Applied Biology of the Cell - BIOL6002 - Nucleic Acids - PDF

Applied Biology of the Cell BIOL6002 Nucleic Acids Dr MaryAnne Hurley 4 Nucleic Acids DNA Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of monomers called nuc...

Applied Biology of the Cell BIOL6002 Nucleic Acids Dr MaryAnne Hurley 4 Nucleic Acids DNA Nucleic acids are biopolymers, or large biomolecules, essential to all known forms of life. They are composed of monomers called nucleotides Each nucleotide has three components: 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). 5 Nucleic Acids DNA They play important role in living organism: Storage of genetic information for creating proteins; e.g. DNA Storage of genetic information for creating new cells; e.g. DNA Transfer of genetic information; e.g. RNA Storage of energy for cell processes; e.g. ATP (adenosine triphosphate) What is DNA? DNA = Deoxyribonucleic Acid a biomolecule that contains the biological instructions that allow the organism to develop, survive and reproduce. DNA, along with the instructions it contains, is passed from adult organisms to their offspring during reproduction. Where is the DNA found? In eukaryotes, DNA can be found in nucleus (chromosomal DNA) and mitochondria (mitochondrial DNA) In prokaryotes, DNA can be found in nucleoid (chromosomal DNA) and plasmids 7 DNA DNA See more here: https://youtu.be/V6bKn34nSbk Discovered by Friedrich Miescher in 1869 – isolated a compound from cell’s nuclei which he called nuclein Solving DNA structure: 1950s: Erwin Chargaff - found that the ratios of adenine (A) to thymine (T) and guanine (G) to cytosine (C) in DNA are equal. Rosalind Franklin and Maurice Wilkins – described the helix structure of DNA using X-ray crystallography. Francis Crick and James Watson – described the 3-D, double helix model of DNA and suggested the mechanism for DNA replication Francis Crick and James Watson – Nobel Prize winners for medicine in 1962, along with Wilkins 11 DNA DNA ◼ Think of DNA as a type of language, made up of a four letter alphabet: A, T, G, C ◼ These letters are called nitrogenous bases  A = Adenine  T = Thymine  G = Guanine  C = Cytosine ◼ The order and combination of bases creates a long, continuous sequence, like words and sentences with different meanings. This sequence of bases in the organism is known as the genome or genetic code ◼ E. coli genome contains ~4.6 million bases/ Human genome ~6 billion bases ◼ Genome contains all the instructions for life (blueprint of life) 12 DNA DNA  DNA present in the cells of all living organisms Contains: i. The genetic information necessary to reproduce an identical copy of the organism ii. The genetic information for all the functions of the cell DNA is the genetic material that stores instructions for to create, grow, function and reproduce life by providing a code by which amino acids are to be joined to make a protein. Structure of DNA Double stranded molecule (helix) containing: phosphate group + sugar + nitrogen base Adenine (A)-Thymine (T) Guanine (G)-Cytosine (C) 14 StructureNucleotide of DNA Components (3) Phosphate Group 1. Sugar – deoxyribose (deoxy – no oxygen on 2’ carbon) What kind of sugar is it 15 StructureNucleotide of DNA Components (3) Phosphate Group 2. Phosphate group – negatively charged, gives DNA overall negative charge Allows to link multiple monomers together 16 StructureNucleotide of DNA Components (3) Phosphate Group 3. Nitrogenous base – organic molecules containing nitrogen Allows “pairing” of DNA strands (through hydrogen bonds) to form double helix 17 Structure of DNA Nucleotides in DNA can contain one of four bases: Adenine, Thymine, Guanine or Cytosine BUT…the sugar and phosphate backbone will remain the same Two types of organic bases occur in nucleotides. 1. Purines – large double-ring molecules Adenine Guanine 2. Pyrimidines – smaller, single-ring molecules Cytosine Thymine 18 StructureNucleotide of DNAComponents (3) Phosphate Group 3. Nitrogenous base – bases in DNA are complementary Adenine (A) Thymine (T) Cytosine (C) Guanine (G) 21 Structure of DNA DNA DNA molecules in organisms exist as a double strand (2 chains). deoxyribose PO4 adenine thymine PO4 deoxyribose The sugar + phosphates form a chain like the “handrails” of a spiral staircase and the bases, attached to each sugar, protrude into the centre (like steps) and bond via hydrogen bonding 22 10 Structure of DNA The bases always pair up in the same way (complementary) Adenine always bonds with Thymine 2 Hydrogen bonds Adenine Thymine Cytosine always bonds with Guanine 3 Hydrogen bonds Cytosine Guanine 23 Structure of DNA Double Helix Two DNA polymers (strands) wind around each other like the outside and inside rails of a circular staircase. Such a winding shape is called a helix. Two chains winding around one another as in DNA are called a double helix. The bases that participate in base pairing are said to be complementary to each other as they bind with each other in a characteristic way (A-T and C-G): by knowing the sequence of one strand we can deduct the sequence of the second strand: e.g. 24 What is RNA? RNA RNA = Ribonucleic Acid There are 3 major types of RNA : mRNA (messenger RNA) rRNA (ribosomal RNA) tRNA (transfer RNA) DNA carries genetic instructions for the cell RNA is carries the biological instructions encoded in DNA and allows to convert them into a specific amino acid sequences in proteins Where is RNA found? In eukaryotes, RNA can be found in nucleus and cytoplasm of the cell In prokaryotes, RNA can be found in cytoplasm 25 RNA RNA RNA is similar to DNA, but is single-stranded and has two major chemical differences: i. The sugar in RNA is ribose. ii. Uracil is used as a nitrogenous base instead of thymine Uracil has the same structure as thymine, except that one of its carbons lacks a methyl (-CH3) group. DNA vs RNA structure  Structure of RNA Single-stranded nucleic acid containing: phosphate group + sugar + nitrogen base OH ribose 28 Structure of RNA RNA  DNA replication A process of producing