Chapter 20: Chromosomes and DNA PDF

# Chapter 20: Chromosomes and DNA ## Chromosomes - **Chromosomes** are thread-like structures that appear inside the nucleus at the time of cell division. - **Discovery**: First observed by Walther Fleming in 1882, while examining the rapidly dividing cells of salamander larvae. - **Number of Chr...

# Chapter 20: Chromosomes and DNA ## Chromosomes - **Chromosomes** are thread-like structures that appear inside the nucleus at the time of cell division. - **Discovery**: First observed by Walther Fleming in 1882, while examining the rapidly dividing cells of salamander larvae. - **Number of Chromosomes in Different Organisms**: - Varies from species to species. - **Penicillium** (a fungus) has only one pair (2 chromosomes) - Some ferns have more than 500 pairs (1000 chromosomes). - **Mosquito**: 3N - **Honeybee**: 16 pairs - **Corn**: 10 pairs - **Sugarcane**: 40 - **Frog**: 13 - **Mouse**: 20 - **Human cells**: 46 chromosomes (23 pairs) - **Function of Chromosomes**: - Each chromosome contains many genes that play key roles in determining body development and function. - The presence of all chromosomes is essential for survival. - Missing part or a whole chromosome can lead to serious consequences and often death. - **Structure of a Typical Chromosome**: - Typically a chromosome consists of two parts: - **Chromatids**: Two replicas. - **Centromere**: Primary constriction, a constricted region on the chromosome. - **Secondary Constriction**: An additional, less pronounced constriction on the arm of the chromosome. - **Karyotype**: - The specific arrangement of chromosomes in an individual. - It is used to classify individuals based on their chromosomal features. - Karyotypes can differ based on: - Size - Staining properties - Location of the centromere - Relative length of the two arms - Position of constricted regions along the arms ### Types of Chromosomes: - **Telocentric**: - Centromere is located at one end. - Both arms are located on one side. - Appear "i" shaped during cell division. - **Acrocentric**: - Centromere is very close to one end. - One arm is very short. - Appear "i" shaped during cell division. - **Sub Metacentric**: - Centromere is displaced from the center. - Arms on both sides are clearly unequal. - Appear "J" shaped. - **Metacentric**: - Centromere is located in the center. - Arms on both sides are equal, or almost equal. - Appear "V" shaped. ## Composition of Chromosomes - Composed of: - **DNA**: - Single long double helical molecule. - Makes up approximately 40% of each chromosome. - **Protein**: - Approximately 60% protein. - Primarily **histones**, which are positively charged (most proteins are negatively charged) due to their abundant basic amino acids (arginine and lysine). - Strongly attracted to the negatively charged phosphate groups of the DNA. - **RNA**: - Significant amount of RNA associated with chromosomes. - Serves as the site of synthesis for all types of RNA. ### Structure of DNA * The DNA of a chromosome is one long double-stranded fiber that extends unbroken through the entire length of the chromosome. * **Nucleosomes:** * Small bead-like structures formed by the attachment of DNA and histone proteins. * When examined with an electron microscope, eukaryotic chromatin resembles a string of beads. * Every 200 nucleotides, the DNA duplex coils around a core of eight histone proteins (histone octamer), forming a complex known as a nucleosome. * Each nucleosome is approximately 10nm in diameter. * **Condensation:** * The process of converting the thin, long chromatin into thicker, rod-like chromosomes. * Involves coiling and supercoiling of the chromatin thread. * Occurs at the onset of division. * The histone cores act as "magnetic forms" that promote and guide coiling. * Further coiling occurs when the string of nucleosomes is wrapped up into higher-order coils called supercoils. ### Types of Condensed Chromatin: - **Heterochromatin**: - Portions of chromatin that remain densely condensed. - DNA in heterochromatin is often not expressed. - **Euchromatin**: - Portions of chromatin that condense only during cell division. - Is present in an open configuration at other times. - Genes in euchromatin can be expressed. ## The Chromosomal Theory of Inheritance - **Statement:** Genes are physical units located on chromosomes. - **Contribution of Karl Correns**: Provided the first suggestion of a central role for chromosomes in heredity (1900). - **Contribution of Walter Sutton**: - Formulated the chromosomal theory of inheritance in 1902. - Proposed that the two gametes (sperm and egg) make equal hereditary contributions. - Observed that homologous chromosomes separate