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Introduction to Biochemistry

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Title: Introduction to Biochemistry


1
Introduction to Biochemistry
  • Andy Howard
  • Biochemistry, Fall 2008IIT

2
What is biochemistry?
  • By the end of this course you should be able to
    construct your own definition but for now
  • Biochemistry is the study of chemical reactions
    in living tissue.

3
Plans
  • Classes of small molecules
  • Classes of macromolecules
  • Water
  • Catalysis
  • Energetics
  • Regulation
  • Molecular biology
  • Evolution
  • What is biochemistry?
  • Cells
  • Cell components
  • Organic and biochemistry
  • Concepts from organic chemistry to remember
  • Small molecules and macromolecules

4
What will we study?
  • Biochemistry is the study of chemical reactions
    in living tissue, both within cells and in
    intercellular media.
  • As such, it concerns itself with a variety of
    specific topics

5
Topics in biochemistry
  • What reactions occur
  • The equilibrium energetics and kinetics of those
    reactions
  • How the reactions are controlled, at the chemical
    and cellular or organellar levels
  • How the reactions are organized to enable
    biological function within the cell and in
    tissues and organisms.

6
Organic and biological chemistry
  • Most molecules in living things (other than H2O,
    O2, and CO2) contain C-C or C-H bonds, so
    biochemistry depends heavily on organic chemistry
  • But the range of organic reactions that occur in
    biological systems is fairly limited compared to
    the full range of organic reactions

7
Why we use only a subset of organic chemistry in
biochemistry
  • Biochemical reactions arealmost always aqueous.
  • They occur within a narrow temperature and
    pressure range.
  • They occur within narrowly buffered pH ranges.
  • Many of the complex reaction mechanisms
    discovered and exploited by organic chemists
    since the 1860's have no counterparts in the
    biochemical universe.

Frederich Wöhler
8
Cells
  • Most biochemical reactions (but not all!) take
    place within semi-independent biological entities
    known as cells
  • Cells in general contain replicative and
    protein-synthetic machinery in order to reproduce
    and survive
  • They often exchange nutrients and information
    with other cells

9
Cell components
  • Cells are separated from their environments via a
    selectively porous membrane
  • Individual components (often called organelles)
    within the cell may also have membranes
    separating them from the bulk cytosol and from
    one another

10
Eukaryotes and prokaryotes
  • The lowest-level distinction among organisms is
    on the basis of whether their cells have defined
    nuclei or not
  • Cells with nuclei are eukaryotic
  • Cells without nuclei are prokaryotic
  • Eubacteria and archaea are prokaryotic
  • Other organisms (including some unicellular
    ones!) are eukaryotic

11
Eukaryotic organelles I
  • Nucleus contains genetic information site for
    replication and transcription
  • Endoplasmic reticulum site for protein synthesis
    and protein processing
  • Ribosome protein-synthetic machine
  • Golgi apparatus site for packaging proteins for
    secretion and delivery

12
Eukaryotic organelles II
  • Mitochondrion site for most energy-producing
    reactions
  • Lysosome digests materials during endocytosis
    and cellular degradation
  • Peroxisome site for oxidation of some nutrients
    and detoxification of the H2O2 created thereby
  • Cytoskeleton network of filaments that define
    the shape and mobility of a cell

13
Eukaryotic organelles III
  • Chloroplast site for most photosynthetic
    reactions
  • Vacuoles sacs for water or other nutrients
  • Cell wall bacterial or plant component outside
    cell membrane that provides rigidity and
    protection against osmotic shock

14
Concepts from organic chemistry
  • There are some elements of organic chemistry that
    you should have clear in your minds.
  • All of these are concepts with significance
    outside of biochemistry, but they do play
    important roles in biochemistry.
  • If any of these concepts is less than thoroughly
    familiar, please review it

15
Organic concepts I
Image courtesy Michigan State U.
  • Covalent bond A strong attractive interaction
    between neighboring atoms in which a pair of
    electrons is roughly equally shared between the
    two atoms.
  • Covalent bonds may be single bonds, in which one
    pair of electrons is shared double bonds, which
    involve two pairs of electrons or triple bonds,
    which involve three pairs (see above).
  • Single bonds do not restrict the rotation of
    other substituents around the bond double and
    triple bonds do.

16
Organic concepts II
  • Ionic bond a strong attractive interaction
    between atoms in which one atom or group is
    positively charged, and another is negatively
    charged.

