DNA, RNA, and Chromosomes PDF

Information System Information must be transmitted within and between individuals by: 1) DNA: Chemical substances transmit information from one generation to the next one. 2) Chemical and electrical signals: Chemical Signals: One of the most common forms of cellular commu...

Information System Information must be transmitted within and between individuals by: 1) DNA: Chemical substances transmit information from one generation to the next one. 2) Chemical and electrical signals: Chemical Signals: One of the most common forms of cellular communication involves the release and reception of chemical signals. These chemical signals, known as ligands or signaling molecules, can be secreted by a cell and travel through the extracellular fluid to reach other target cells. Examples of chemical signals include neurotransmitters, hormones  Hormones: Hormones are the chemical signaling molecules produced by the endocrine glands and secreted directly into the bloodstream. They travel through the blood to distant tissues and organs. Although hormones reach all parts of the body, only target cells with compatible receptors are equipped to respond. Neurotransmitters: Many animals use electrical signals to transmit information. Nervous system transmits information by way of chemical compounds called neurotransmitters and electrical impulses. Chromosomes  Chromosomes Chromosomes are thread like bodies present in the nucleoplasm of the living cells, which help in the inheritance (transmission) of genetic material in form of Genes from generation to generation. That genetic material, which determines how an organism develops, is a molecule of deoxyribonucleic acid (DNA). In prokaryotes, or cells without a nucleus, the chromosome is merely a circle of DNA. In eukaryotes, or cells with a distinct nucleus, chromosomes are much more complex in structure.  The eukaryotic genome is made up of a number of chromosomes. In diploid organisms such as human, there are two copies of each chromosome. These “pairs” of chromosomes are similar in that they have all of the same genes in the same order, but they often carry different versions of the genes, which are known as alleles..  Chromosomes vary widely between different organisms. The number of chromosomes per organism is always a definite number. Chromosomes are the essential unit for cellular division and must be replicated, divided, and passed successfully to their daughter cells. They control the growth and development of the organism. The structure of chromosomes and chromatin varies through the cell cycle.  In interphase chromosomes are packaged by proteins into a condensed structure called chromatin. This allows the very long DNA molecules to fit into the cell nucleus. Chromosomes can be detected by staining cells with dyes in mitosis, where the chromosomes are condensed.  Each chromosome is made up of DNA tightly coiled many times around proteins called histones that support its structure. Each chromosome has a constriction point called the centromere, which divides the chromosome into two sections, or “arms.” The short arm of the chromosome is labeled the “p arm.” The long arm is labeled the“q arm.” The position of the centromere on each chromosome gives the chromosome its characteristic shape, and can be used to help describe the location of specific genes.  Chromosome Structure The chemical composition of a chromosome is histone proteins and DNA. Chromosomes are made up of chromatin, which contains a single molecule of DNA and associated proteins. Each chromosome contains hundreds and thousands of genes that can code for several proteins in the cell. Structure of a chromosome can be best seen during cell division Main parts of chromosomes are: Chromatid: Each chromosome has two symmetrical structures called chromatids Each chromatid contains a single DNA molecule At the anaphase of mitotic cell division, sister chromatids separate and migrate to opposite poles  Centromere and kinetochore: Sister chromatids are joined by the centromere. Spindle fibres during cell division are attached at the centromere The number and position of the centromere differs in different chromosomes The centromere is called primary constriction Centromere divides the chromosome into two parts, the shorter arm is known as ‘p’ arm and the longer arm is known as ‘q’ arm. The kinetochore is a giant protein complex assembled on the centromere of eukaryotes just before cell division. Each chromosome contains two kinetochores on either side of the centromere during metaphase. During cell division, the kinetochore complex serves as an interface between chromosomes and spindle microtubules. The main functions of kinetochore are: Kinetochore pulls the chromosomes apart during the anaphase phase of the cell division. It helps in distributing the sister chromatids equally into the daughter cells.  