during meiosis, and each pair orients on the metaphase plate independently of other pairs. ### Problem with the Theory - The number of characters that assort independently in an organism often exceeds the number of chromosome pairs, which led to skepticism about the theory. ## DNA as Hereditary Material - **Contribution of Griffith**: - The first evidence for the hereditary nature of DNA came from Frederick Griffith (1928). - Griffith observed unexpected phenomena while studying two related strains of *Streptococcus pneumoniae* bacteria: - A **virulent strain** (S-type) forms smooth colonies on a culture dish and is pathogenic. - A **mutant strain** (R-type) forms rough colonies and is non-virulent. - Griffith's experiments demonstrated that: - Heat-killed virulent bacteria could transform live, non-virulent bacteria into virulent bacteria. - This process was termed **transformation**, the transfer of genetic material from one cell to another. - **Contribution of Avery, McLeod, and McCarty**: - In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty provided further evidence that DNA was the transforming principle. - They: - Prepared mixtures of heat-killed virulent *Streptococcus pneumoniae* bacteria and live non-virulent bacteria. - Removed most of the protein from the mixtures, finding that the transforming activity remained. - Used enzymes to further isolate the transforming principle, discovering that DNA was responsible for the transformation. - **Experiment of Hershey and Chase**: - In 1952, Alfred Hershey and Martha Chase conducted experiments with bacteriophages (viruses that infect bacteria) to confirm that DNA is the genetic material. - They labeled bacteriophages with either radioactive phosphorus (32P), which is found in DNA, or radioactive sulfur (35S), which is found in protein coats. - They infected bacteria with the labeled phages and then separated the bacteria from the phage coats. - The results showed that radioactive phosphorus (32P) was found inside the bacteria, while radioactive sulfur (35S) remained outside. - This demonstrated that DNA, and not protein, was the genetic material that entered the bacterial cells during infection. ## Chemical Nature of DNA - **Discovery of DNA:** - Friedrich Miescher discovered DNA in 1869, while extracting a white substance from the nuclei of human cells and fish sperm. - He initially called it "nuclein," because it seemed to be specifically associated with the nucleus. - Later, it was recognized as **nucleic acid** due to its acidic nature. - **Work of P. A. Levene**: - Determined the main components of DNA: - Phosphate (PO4) groups - Five-carbon sugar (deoxyribose) - Nitrogen-containing bases: - **Purines**: Adenine (A) and Guanine (G) - **Pyrimidines**: Thymine (T) and Cytosine (C) (RNA contains Uracil, U, instead of T). - **Structure of a Typical Nucleotide**: - **Nucleotides** are the repeating units of DNA and RNA. - Each nucleotide consists of: - **Nitrogenous base**: Attached to carbon number 1 of the pentose sugar. - **Pentose sugar**: A five-carbon sugar (deoxyribose in DNA, ribose in RNA). The phosphate group is attached to carbon number 5 of the sugar. In addition, a free hydroxyl (-OH) group is attached to carbon number 3 of the sugar. - **Phosphate group**: Attached to carbon number 5 of the sugar. ## Formation of the Polynucleotide Chain - **Phosphodiester Linkage**: - The reaction that links nucleotides together. - A dehydration synthesis that eliminates water molecules and forms a covalent bond. - Links the phosphate group of one nucleotide to the hydroxyl group of the next nucleotide, creating a "phosphodiester bond." - **Polynucleotide Chains**: - Thousands of nucleotides can link together in long chains. - Each chain has a free 5' phosphate group at one end and a free 3' hydroxyl group at the other end. ## Work of Chargaff - **Erwin Chargaff** discovered that: - The amount of adenine (A) in DNA always equals the amount of thymine (T). - The amount of guanine (G) in DNA always equals the amount of cytosine (C). - This "Chargaff's rule" indicated that bases occur in pairs, meaning that the two strands of DNA are complementary. ## Work of Wilkins and Franklin - **Rosalind Franklin** and **Maurice Wilkins** used X-ray diffraction to study the structure of DNA. - They were both working on the same problem at the same time, but were not collaborating.. - The X-ray diffraction patterns suggested that DNA was a helix with: - A diameter of ~2 nm - A complete helical turn every ~3.4 nm ## Double-Helical Structure of DNA (Watson-Crick Model) - **James Watson** and **Francis Crick** proposed the model of the DNA double helix in 1953. - The model explained: - The DNA