PATH1002 Structure of Nucleotides and Nucleic Acid Handout 2024 PDF

Learning Objectives Understand the basic structure and function of DNA and RNA Relate the structure of DNA and RNA to their roles in storing and expressing genetic information Describe the process of DNA replication and appreciate the importance of accurate replication Structure of Nucleot...

Learning Objectives Understand the basic structure and function of DNA and RNA Relate the structure of DNA and RNA to their roles in storing and expressing genetic information Describe the process of DNA replication and appreciate the importance of accurate replication Structure of Nucleotides and Nucleic Acid Learning Objectives – Lecture 1 At the end of this lecture you should be able to: – Describe in detail the structure of DNA and RNA including their chemical components – Explain what a chromosome is and outline packaging of DNA in the nucleus – Compare and contrast DNA and RNA structure  Deoxyribonucleic acid (DNA) is the genetic material that is transmitted from cell to cell at cell division from generation to generation through reproductive cells Instructions are stored in DNA in the nucleus in every dividing cell Ribonucleic acid (RNA) – information stored in DNA is converted to RNA Many different functional types of RNA broadly grouped as protein coding RNA and non- coding RNA Genetics in healthcare Pharmacogenomics Deoxyribonucleic Acid Two long polynucleotide chains composed of 4 types of nucleotides subunits. Two strands wind around each other to make a double helix, which looks like a spiral staircase. Nucleotide– basic unit of DNA Each nucleotide has 3 components Five- carbon sugar phosphate group one of 4 nitrogen containing bases Guanine (G) Adenine (A) Cytosine (C) Thymine (T) Figure 5-2a Essential Cell Biology (© Garland Science 2010) Nucleotides Adenosine Adenosine monophosphate  Figure 5-2b Essential Cell Biology (© Garland Science 2010) Linear backbone of alternating sugar and phosphates with a base attached to the sugar residue Adjacent nucleotides held together by strong covalent bonds between atoms of linear backbone Order of nucleotides specify the instructions Figure 5-2c Essential Cell Biology (© Garland Science 2010)  Non random base pairing allows us to determine individual nucleotide composition If a piece of double stranded DNA has 42% GC content – what are individual base compositions?  DNA is antiparallel DNA has chemical polarity In a DNA sequence the 2 ends are not chemically identical Figure 5-2b Essential Cell Biology (© Garland Science 2010) Numbering of the carbon atoms run clockwise following organic chemistry rules.  Nucleic acid can only be synthesized in a 5’ to 3’ direction New incoming nucleotides attach to the 3’ OH of the preceding nucleotide Nucleotides are linked via 3’, 5’ phosphodiester bond  DNA is always written in 5’ to 3’ direction unless explicitly stated What is the sequence on the complementary strand of: 5’ AGGCCTTTAG 3’ Function of DNA Transmit information Requires accurate copying of DNA Store information Specified through the order or sequence of nucleotides - gene expression Ribonucleic Acid Figure 7–4 Uracil forms a base pair with adenine. RNA Function of RNA Transient carriers of molecular instruction from DNA Protein synthesis Regulation of gene expression Base pairing rules are critical for DNA replication and gene expression  DNA Organisation 1 human cell contains about span 2m of DNA stretched out  Packaging of DNA into chromosomes requires multiple hierarchies of folding Specialised proteins bind and fold DNA into series of loops and coils to give order allowing DNA to be accessible to enzymes that repair and replicate it and cause gene expression What is a chromosome Duplicated chromosome Each chromosome consists of a single very long piece of DNA and associated proteins that fold and pack the DNA into more compact structure - chromatin  Nucleosome Nucleosome is most fundamental unit of packaging where negatively charged DNA is bound by positively charged highly conserved proteins Consists of central core of 8 histone proteins - small proteins (102-135 amino acids) Each core consists of 2 molecules each of H2A, H2B, H3 and H4 around which 147bp DNA is coiled Adjacent nucleosomes linked by short length spacer DNA “string of beads”  N terminal tails of core histones protrude from the nucleosome and specific amino acids in the tail can be modified to affect how the chromatin is packed Figure 5-22 Essential Cell Biology (© Garland Science 2010) Further packaging of nucleosomes depends on H1 which pulls nucleosomes together to form a 30nm chromatin fiber The chromatin in human chromosomes is folded into looped domains by special nonhistone chromosomal proteins that bind to specific DNA sequences, creating a clamp at the base of each loop Essential Cell Biology, Fifth Edition Copyright © 2019 W. W. Norton & Company Further packaging of nucleosomes depends on H1 which pulls nucleosomes together to form a 30nm chromatin fiber Regulation of Chromosome Structure Eucaryotic cells can rapidly adjust the local structure of their chromatin to expose localised areas of DNA ATP dependent Chromatin remodelling complexes to change the position of the nucleosome on the DNA Reversible histone modification by histone modifying enzymes Histone tails can be chemically modified by addition of acetyl, methyl or phosphate groups eg acetylation of lysine can reduce affinity of histone tail for adjacent nucleosomes thereby loosening chromatin  Chromatin remodelling cell alters its chromatin structure to allow rapid access to DNA Figure 5-24 Essential Cell Biology (5th Edition) The complexes use energy derived from ATP to loosen the nucleosomal DNA and push it along the histone octamer. In this way, the enzyme can expose or hide a sequence of DNA, controlling its availability to other DNA-binding proteins  Fig ure 3. Euk aryo tic gene s are locat ed on mult iple linea r chro mos ome s pack ed into a com plex with histo ne prot eins to form chro mati n. Hist ones are the prim ary regu lator of the chro mati n stru ctur e, whic h is dyna mic, exist ing in eithe ra hete roch rom atin (con dens ed) or euch rom atin (ope n) state. Whe ther chro mati n is activ e or inact ive is larg ely depe nden t on the post - tran scri ption al mod ifi catio ns of the histo ne tails, inclu ding acet ylati on, met hylat ion, and phos phor ylati on. Histone tails can be reversibly modified Modifications are important in regulating chromatin structure Acetylation loosens chromatin leading to more euchromatin (open) Methylation can lead to more condensed heterochromatin (closed) Summary DNA structure - antiparallel double stranded molecular where 2 strands held together by H bonds between complementary base pairs Nucleotides on a strand of DNA joined together by phophodiester bonds Differences between DNA and RNA Packaging DNA