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    Lec3 1ppt

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    Shannon Marie
    The document provides an introduction to nucleic acids and proteins, covering topics like nucleic acid structure and nomenclature, the central dogma, molecular interactions, DNA and RNA structure, protein structure levels from primary to quaternary, amino acid properties, and protein synthesis.

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    Lec3 1ppt

    Uploaded by

    Shannon Marie
    9 views36 pages
    The document provides an introduction to nucleic acids and proteins, covering topics like nucleic acid structure and nomenclature, the central dogma, molecular interactions, DNA and RNA structure, protein structure levels from primary to quaternary, amino acid properties, and protein synthesis.

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    lec3_1ppt

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    The document provides an introduction to nucleic acids and proteins, covering topics like nucleic acid structure and nomenclature, the central dogma, molecular interactions, DNA and RNA structure, protein structure levels from primary to quaternary, amino acid properties, and protein synthesis.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    9 views36 pages

    Lec3 1ppt

    Uploaded by

    Shannon Marie
    The document provides an introduction to nucleic acids and proteins, covering topics like nucleic acid structure and nomenclature, the central dogma, molecular interactions, DNA and RNA structure, protein structure levels from primary to quaternary, amino acid properties, and protein synthesis.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    of 36

    Lecture 3

    Introduction to Nucleic Acids & Proteins

    1
    Lecture 3

    Introduction to Nucleic Acids & Proteins


    Lecture outline: Readings:
    1) Molecular Interactions Alberts textbook,Ch
    2) P
    Properties
    ti off nucleic
    l i 2 pp.
    2, pp 51
    51-64
    64
    acids Ch 3, pp. 125-152
    3) Intro to proteins
    4) Amino acid structure
    5) Protein structure
    2
    Nucleic Acid Nomenclature
    To review from last lecture…….
    1) Nucleoside
    monophosphate:
     Sugar + base + 1P
    2) Nucleoside
    diphosphate:
     Sugar
    g + base + 2P
    3) Nucleoside triphosphate:
     Sugar + base + 3P

    3
    “Central
    Ce t a Dogma”
    og a
    DNA

    mRNA tRNA rRNA

    translation

    transport AA’s p of the


    part
    protein
    ribosome

    Messenger RNA (mRNA)


    Transfer RNA (tRNA)
    Ribosomal RNA (rRNA)
    4
    Molecular Interactions
    Interactions between individual molecules
    usually mediated by noncovalent attractions
    • Electrostatic
    El t t ti attractions
    tt ti
    • Hydrogen
    y g bonds
    • van der Waals attractions
    • Hydrophobic
    H d h bi fforce
    Individually,
    y, veryy weak forces but can sum to
    generate strong binding between molecules

    5
    Overview

    Alberts, Figure 6-2 6


    Nucleic
    uc e c ac
    acid
    d cchains
    a s
    1) DNA is synthesized from
    deoxyribonucleoside
    triphosphates, otherwise
    known as:
     dNTP’s

    2) RNA is synthesized from


    ribonucleoside triphosphates,
    p p ,
    or:
     NTP’s
    3) Nucleotides are linked by:
     phosphodiester bonds

    7
    Alberts, Figure 6-4c
    Base Pairing
    g
    1) Holds the DNA
    double helix
    together
    2) A - T
     2 H-bonds
    H bonds

    G-C
     3 H-bonds

    Alberts, Figure 4-4 8


    Three forces that keep
    p DNA together…
    g

    1. Hydrogen
    bonds

    2. Van der Waals


    attractions

    3. Hydrophobic
    interactions

    9
    Alberts, Figure 4-5b
    DNA Structure

    Minor Groove

    Major Groove

    Alberts, Figure 4-3


    10
    Review
    antiparallel
    1)The strands in a double helix are ____________.

    This means that one strand is 5’ 3’ while it’s


    partner is 3’ 5’
    2) What are the two ends of the DNA
    strand composed of?

    5’ =  Phosphate group (-PO4)


    3’ =
    3  Hydroxyl
    H d l group (OH)

    11
    The sequence of the This is important for:
    two strands are:  DNA replication
     complementary  RNA synthesis
    The strands can be:
     unzipped
    12
    Unzipping the helix
    1) Heating denatures double
    double-stranded
    stranded DNA by:
     disrupting H-bonds between bases

    2) The temperature at which DNA denatures is


    called the:
     Tm and varies between species
    p
    reversible
    3) Denaturation of DNA is a ____________
    process

    13
    Application of DNA denaturation/renaturation capacity

    DNA amplification
    p by
    y Polymerase
    y Chain Reaction ((PCR))