molecule is a double helix consisting of two complementary strands that run in opposite directions (antiparallel). - The strands are held together by hydrogen bonds that form between nitrogenous bases on the two strands. - The base pairs always consist of a purine (adenine or guanine) paired with a pyrimidine (thymine or cytosine). - **Adenine always pairs with thymine** (A-T) with two hydrogen bonds. - **Guanine always pairs with cytosine** (G-C) with three hydrogen bonds. - The double helical structure is stabilized by hydrophobic interactions that stack the base pairs, creating a stable, compact form. ## DNA Replication - **Definition:** The process of creating a new DNA molecule from an existing DNA molecule. - **Models of DNA Replication**: - Three models were proposed: - **Semi-conservative model**: - Each new DNA molecule consists of one original strand and one new strand. - **Conservative model**: - The original DNA molecule remains intact, and a completely new molecule is created. - **Dispersive model**: - Each new DNA molecule is a mixture of old and new DNA segments. - **Meselson-Stahl Experiment** - In 1958, Matthew Meselson and Franklin Stahl provided strong evidence for the semi-conservative model of DNA replication. - They grew bacteria in a medium containing heavy nitrogen (N15) to label their DNA. - They transferred the bacteria to a medium containing light nitrogen (N14) and collected DNA samples at different time points. - The density of the DNA was analyzed using a cesium chloride gradient. - The results showed that: - After one round of replication, the DNA was a mixture of "heavy" and "light" strands. - After two rounds of replication, one-half of the DNA molecules contained only light strands, while the other half contained one heavy strand and one light strand. - This supported the semi-conservative model. ### The Replication Process - **Definition**: The process of DNA replication starts at one or more sites on the DNA molecule, called **replication origins**. - **Key Enzymes involved in DNA Replication:** - **Helicases**: Unwind and separate the two DNA strands. - **Single-strand binding proteins (SSBPs)**: Stabilize and protect the single strands from cleavage and prevent them from rewinding. - **DNA polymerases**: Synthesize new DNA strands by adding nucleotides in the 5'→3' direction. - **DNA polymerase I**: Plays a supporting role in DNA replication. - **DNA polymerase II**: Involved in DNA repair. - **DNA polymerase III**: The main replicating enzyme. - **Primase**: Synthesizes short RNA primers to initiate DNA synthesis. - **DNA ligase**: Joins together the Okazaki fragments synthesized on the lagging strand. - **Steps in DNA Replication**: 1. **Initiation**: - Replication begins at the replication origin. - **Initiator proteins** recognize and bind to the origin sequence. - **Helicases** unwind the DNA double helix, separating the two strands. - **Single-strand binding proteins** stabilize the separated strands. - **Primase** synthesizes a short RNA primer to which DNA polymerase can attach. 2. **Elongation**: - **DNA polymerases** add nucleotides to the new DNA strands, following the base pairing rules. - **Leading strand synthesis**: Occurs continuously, as the DNA polymerase moves in the same direction as the unwinding helix. - **Lagging strand synthesis**: Occurs discontinuously. - A series of short segments, called **Okazaki fragments**, are synthesized in the opposite direction. - **DNA ligase** connects the Okazaki fragments together. 3. **Termination**: - Occurs when the polymerase reaches the end of the template strand. - **Release factors** disengage the polymerase and separate the newly synthesized DNA molecules ## Genetic Code - **Definition**: The linear sequence of nucleotide triplets in DNA that specifies the sequence of amino acids in a polypeptide chain. - **The Genetic Code is**: - **Triplet**: Each codon is a sequence of three nucleotides. - **Degenerate**: Most amino acids are specified by more than one codon. - **Non-overlapping**: The code is read continuously, without punctuation, beginning at a specific start codon and ending at a stop codon. - **Universal**: The genetic code is largely the same in all known organisms. - **Commaless**: There are no special punctuation marks separating codons. ### Discovery of the Genetic Code - Marshall Nirenberg, Philip Leder, and Har Gobind Khorana were key researchers in deciphering the genetic code. - Nirenberg and Leder used a cell-free system to synthesize proteins by providing an artificial mRNA and a mixture of amino acids. - Khorana synthesized artificial mRNAs with specific codon sequences. - These experiments ultimately determined the