17
Organic concepts III
  • Hydrogen bond A weak attractive interaction
    between neighboring atoms in which a hydrogen
    atom carrying a slight, partial positive charge
    shares that positive charge with a neighboring
    electronegative atom.
  • The non-hydrogen atom to which the hydrogen is
    covalently bonded is called the hydrogen-bond
    donor
  • the neighboring atom that takes on a bit of the
    charge is called the hydrogen-bond acceptor

Cartoon courtesy CUNY Brooklyn
18
Organic concepts IV
  • Van der Waals interactionA weak attractive
    interaction between nonpolar atoms, arising from
    transient induced dipoles in the two atoms.

Image courtesyColumbia U. Biology Dept.
19
Organic Concepts V
  • Chirality The property of a molecule under which
    it cannot be superimposed upon its mirror image.

Image courtesy DRECAM, France
20
Organic Concepts VI
acetone
propen-2-ol
  • Tautomerization The interconversion of two
    covalently different forms of a molecule via a
    unimolecular reaction that proceeds with a low
    activation energy. The two forms of the molecule
    are known as tautomers because of the low
    activation barrier between the two forms, we will
    typically find both species present.

21
Organic Concepts VII
  • Nucleophilic substitution a reaction in which an
    electron-rich (nucleophilic) molecule attacks an
    electron-poor (electrophilic) molecule and
    replaces group or atom within the attacked
    species.
  • The displaced group is known as a leaving group.
  • This is one of several types of substitution
    reactions, and it occurs constantly in biological
    systems.

22
Organic Concepts VIII
  • Polymerization creation of large molecules by
    sequential addition of simple building blocks
  • often by dehydration, i.e., the elimination of
    water from two species to form a larger
    oneR1-O-H HO-R2-X-H ? R1-X-R2-OH H2O
  • The product here can then react withHO-R3-X-H to
    formR1-X-R2-X-R3-OH with elimination of another
    water molecule, and so on.

23
Organic Concepts IX
  • Equilibrium in the context of a chemical
    reaction, the state in which the concentrations
    of reactants and products are no longer changing
    with time because the rate of reaction in one
    direction is equal to the rate in the opposite
    direction.
  • Kinetics the study of the rates at which
    reactions proceed.
  • Conventionally, we use the term thermodynamics to
    describe our understanding of the energetics of
    equilibrium systems

24
Organic Concepts X
  • Catalysis the lowering of the energetic barrier
    between substrates and products in a reaction by
    the participation of a substance that ultimately
    is unchanged by the reaction
  • It is crucial to recognize that catalysts
    (chemical agents that perform catalysis) do not
    change the equilibrium position of the reactions
    in which they participate
  • they only change the rates (the kinetics) of the
    reactions they catalyze.
  • Zwitterion a compound containing both a positive
    and a negative charge

25
Classes of small molecules
  • Small molecules other than water make up a small
    percentage of a cell's mass, but small molecules
    have significant roles in the cell, both on their
    own and as building blocks of macromolecules. The
    classes of small molecules that play significant
    roles in biology are listed below. In this list,
    "soluble" means "water-soluble".

26
iClicker quiz (for attendance)
  • How many midterms will we have?
  • (a) 1
  • (b) 2
  • (c ) 3
  • (d) 4
  • (e) I dont care.

27
Biological small molecules I
  • Water Hydrogen hydroxide. In liquid form in
    biological systems. See below.
  • Lipids Hydrophobic molecules, containing either
    alkyl chains or fused-ring structures. A
    biological lipid usually contains at least one
    highly hydrophobic moeity.

28
Biological small molecules II
  • Carbohydrates Polyhydroxylated compounds for
    which the building blocks are highly soluble.
  • The typical molecular formula for the monomeric
    forms of these compounds is (CH2O)n, where 3 lt n
    lt 9,
  • but usually n 5 or 6.

29
Biological small molecules III
  • Amino acids Compounds containing an amine (NH3)
    group and a carboxyl (COO-) group.
  • The most important biological amino acids are
    a-amino acids, in which the amine group and the
    carboxyl group are separated by one carbon, and
    that intervening carbon has a hydrogen attached
    to it. Thus the general formula for an a-amino
    acid is
  • H3N - CHR - COO-

30
Biological small molecules IV
  • Nucleic acids Soluble compounds that include a
    nitrogen-containing ring system.
  • The ring systems are derived either from purine
    or pyrimidine.
  • The most important biological nucleic acids are
    those in which the ring system is covalently
    attached to a five-carbon sugar, ribose, usually
    with a phosphate group attached to the same
    ribose ring.