    Description of process in MBoC,


    MBoC pp 544-546
    Application of DNA denaturation/renaturation capacity
    Typical
    yp PCR Thermocycler
    y
    Introduction
    t oduct o to Protein
    ote StStructure
    uctu e
    Examples:
    Primary (sequence)  AA sequence

    Secondary (local folding)  α helix, β sheet

    Tertiary (long-range folding)  3D structure

    Quaternary (multimeric organization) Multiple polypeptide chains

    Large scale
    Supramolecular (large-scale assembly)  protein
    assemblies
    17
    Protein Structure

    1) Proteins
    P i are composed d off
    amino acids
    2)) The amino acid side-chain,, or
    R
    _______group is variable, and
    determines the type of amino
    acid
    3) 4 major categories of amino
    acids:
     basic
    b i
    Panel 3-1, MBoC
     acidic
     uncharged polar
     non-polar

    18
    Examples
    p of basic and acidic AAs

    Basic Acidic
    Examples
    p of p
    polar and non-polar
    p AA’s

    Polar Non-Polar
    Cysteine
    y and Disulphide
    p Bonds

    Reduced conditions Oxidized conditions


    Structure of the genetic code
    Groups of basic, acidic, hydrophobic AA’s:

    22
    Mutational steps
    p between codons
    AA: Pro Cys
    y
    Codons: CCC UGC
    CCU UGU
    CCA
    CCG

    1) What is the minimum number of mutational steps


    between amino acids?
     # mutations betw codons for diff AA’s
    2) How many mutational steps required to get from a
    codon for
    f proline to one for
    f cysteine, minimum? ?
     2
    3) … maximum?
    i 3
    ? ___
    23
    Review
    e e
    1) Groups of AA’s
    AA s with similar properties tend to be
    ________
    clustered in the codon table
    2) Codons of AA’s
    AA s with similar properties tend to have
    fewer mutational steps between them
    _____
    3)) One random mutation in a codon is _____less likelyy to
    result in a dramatic change in amino acid
    properties than two random mutations

    24
    Synthesis
    y of Proteins

    N-term C-term

    = -carbon

    Alberts, Figure 3-1 25


    The order of AA’s is important
    p

    This is Leu-Enkephalin - a pentapeptide of Tyr-Gly-Gly-Phe-Leu


     It
    I is
    i a naturall opioid
    i id peptide
    id which
    hi h down
    d modulates
    d l the
    h
    perception of PAIN …….aaaaaahhhhhhhh…..
    The pentapeptide
    Th t tid Leu-Phe-Gly-Gly-Tyr
    L Ph Gl Gl T has h no pharmacological
    h l i l
    effects. The NH2 – COOH orientation of the peptide is essential for
    function
    The Alpha
    p Helix

    3.6
    3 6 amino
    acids / turn

    Figure 3-7a,b,c Molecular Biology of the Cell (© Garland Science 2008)


    The β Sheet

    Figure 3-7d,e,f Molecular Biology of the Cell (© Garland Science 2008)


    H-bonding
    g in Secondary
    y Structures

    1) Which atoms are H-bonded?


     Carbonyl
    y oxygen,
    yg , amide hydrogen
    y g
    2) Alpha helices
     4 AA’s apart and within the same strand
    3)) Beta sheet
     Between AA’s in different strands

    29
    A specialized
    p alpha
    p helix: coiled coil motif

    Whatt kind
    Wh ki d off
    alpha helix is
    this?
     amphipathic

    Alberts, Figure 3-9

    30
    Tertiary
    e t a y St
    Structure:
    uctu e Rhodopsin
    odops

    1) 3D overall structure of
    a protein
    2) Held together by:

     hydrophobic interactions
     non-covalent bonds
     covalent disulfide bonds

    31
    4 Domains
    o a so of tthe
    eSSrc
    cpprotein
    ote
    functions
    The domains are specialized for different ___________

    Alberts, Figure 3-10 32


    Quaternary
    y Structure: Hemoglobin
    g

    heme
    * *
    Alberts, Figure 3-22
    3 22

    2  , 2
    1) Hemoglobin protein formed from different subunits: ______
    2)) Each subunit = separate
    p polypeptide
    p yp p
    __________
    mutation in the  subunit
    3) Sickle cell anemia is caused by a ________ 33
    Hemoglobin
    g function

    1) Transports ____O2 from lungs to tissues


    2) Heterozygotes for the sickle cell
    anemia mutation in the  globin gene
    are partially protected against ______
    malaria
    3) Frequency of the sickle cell allele has
    reached highest levels in ___________
    Africa + India
    4) Related molecule, ________
    myoglobin has only
    one subunit and is found in muscle
    tissue
    34
    Large Scale Protein Assemblies

    Alberts Figure 3-31


    Alberts, 3 31

    35
    The
    e End
    d

    36

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