codons that specify all 20 amino acids. ## Transcription - **Definition**: The process of creating a messenger RNA (mRNA) molecule from a DNA template. - **Key Enzymes and Factors**: - **RNA Polymerase**: Synthesizes mRNA. - **Promoter**: A sequence of DNA that signals the starting point for transcription. - **Sigma factor**: In bacteria, a subunit of RNA polymerase that is required for the initiation of transcription. - **Core enzyme**: The main part of RNA polymerase that catalyzes the synthesis of mRNA. ### Steps in Transcription: 1. **Initiation**: - RNA polymerase binds to a specific promoter sequence on the DNA template strand. - The DNA helix unwinds, forming a transcription bubble. - The first nucleotide of the new RNA strand is added to the template strand. 2. **Elongation**: - RNA polymerase moves along the DNA template strand, adding complementary RNA nucleotides to the growing mRNA molecule. 3. **Termination**: - Transcription ends when the polymerase recognizes a termination signal sequence on the DNA template. - The mRNA detaches from the DNA template. ## Post-Transcriptional Modifications in Eukaryotes - Eukaryotic mRNA undergoes several processing steps before it is translated. - These modifications include: - **Addition of a 5' cap**: A modified guanine nucleotide added to the 5' end of the mRNA for protection and stability. - **Addition of a 3' poly(A) tail**: A sequence of adenine nucleotides added to the 3' end of the mRNA for protection and stability. - **Splicing**: The removal of introns (non-coding regions) from the mRNA ## Translation - **Definition**: The process of synthesizing a protein from an mRNA molecule. - **Key Components**: - **Ribosomes**: Sites of protein synthesis. - **tRNA**: Carries amino acids to the ribosome. - **Aminoacyl-tRNA synthetase**: Attaches the correct amino acid to its corresponding tRNA. - **mRNA**: Contains the genetic code that specifies the sequence of amino acids in the protein. - **Initiation factors**: Help to assemble the ribosome with the mRNA and the first tRNA. - **Elongation factors**: Help to move the ribosome along the mRNA. - **Release factors**: Cause the ribosome to release the completed polypeptide chain. ### Steps in Translation: 1. **Initiation**: - The small ribosomal subunit binds to the mRNA. - The initiator tRNA (carrying methionine) binds to the start codon (AUG). - The large ribosomal subunit joins the complex. 2. **Elongation**: - tRNAs carrying amino acids bind to the mRNA codons in the A site. - A peptide bond forms between the adjacent amino acids, adding the new amino acid to the growing polypeptide chain. - The ribosome translocates to the next codon, moving along the mRNA. 3. **Termination**: - The ribosome reaches a stop codon (UAG, UAA, or UGA). - A release factor binds to the stop codon, causing the polypeptide chain to detach from the ribosome. - The ribosomal subunits dissociate. ## Mutations - **Definition:** A change in the sequence of DNA. - **Causes of Mutations:** - **Errors in DNA replication:** Can lead to permanent changes in the DNA sequence if not repaired. - **Exposure to mutagens:** Certain environmental factors, like radiation or chemicals, can damage DNA. ### Types of Mutations 1. **Chromosomal Aberrations:** - Involve changes in the number or structure of chromosomes. - **Changes in chromosome number**: Can result from the loss or gain of entire chromosomes or sets of chromosomes. - **Aneuploidy:** An abnormal number of chromosomes. - **Polyploidy:** More than two sets of chromosomes. - **Changes in chromosome structure**: Can involve deletions, insertions, duplications, or rearrangements of chromosome segments. 2. **Point Mutations**: - Changes in a single nucleotide in the DNA sequence. - **Types of Point Mutations**: - **Substitution**: One nucleotide is replaced by a different nucleotide. - **Insertion**: An extra nucleotide is added. - **Deletion**: A nucleotide is removed. ### Effects of Mutations - **Harmful**: Mutations can disrupt gene function and lead to disorders or disease. - **Beneficial**: Mutations are the source of genetic variation, which is essential for evolution. - **Neutral**: Some mutations may have no noticeable effect. ## Central Dogma - The central dogma of molecular biology describes the flow of genetic information from DNA to RNA to protein. - It is a guiding principle in understanding how genes are expressed and regulated. - **Steps in the Central Dogma**: 1. **Transcription:** DNA is transcribed into RNA (mRNA). 2. **Translation:** mRNA is translated into protein. ## References - Biology (F.Sc. Part-II) textbook. - Campbell Biology (any recent edition) - Molecular Biology of the Cell (any recent edition)