Secondary constriction and nucleolar organisers: Other than centromere, chromosomes possess secondary constrictions. – Secondary constrictions can be identified from centromere at anaphase because there is bending only at the centromere (primary constriction) – Secondary constrictions, which contain genes to form nucleoli are known as the nucleolar organiser Telomere: - Terminal part of a chromosome is known as a telomere. Telomeres are polar, which prevents the fusion of chromosomal segments Each time a cell divides, the telomeres become slightly shorter and the cell stop dividing. Satellite: It is an elongated segment that is sometimes present on a chromosome at the secondary constriction.The chromosomes with satellite are known as sat-chromosome Telomere  Chromatin: Chromosome is made up of chromatin. Chromatin is made up of DNA, RNA and proteins. At interphase, chromosomes are visible as thin chromatin fibres present in the nucleoplasm. During cell division, the chromatin fibres condense and chromosomes are visible with distinct features. – The darkly stained, condensed region of chromatin is known as heterochromatin. It contains tightly packed DNA, which is genetically inactive – The light stained, diffused region of chromatin is known as euchromatin. It contains genetically active and loosely packed DNA – At prophase, the chromosomal material is visible as thin filaments known as chromonemata  Structural Organisation of Chromatin Chromatin consists of DNA and associated proteins. DNA is packaged in a highly organised manner in chromosomes Nucleosomes are the basic unit of chromatin. It is 10 nm in the diameter – DNA packing is facilitated by proteins called histones. DNA is wound around histone proteins to form a nucleosome – There are 5 types of histone proteins in the eukaryotic chromosomes. – Histones are positively charged due to the presence of amino acids with basic side chains and it associates with negatively charged DNA due to the presence of phosphate groups – Histone proteins play an important role in gene regulation – A typical nucleosome contains 200 base pairs( bp )of DNA helix. The core particle of the nucleosome consists of DNA coiled around a core of eight histone molecules (2 molecules of 4 histone proteins). That is linked by linker DNA. – Nucleosomes prevent DNA from getting tangled  Linker DNA and the fifth histone pack adjacent nucleosomes to a 30 nm compact chromatin fibre These fibres form a large coiled loop held together by non-histone proteins (actin, 𝛂 and 𝛃 tubulin, myosin) called scaffolding proteins to form extended chromatin which is 300 nm in diameter Metacentric Sub-metacentric Types of Chromosomes Acrocentric Telocentric 1. Telocentric (at one end of the chromosome. It has one arm) 2. Acrocentric (almost terminal. It has one large and another very small arm) 3. Metacentric (in the center of the chromosome. So the arms are equal) 4. Sub-metacentric(not at the middle position of the chromosomes. So the arms are unequal) The structure of DNA and RNA Deoxyribonucleic acid and ribonucleic acid are the main groups of the nucleic acids. They are made of subunits called nucleotides.  Deoxyribonucleic acid (DNA) Deoxyribonucleic acid (DNA) contains the biological instructions that make each species unique. Genes are nothing but the segments of DNA DNA is passed from adult organisms to their offspring during reproduction.. Where DNA is found?  What is DNA made of? DNA is a polymer. The monomer units of DNA are nucleotides. Each nucleotide consists of three parts: a phosphate group, a sugar group and one of four types of nitrogen bases. To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating What is DNA made of? DNA is made of chemical building blocks called nucleotides. These building blocks are made of three parts: a phosphate group, a sugar group and one of four types of nitrogen bases. To form a strand of DNA, nucleotides are linked into chains, with the phosphate and sugar groups alternating.  