two identical copies of DNA from one original DNA molecule DNA replication occurs in all living organisms – essential part cells growth and reproduction. How? DNA unique sequence enables the molecule to copy itself: the DNA double helix splits into two single strands, each serving as a template for building two new, double-stranded DNA molecules DNA replication enabled by the specific nature of DNA pairing( i.e., A-T and C-G) knowing the sequence of one strand the sequence of the other strand can be reproduced, creating two identical replicas of the original strand. Enzymatic process (carried out by specific enzymes) e.g. helicase, DNA polymerase See more here: https://youtu.be/TNKWgcFPHqw DNA replication Why does DNA need to be copied? Organisms may require to copy the DNA for the following purposes: To proliferate cells (increase numbers) – create new cells from one “parent” cell (mitosis) To reproduce– create offsprings and reproduce (meiosis) DNA profiling Take a sample of cell-containing material, e.g. a cheek cell or semen. Extract the DNA from the cells. Treat the extracted DNA with special enzymes. This produces DNA fragments. The DNA fragments are placed at one end of a gel. An electric charge is passed through the gel and the fragments move. The distance travelled by the pieces of DNA is seen by putting a stain onto the gel. The result is a series of bands.  Chromosomes In sexual reproduction, offspring gets information from each parent. Special cells, or gametes, are produced that contain only one copy of each chromosome and thus each gene. A cell is haploid (n) when it has only one copy of each chromosome or gene. Fertilisation occurs when the nuclei of two gametes fuse and the resultant cell (zygote) has two copies of each gene. DNA replication The messages that the DNA carries are vital for the survival of the cell. When a cell replicates, it produces an identical copy of itself. Replication is the production of an identical copy of the DNA. The structure of DNA allows it to make an exact copy of itself. Enzymes control the entire process. Takes place during interphase of the cell cycle Requires enzymes and energy (ATP) Requires ‘free’ nucleotides  Central Dogma of Molecular Biology DNA RNA Protein 2024-10-08 38  Protein synthesis DNA must be able to convert its message into proteins. These proteins will then ‘run’ the cell. Proteins are made of amino acid chains. About 20 amino acids are used to make up the majority of cell proteins. The number and order of amino acids determines the type of protein made. The DNA molecule controls both of these. The DNA has a code on one side of the double strand. This code is made up of groups of three bases in sequence. Each group of three bases codes for a specific amino acid. This is called the codon.  Transcription DNA: Transcription and Translation A process in which gene DNA sequence is copied (transcribed) to create RNA molecule. Transcription occurs in all living organisms – essential part of protein synthesis. Transcription (DNA to mRNA) occurs in the nucleus of the cell in eukaryotes (plants, fungi, animals, etc.) and in the cytoplasm of bacteria. Enzymes are involved in the process: i. DNA helicase separates the two strands of DNA ii. RNA polymerase moves along the DNA strand creating a complementary RNA strand. The complementary strand is known as messenger RNA (mRNA) and it holds the information needed to make the amino acid sequence of the protein Translation DNA: Transcription and Translation A process in which the sequence of mRNA is converted to sequence of amino acids during protein synthesis. Translation occurs in all living organisms – essential part of protein synthesis. mRNA sequence enables the creation of protein by converting the genetic code (codons) to amino acid sequence. Occurs in ‘protein factories’ called ribosomes in the cytoplasm of the cell – ribosomes bind to mRNA and carry out the translation process. tRNA (transfer RNA) molecules “bring in” the appropriate amino acid, as defined by the sequence, where ribosomes incorporate it into the protein See more here: https://youtu.be/gG7uCskUOrA Amino acid sequence Amino acid sequence in the protein is determined by the DNA sequence of the gene encoding the protein (genetic code). How are the amino acids encoded? The genetic code is read in 3-letter “words” (called codons) - a sequence of 3 nucleotides in DNA or RNA that corresponds to a specific amino acid: → There are 64 combinations of the 3-letter codes possible with the 4 nitrogenous bases present in the DNA/RNA → There are 20 amino acids universally encoded by most organisms → Some amino acids are coded by more than one codon → Each codon codes only for one specific amino acid → The codes are universal irrespective of the type of organism  Genetic Code → There are 61 codons coding for individual amino acids and 3 are STOP codons → E.g. ACU = Threonine 2024-10-08 44 45 ATP (Adenosine Triphosphate). Adenosine triphosphate (ATP) is a nucleic acid molecule that remains a single nucleotide. Unlike a DNA or RNA nucleotide, the ATP nucleotide has three phosphate groups attached to its ribose sugar and adenine as the nitrogenous base. ATP is a “energy currency” of the cell – all living organisms run their cells on ATP ATP is a high-energy molecule because the last two phosphate bonds are unstable, negatively-charged and are easily broken. ATP can store energy from cellular processes and provide energy when needed by attaching/detaching the phosphate group. 46 ATP (Adenosine Triphosphate). 47 Questions for revision 1. What are the functions of nucleic acids? 2. What are the nucleic acids monomers called and what are they composed of? 3. Give an example of a nucleic acid. 4. Describe how DNA double helix is formed. 5. What is the structure and function of RNA? 6. Describe the process of DNA replication. 7. What two processes are involved in protein synthesis? 8. What is a genetic code and how is encoding the amino acid sequence? 9. What is the function of ATP?