrogen bonds) | | Location | DNA is **found in the nucleus** | RNA forms in the nucleolus, and then moves to the **cytoplasm depending on the type of RNA formed.** | | Reactivity| Due to its deoxyribose sugar, which contains one less oxygen-containing hydroxyl group, DNA is a more stable molecule than RNA, which is useful for a molecule which has the task of keeping genetic information safe. | RNA, containing a ribose sugar, is **more reactive than DNA** and is not stable in alkaline conditions. RNA's larger helical grooves mean it is more easily subject to attack by enzymes. | ## Types of RNA - **Messenger RNA (mRNA)** copies portions of genetic code, a process called **transcription**, and transports these copies to ribosomes, which are the cellular factories that facilitate the production of proteins from this code. - **Transfer RNA (tRNA)** is responsible for bringing amino acids, basic protein building blocks, to these protein factories (Ribosomes), in response to the coded instructions introduced by the mRNA. This protein-building process is called **translation**. - **Ribosomal RNA (rRNA)** is a component of the ribosome factory itself without which protein production would not occur ## DNA Supercoiling - DNA does not only exist as secondary structures such as double helices, but it can fold up on itself to form tertiary structures by supercoiling. Supercoiling allows for the compact packing of circular DNA. Circular DNA still exists as a double helix, but is considered a closed molecule because it is connected in a circular form. A superhelix is formed when the double helix is further coiled around an axis and crosses itself. - Supercoiling changes the shape of DNA. The benefit of a supercoiled DNA molecule is its compactibility. In comparison to a relaxed DNA molecule of the same length, a supercoiled DNA is more compact. - **DNA topoisomerases** - These enzymes act to regulate DNA supercoiling by catalysing the winding and unwinding of DNA strands. They do this by making an incision that breaks the DNA backbone - **Class I DNA topoisomerases** break one strands of a DNA helix. - **Class II dna topoisomerases** break two strands of a dna helix. ## DNA Supercoiling - **Class I DNA Topoisomerases**: causing single-strand breaks and relegation. Does not need ATP. Topoisomerase I is a monomer. - **Class II DNA Topoisomerases (Gyrase)**: causing double strands break and relegation. Must need ATP hydrolyzing for its function. Topoisomerase II is a heterodimer. ## Online Tutorial - https://goo.gl/forms/8tLievmGE7eZih793 ## The Flow of Genetic Information - **Replication (DNA SYNTHESIS)** - **Protein Expression** - **Transcription (RNA SYNTHESIS)** - **Translation (PROTEIN SYNTHESIS)** ## DNA Replication - DNA replication is the process by which DNA makes a copy of itself during cell division. Replication is: - **Semi-discontinuous** - **Semi-conservative**: Semiconservative as it produces two copies that each contained one of the original strands and one new strand. - The DNA Replication occur in 3 steps: - **Initiation** - **Propagation** - **Termination** ### Replication Step 1: Initiation - The point at which the replication begins is known as the origin of replication (oric). Helicase brings about the procedure of strand separation, which leads to the formation of the Y shape replication fork. - **Enzymes in replication fork** - **Helicase**: responsible strand separation, which leads to the formation of the replication fork. - **SSB protein:** next step is for the single-stranded dna binding protein to bind to the single-stranded dna. Its job is to stop the strands from binding again. - **DNA polymerase III**: this enzyme makes the new strand by reading the nucleotides on the template strand and specifically adding complementary one nucleotide after the other on the daughter strand. If it reads an adenine (A) on the template, it will only add a thymine (T). - **Dna primase**: a primer is required to bind at the origin. Primers are short sequences of RNA, around 10 nucleotides in length. Primase synthesizes the primers. - **Ligase**: join okazaki fragments ### Replication Step 2: Elongation - **DNA POLYMERASEIII HAS DIFFERENT FUNCTIONS**: - DNA POLYMERASE ADDING NUCLEOTIDES TO THE NEW STRAND IN THE 3' DIRECTION (FROM 5' TO 3') - 3'-5' EXONUCLEASE ACTIVITY (PROOF READING TO INCREASE FIDELITY) - 5'-3' EXONUCLEASE ACTIVITY (REMOVE RNA PRIMERS OR DAMAGE DNA ON ITS PATH) - **REPLICATION IS SEMI-DISCONTINUOUS**: - The mechanism of DNA replication allows only for synthesis in a 5'-3' direction. Since the two strands are antiparallel, how is the parental strand that runs 5'-3' copied! - The leading strand is made continuously in a 5'-3' direction. - The lagging strand is initiated at the replication fork and proceeds 5'-3' back towards the origin to form the first okazaki fragment. - As the replication fork progresses the leading strand continues to be made as a single strand while further lagging strand fragment are made in a discontinuous fashion. - DNA pol I replace rna primers with dna nucleotides & the fragments are joined together by ligase. ### Replication Step 3: Termination - HE PROGRESS OF THE DNA REPLICATION FORK MUST STOP OR BE BLOCKED. TERMINATION AT A SPECIFIC LOCUS, WHEN IT OCCURS, INVOLVES THE INTERACTION BETWEEN TWO COMPONENTS: - A TERMINATION SITE SEQUENCE IN THE DNA - A PROTEIN WHICH BINDS TO THIS SEQUENCE TO PHYSICALLY STOP DNA REPLICATION ## IL 1 - WHY DOES DNA CONTAIN T RATHER THAN U? - PLZ ANSWER ON THE FOLLOWING LINK: HTTPS://GOO.GL/FORMS/GF6RTQIB2WZW1RIT2