The four different types of nucleotides found in DNA, differing only in the nitrogenous base. Purines are the larger of the two types of bases and pyrimidines are the smaller. The order, or sequence, of these bases determines what biological instructions are contained in a strand of DNA. For example, the sequence ATCGTT might instruct for blue eyes, while ATCGCT might instruct for brown. What does DNA do? DNA contains the instructions needed for an organism to develop, survive and reproduce. To carry out these functions, DNA sequences must be converted into messages that can be used to produce proteins, that do most of the work in our bodies. Each DNA sequence that contains instructions to make a protein is known as a gene. The size of a gene may vary greatly, ranging from about 1,000 bases to 1 million bases in humans. Genes only make up about 1 percent of the DNA sequence What is the DNA double helix? Scientist use the term "double helix" to describe DNA's winding, two-stranded structure. This shape looks like a twisted ladder To understand DNA's double helix : The sides of the ladder are strands of alternating sugar and phosphate groups ,the strands run in opposite directions. Each rung of the ladder is made up of two nitrogen bases, paired together by weak thermodynamic forces (Hydrogen bonds ). Nucleotide binding & bonding  Nucleotides bind using sugar, phosphate groups (phosphate group on 5th carbon of sugar binds covalently to 3rd carbon of sugar ) sugar- phosphate backbone.  Nucleotides form hydrogen bonds with bases on opposing strand. Complementary base pairing A pairs with T (2hydrogen bonds), C pairs with G ( 3 hydrogen bonds), and they are called complementary bases.  It is notice is that a smaller base is always paired with a bigger one.  A - T and G - C base pairs are occupy the same space within a DNA double helix.  The effect of this is to keep the two chains at a fixed distance from each other and keep the backbone strands parallel.  Therefore the DNA molecule has a uniform diameter. Base Pairs Within the DNA double helix, A forms 2 hydrogen bonds with T on the opposite strand, and G forms 3 hyrdorgen bonds with C on the opposite strand. DNA Backbone The DNA backbone is a polymer with an alternating sugar-phosphate sequence. The deoxyribose sugars are joined at both the 3'-hydroxyl and 5'- hydroxyl groups to phosphate groups in ester links. Features of the DNA Double Helix DNA (Watson and Crick ,1953) Two DNA strands form a helical spiral, winding around a helix axis. The two polynucleotide chains run in opposite directions. The bases of the individual nucleotides are on the inside of the helix, stacked on top of each other like the steps of a spiral staircase A final structure for DNA Notice that the two chains run in opposite directions, and the right-hand chain is essentially upside-down.  RNA Ribonucleic acid consists of: Ribose (a pentose = sugar with 5 carbons) Phosphoric Acid Nitrogenous bases: Purines(Adenine and Guanine ) and Pyrimidines (Cytosine and Uracil ) RNA structure RNA typically is a single-stranded biopolymer. The primary structure of RNA is composed of nucleotides attached by 5’-3’ phosphodiester bonds between ribose sugars. RNA differs from DNA in that it contains a uracil nucleotide instead of thymine and carries a 2’ hydroxyl group rather than a 2’ hydrogen. However, the presence of self-complementary sequences in the RNA strand leads to intrachain base-pairing and folding of the ribonucleotide chain into complex structural forms consisting of bulges and helices.  How is it made? RNA polymerases synthesize RNA from DNA through a process called transcription. To initiate transcription, an RNA polymerase enzyme binds to a promoter region on DNA, and the DNA double helix unwinds into a template strand and non-coding strand. During transcription, an RNA polymerase uses the 3’-5’ DNA template strand to synthesize a 5’-3’ RNA strand with complementary nucleotides. The newly synthesized RNA strand is nearly identical to the non-coding strand of DNA except for uracil substituting thymine.  RNA is found in the nucleus, where it is synthesized, and in the cytoplasm , as messenger RNA, transfer RNA or ribosomal RNA. All these forms of RNA are involved in the protein synthesis. 1. messengerRNA or m RNA: a copy of a section of DNA and serves as a template and carries the genetic information out of the nucleus for protein synthesis. 