31
Small molecules V
  • Inorganic ions Ionic species containing no
    carbon but containing one or more atoms and at
    least one net charge.
  • Ions of biological significance includeCl-, Na,
    K, Mg2, Mn2, I-, Ca2, PO4-3, SO4-2, NO3-,
    NO2-, and NH4.
  • Phosphate (PO4-3) is often found in partially
    protonated forms HPO4-2 and H2PO4-
  • Ammonium ions occasionally appear as neutral
    ammonia (NH3), particularly at higher pH values

32
Biological Small Molecules VI
  • Cofactors This is a catchall category for
    organic small molecules that serve in some
    functional role in biological organisms. Many are
    vitamins or are derived from vitamins a vitamin
    is defined as an organic molecule that is
    necessary for metabolism but cannot be
    synthesized by the organism. Thus the same
    compound may be a vitamin for one organism and
    not for another.
  • Ascorbate (vitamin C) is a vitamin for humans and
    guinea pigs but not for most other mammals.
  • Cofactors often end up as prosthetic groups,
    covalently or noncovalently attached to proteins
    and involved in those proteins' functions.

33
Biological macromolecules
  • Most big biological molecules are polymers, i.e.
    molecules made up of large numbers of relatively
    simple building blocks.
  • Cobalamin is the biggest nonpolymeric biomolecule
    I can think of (MW 1356 Da)

Structure courtesy Wikimedia
34
Categories of biological polymers
  • Proteins
  • Nucleic acids
  • Polysaccharides
  • Lipids (sort of)
  • 2-3 chains of aliphatics attached to a polar head
    group, often built on glycerol
  • Aliphatic chains are usually 11-23 Cs

35
Polymers and oligomers
  • These are distinguished only by the number of
    building-blocks contained within the multimer
  • Oligomers typically lt 50 building blocks
  • Polymers ? 50 building blocks.

36
Categories of biopolymers
37
Water a complex substance
  • Oxygen atom is covalently bonded to 2 hydrogens
  • Single bond character of these bonds means the
    H-O-H bond angle is close to 109.5º acos(-1/3)
    actually more like 104.5º
  • This contrasts with OCO (angle180º) or urea
    ((NH2)2-CO) (angles120º)
  • Two lone pairs available per oxygenthese are
    available as H-bond acceptors

38
Water is polar
  • Charge is somewhat unequally shared
  • Small positive charge on Hs (d) small negative
    charge on O (2d-) (Why?)
  • A water molecule will orient itself to align
    partial negative charge on one molecule close to
    partial positive charges on another.
  • Hydrogen bonds are involved in this.

39
Liquid water is mobile
  • The hydrogen-bond networks created among water
    molecules change constantly on a sub-picosecond
    time scale
  • At any moment the H-bonds look like those in
    crystalline ice
  • Solutes disrupt the H-bond networks

40
Water in reactions
  • Water is a medium within which reactions occur
  • But it also participates in reactions
  • Enzymes often function by making water oxygen
    atoms better nucleophiles or water Hs better
    electrophiles
  • Therefore water is a direct participant in
    reactions that wouldnt work in a nonenzymatic
    lab setting!

41
Waters physical properties
  • High heat capacitystabilizes temperature in
    living things
  • High surface tension
  • Nearly incompressible (density almost independent
    of pressure)
  • Density max at 3.98ºC

42
Catalysis
  • Catalysis is the lowering of the activation
    energy barrier between reactants and products
  • How?
  • Physical surface on which reactants can be
    exposed to one another
  • Providing moieties that can temporarily
    participate in the reaction and be restored to
    their original state at the end

43
Biological catalysts
  • 1890s Fischer realized that there had to be
    catalysts in biological systems
  • 1920s Sumner said they were proteins
  • It took another 10 years forthe whole community
    to accept that
  • Its now known that RNA can be catalytic too
  • Can catalyze modifications in itself
  • Catalyzes the key step in protein synthesis in
    the ribosome

44
Energy in biological systems
  • We distinguish between thermodynamics and
    kinetics
  • Thermodynamics characterizes the energy
    associated with equilibrium conditions in
    reactions
  • Kinetics describes the rate at which a reaction
    moves toward equilibrium

45
Thermodynamics
  • Equilibrium constant is a measure of the ratio of
    product concentrations to reactant concentrations
    at equilibrium
  • Free energy is a measure of the available energy
    in the products and reactants
  • Theyre related by DGo -RT ln Keq

46
Kinetics
  • Rate of reaction is dependent on Kelvin
    temperature T and on activation barrier DG
    preventing conversion from one site to the other
  • Rate Qexp(-DG/RT)
  • Job of an enzyme is to reduce DG

Svante Arrhenius
47
Regulation
  • Biological reactions are regulated in the sense
    that theyre catalyzed by enzymes, so the
    presence or absence of the enzyme determines
    whether the reaction will proceed
  • The enzymes themselves are subject to extensive
    regulation so that the right reactions occur in
    the right places and times

48
Typical enzymatic regulation
  • Suppose enzymes are involved in converting A to
    B, B to C, C to D, and D to F. E is the enzyme
    that converts A to B (E) A ? B ? C ? D ? F
  • In many instance F will inhibit (interfere) with
    the reaction that converts A to B by binding to a
    site on enzyme E so that it cant bind A.
  • This feedback inhibition helps to prevent
    overproduction of Fhomeostasis.

