Chapter 04_Upload.pptx

Biological Science Seventh Edition Chapter 4 Nucleic Acids Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Admin There is an online quiz on Chapter 4 due tonight We will do group work on Monday Chapter 4 Opening Roadmap Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved 4.1 What is a Nucleic Acid? Nucleic acid—polymer of nucleotide monomers Three components of nucleotide: 1. Phosphate group 2. Five-carbon sugar 3. Nitrogenous (nitrogen-containing) base Phosphate group and nitrogenous base are bonded to sugar molecule Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved What is a Nucleic Acid? (1 of 2) Ribonucleotides are monomers of RNA: – Have ribose as their sugar – Has an group bonded to the 2′ carbon Deoxyribonucleotides are the monomers of DNA: – Sugar is deoxyribose (deoxy = “lacking oxygen”) – Has H instead at 2′ carbon Both sugars have group bonded to 3′ carbon Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved What is a Nucleic Acid? (2 of 2) Two groups of nitrogenous bases: 1. Purines—contain nine atoms in their two rings: ▪ Adenine (A) ▪ Guanine (G) 2. Pyrimidines—contain six atoms in their one ring: ▪ Cytosine (C) ▪ Uracil (U)—found only in ribonucleotides ▪ Thymine (T)—found only in deoxyribonucleotides ▪ Think of it as “CUT of Py” Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.1 The General Structure of a Nucleotide Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Draw a deoxyribonucleotide P 5’ 1’ 4’ deoxyribose 3’ 2’ OH Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved How Do Nucleotides Polymerize to Form Nucleic Acids? Nucleic acids polymerize via condensation reactions Phosphodiester linkage (bond) occurs between: – Phosphate group on 5′ carbon of one nucleotide and – group on the 3′ carbon of another – Polymer produced is RNA Phosphodiester linkages join ribonucleotides together: – Polymer produced is RNA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.2 Nucleotides Polymerize Via Condensation Reactions Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved DNA and RNA Strands Are Directional Phosphodiester linkages form a sugar–phosphate backbone Backbone is directional (5′ → 3′ direction): – One end has unlinked 5′ phosphate group – Other end has unlinked 3′ hydroxyl group Primary structure of DNA written by listing sequence of bases by single-letter abbreviations: – Example: Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.3 Nucleic Acids Have a Sugar–Phosphate Backbone Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Polymerization Requires an Energy Source Nucleic acid polymerization: – Can take place in cells by use of enzymes – Potential energy is raised by adding two additional phosphate groups – Creates nucleoside triphosphates ”activated nucleotides” – Example of activated ribonucleotide: Adenosine triphosphate (ATP) Energy is released when activated nucleotides polymerize: – Makes reaction spontaneous Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.4 Activated Monomers Drive Polymerization Reactions Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved What is the Nature of DNA’s Secondary Structure? Early data provided clues to DNA secondary structure: – DNA polymerized through formation of phosphate linkages – Molecule had sugar–phosphate backbone – Number of purines equaled number of pyrimidines: ▪ Equal number of T’sand A’s; equal number of C’s and G’s – X-ray crystallography used to measure distances between atoms in DNA: ▪ Predicted helical structure Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved DNA Strands Form an Antiparallel Double Helix DNA is put together like a ladder: – Antiparallel sugar–phosphate backbones form ladder side rails – Bases attached to sugars form ladder rungs – Hydrophobic interactions (stacking) cause double-stranded DNA to twist into helix – van Der Waals interactions stabilize strands DNA has two different-sized grooves: 1. Major groove 2. Minor groove Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.6 The Secondary Structure of DNA is a Double Helix Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Hydrogen bonds between nitrogenous bases = “base pairing” (similar for Uracil) Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Cell Biology Video: Stick Model of DNA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Watson, Crick… and Rosalind Franklin Watson and Crick won the Nobel Prize for their paper describing the double helical secondary structure of DNA Their work relied on key observations of a third scientist, Rosalind Franklin, who had X-Ray images showing DNA forming a helix of specific dimensions. Watson and Crick got access to Franklin’s data through one of her colleagues- she only learned of this communication much later- and they did not credit her in their paper. Franklin died before the Nobel prize was awarded, but she remains a symbol of the misogyny and general snobbery which infects the sciences to this day. Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved A look ahead: lead and lag strands during DNA replication DNA strands in a double helix are complementary and antiparallel During replication, each strand will be used as the template to make a new complementary, antiparallel strand But DNA polymerase only “knows” how to add in one direction, so DNA polymerase will travel in opposite directions on opposite strands. For a given opening in the DNA, one strand can be copied continuously, but the other can’t. Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved The Tertiary Structure of DNA DNA forms more compact three-dimensional structures in cells. – Two forms of DNA Tertiary structure – DNA is wound to form coils and supercoils – Eukaryotic DNA wraps around DNA-binding proteins called histones. Prokaryotes also have a system of DNA packaging proteins. Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Packaging of DNA Prokaryotic DNA Eukaryotic DNA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved The DNA Double Helix is a Stable Structure Double helix is highly structured: – Held together by phosphodiester linkages, hydrogen bonds, and hydrophobic interactions – Functional groups participate in chemical reactions ▪ Makes molecule stable and resistant to degradation ▪ Stability of DNA key to effectiveness of reliable information-storage molecule Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Research: Environmental DNA DNA is stable enough to survive detectably for extremely long periods (Diatom chloroplast DNA from 1.4 million-year-old sediments). Living things leave traces of themselves everywhere- in feces/blood/shed skin, but also in the open sea, and even airborne. Environmental DNA is a DNA signal obtained without obvious signs of biological material. Retrieval of DNA signals from environmental samples is achievable thank to advances in polymerase chain reaction (PCR) and bioinformatics Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved The stability of DNA allows it to persist in the environment https://www.science.org/content/article/dna-pulled-thin-air-identifies-nearby-animals Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved DNA Functions as an InformationContaining Molecule DNA is the biological reservoir of information: – Stores information required for organism’s growth and reproduction – Information consists of sequences of nucleotides in nucleic acid: ▪ Four nitrogenous bases function like letters in an alphabet ▪ Sequence of bases has meaning, like order of letters in a word Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved DNA Functions as an InformationContaining Molecule DNA replication has three steps:  Two strands are separated by breaking hydrogen bonds  Free deoxyribonucleotides form hydrogen bonds with complementary bases on original strand of DNA (template strand)  Phosphodiester linkages form to create new strand, called complementary strand  Complementary base pairing allows each strand to be copied exactly producing two identical daughter molecules Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.7 Making a Copy of D NA  A single strand contains the information needed to make the other strand  We will cover this in detail on Wednesday! Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved 4.3 RNA Structure and Function Primary structure of RNA: – Four types of nitrogenous bases extending from sugar–phosphate backbone Primary structure of RNA differs from DNA: 1. RNA contains ribose instead of deoxyribose 2. RNA contains uracil instead of thymine 3. 2′ group on ribose is more reactive than 4. RNA much less stable than D NA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Secondary Structure RNA’s secondary structure results from complementary base pairing: A with U; G with C Bases of RNA typically form hydrogen bonds with complementary bases on the same strand RNA strand folds over, forming hairpin structure: – Bases on one part of RNA strand fold over and align with bases on other part of the same strand – Two sugar–phosphate strands are anti-parallel Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Figure 4.8 Complementary Base Pairing Directs Secondary Structure in RNA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved Tertiary Structure RNA molecules can also have tertiary structure: – Forms when secondary structures fold into more complex shapes – Many nitrogenous bases remain exposed! – Can complex with ions as cofactors! RNA much more diverse in size, shape, and reactivity than DNA A tRNA Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved RNA Can Function as a Catalytic Molecule RNA is much more diverse in size, shape, and reactivity than DNA RNA is highly versatile An information-containing molecule Capable of self-replication Capable of catalyzing reactions: ribozymes © 2017 Pearson Education, Inc. Figure 4.10 Tertiary Structure of the Tetrahymena Ribozyme Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved The “RNA world”: RNA doing the jobs of DNA + protein RNA world RNA-protein world Current world Heredity RNA RNA DNA Messenger (RNA?) RNA RNA Catalyst RNA RNA/Protein Protein/RNA Function: Lots of circumstantial evidence that the most ancient catalysts were RNAs © 2017 Pearson Education, Inc. Table 4.1 DNA and RNA Structure Summary Table 4.1 DNA and RNA Structure Copyright © 2020, 2017, 2014 Pearson Education, Inc. All Rights Reserved

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