2. transferRNA or t RNA: binds to both mRNA and amino acids and brings the correct amino acids to ribosomes during protein formation, based on the nucleotide sequence of the mRNA. 3. ribosomalRNA or r RNA: constitutes 50% of a ribosome, which is a molecular assembly involved in protein synthesis.  The rule A+C=U+G CAN'T be applied in structure of RNA, but it(A+C=T+G) is found in dna structure, WHY?  Protein synthesis The mechanism of RNA translation into protein is carried out in three steps: initiation, elongation, and termination. During initiation, a tRNA and ribosome join an mRNA. The start codon, AUG, codes for methionine and will always be the first amino acid in the sequence. After initiation, the ribosome moves along the mRNA in the 5’-3’ direction, reading the codons and binding tRNAs carrying the respective amino acids for which the codons are coding. The sequence of amino acids progressively becomes longer and terminates upon reaching a stop codon. The stop codons are UAG, UAA, and UGA. The polypeptide is then released from the ribosomal complex and modified into an active protein..  The processes of protein synthesis 1) Transcription: The First Step of Protein Synthesis In this process, a single-stranded mRNA molecule is transcribed from a double-stranded DNA molecule. The mRNA thus formed is used as a template for the next step, translation. The three steps of transcription are: initiation, elongation, and termination. i) Initiation The process of transcription begins when the enzyme RNA polymerase binds to a region of a gene called the promoter sequence with the assistance of certain transcription factors. Due to this binding, the double-stranded DNA starts to unwind at the promoter region. Among the two strands of DNA, one that is used as a template to produce mRNA is called the template, noncoding, or antisense strand. On the other hand, the other one is called the coding or sense strand.  ii) Elongation After the opening of DNA, the attached RNA polymerase moves along the template strand of the DNA, creating complementary base pairing of that strand to form mRNA. iii) Termination Once the mRNA strand is complete, the hydrogen bonds between the RNA-DNA helix break. As a result, the mRNA detaches from the DNA. The mRNA formed at the end of the transcription process is called pre-mRNA, as it is not fully ready prepared to enter translation. So, before leaving the nucleus, it needs to undergo some modifications or processing to transform into a mature mRNA. some modifications or processing to transform into a mature mRNA, including : the addition of a 5' cap and a poly-A tail (polyadenylation) and the removal of introns (non-coding regions). Translation It is the second part of the protein synthesis: RNA → Protein. It is the process in which the genetic code in mRNA is read to make a protein. After mRNA leaves the nucleus, it moves to a ribosome, which consists of rRNA and proteins. The ribosome reads the sequence of codons in mRNA, and molecules of tRNA bring amino acids to the ribosome in the correct sequence. Translation occurs in three stages: Initiation, Elongation and Termination  During initiation: After the mature mRNA leaves the nucleus, it travels to a ribosome. The 5′ methylated cap of the mRNA, containing the strat codon (AUG) binds to the small ribosomal subunit of the ribosome. Next, a tRNA containing anticodons complementary to the start codon on the mRNA attaches to the ribosome. These mRNA, ribosome, and tRNA together form an initiation complex. The ribosome reads the sequence of codons in mRNA, and tRNA bring amino acids to the ribosome in the proper sequence. The large ribosomal subunit then joins, forming a functional ribosome.  Elongation phase: tRNA keep bringing amino acids to the growing polypeptide according to complementary base pairing between the codons on the mRNA and the anticodons on the tRNA. As a tRNA moves into the ribosome, its amino acid is transferred to the growing polypeptide. Once this transfer is complete, the tRNA leaves the ribosome, the ribosome moves one codon length down the mRNA, and a new tRNA enters with its corresponding amino acid. This process repeats and the polypeptide grows.  Termination It occurs when a stop codon (UAA, UAG, or UGA) is encountered on the mRNA. This signals the end of protein synthesis, and the completed polypeptide chain is released from the ribosome. The stop codon doesn’t call for a tRNA, but instead for a type of protein called a release factor, which will cause the entire complex (mRNA, ribosome, tRNA, and polypeptide) to break apart, releasing all of the components.