49
Molecular biology
  • This phrase means something much more specific
    than biochemistry
  • Its the chemistry of replication, transcription,
    and translation, i.e., the ways that genes are
    reproduced and expressed.
  • Most of you have taken biology 214 or its
    equivalent well review some of the contents of
    that course here, mostly near the end of the
    semester.

50
The molecules ofmolecular biology
  • Deoxyribonucleic acid polymer backbone is
    deoxyribose-phosphate side chains are
    nitrogenous ring compounds
  • RNA polymer backbone is ribose-phosphate side
    chains as above
  • Protein polymer backbone isNH-(CHR)-CO side
    chains are 20 ribosomally encoded styles

51
Steps in molecular biologythe Central Dogma
  • DNA replication (makes accurate copy of existing
    double-stranded DNA prior to mitosis)
  • Transcription (RNA version of DNA message is
    created)
  • Translation (mRNA copy of gene serves as template
    for making protein 3 bases of RNA per amino acid
    of synthesized protein)

52
Evolution and Taxonomy
  • Traditional studies of interrelatedness of
    organisms focused on functional similarities
  • This enables production of phylogenetic trees
  • Molecular biology provides an alternative,
    possibly more quantitative, approach to
    phylogenetic tree-building
  • More rigorous hypothesis-testing possible

53
Quantitation
  • Biochemistry is a quantitative science.
  • Results in biochemistry are rarely significant
    unless they can be couched in quantifiable terms.
  • Thermodynamic kinetic behavior of biochemical
    systems must be described quantitatively.
  • Even the descriptive aspects of biochemistry,
    e.g. the compartmentalization of reactions and
    metabolites into cells and into particular parts
    of cells, must be characterized numerically.

54
Mathematics in biochemistry
  • Ooo I went into biology rather than physics
    because I dont like math
  • Too bad. You need some herebut not much.
  • Biggest problem in past yearsexponentials and
    logarithms

55
Exponentials
  • Many important biochemical equations are
    expressed in the formY ef(x)
  • which can also be writtenY exp(f(x))
  • The number e is the base of the natural logarithm
    system and is, very roughly, 2.718281828459045
  • I.e., its 2.7 1828 1828 45 90 45

56
Logarithms
  • First developed as computational tools because
    they convert multiplication problems into
    addition problems
  • They have a fundamental connection with raising a
    value to a power
  • Y xa ? logx(Y) a
  • In particular, Y exp(a) ea?lnY loge(Y) a

57
Algebra of logarithms
  • logv(A) logu(A) / logu(v)
  • logu(A/B) logu(A) - logu(B)
  • logu(AB) Blogu(A)
  • log10(A) ln(A) / ln(10) ln(A) /
    2.30258509299 0.4342944819 ln(A)
  • ln(A) log10(A) / log10e log10(A) /
    0.4342944819 2.30258509299 log10(A)

58
Course structure
  • Two midterms plus a final
  • All exams will be closed-book, closed-notes
    exams. Calculators are not allowed.
  • Each exam will be accompanied by a help-sheet
    with many helpful facts
  • Gauge your memorization with the help-sheet
    before you whats on the help sheet doesnt need
    to be memorized
  • My exams tend to be long but easybudget your
    time carefully!

59
Grading
  • Im a moderately tough grader, but I do curve
    this course
  • The cutoff for an A is likely to be around an 82,
    but its uncertain
  • Homework, literature assignments, iClicker
    quizzes, and discussion-board participation count
  • Internet students will get a substitute
    assignment to replace iClicker quizzes

60
Textbook and Lecture Notes
  • Garrett Grisham is a detail-rich and
    well-written text read it!
  • Many of my lectures are derived from Horton et al
    rather than from Garrett Grisham, particularly
    in the version that Ive already posted to the
    Internet
  • Be prepared for the lecture notes themselves to
    evolve during the course

61
Office Hours
  • I should be available 330-5pm Tuesdays and
    Thursdays in most cases
  • If that doesnt work, make an appointment
  • The discussion board is another good way to reach
    me and the rest of the class as well!

62
Assignments
  • Regular homeworks will be due weekly, probably on
    Fridays
  • But no assignment due tomorrow
  • Literature assignments are due weekly, probably
    on Tuesdays
  • Specific readings already posted will be
    augmented but not deleted
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