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Introduction to Biochemistry. Andy Howard Biochemistry, Fall 2008 IIT. 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. What is biochemistry? Cells

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introduction to biochemistry

Introduction to Biochemistry

Andy Howard

Biochemistry, Fall 2008IIT

Biochemistry: Introduction

what is biochemistry
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.

Biochemistry: Introduction

plans
What is biochemistry?

Cells

Cell components

Organic and biochemistry

Concepts from organic chemistry to remember

Small molecules and macromolecules

Classes of small molecules

Classes of macromolecules

Water

Catalysis

Energetics

Regulation

Molecular biology

Evolution

Plans

Biochemistry: Introduction

what will we study
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:

Biochemistry: Introduction

topics in biochemistry
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.

Biochemistry: Introduction

organic and biological chemistry
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:

Biochemistry: Introduction

why we use only a subset of organic chemistry in biochemistry
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

Biochemistry: Introduction

cells
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

Biochemistry: Introduction

cell components
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

Biochemistry: Introduction

eukaryotes and prokaryotes
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

Biochemistry: Introduction

eukaryotic organelles i
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

Biochemistry: Introduction

eukaryotic organelles ii
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

Biochemistry: Introduction

eukaryotic organelles iii
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

Biochemistry: Introduction

concepts from organic chemistry
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:

Biochemistry: Introduction

organic concepts i
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.

Biochemistry: Introduction

organic concepts ii
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.

Biochemistry: Introduction

organic concepts iii
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

Biochemistry: Introduction

organic concepts iv
Organic concepts IV
  • Van der Waals interaction:A weak attractive interaction between nonpolar atoms, arising from transient induced dipoles in the two atoms.

Image courtesyColumbia U. Biology Dept.

Biochemistry: Introduction

organic concepts v
Organic Concepts V
  • Chirality: The property of a molecule under which it cannot be superimposed upon its mirror image.

Image courtesy DRECAM, France

Biochemistry: Introduction

organic concepts vi
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.

Biochemistry: Introduction

organic concepts vii
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.

Biochemistry: Introduction

organic concepts viii
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 one:R1-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.

Biochemistry: Introduction

organic concepts ix
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

Biochemistry: Introduction

organic concepts x
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

Biochemistry: Introduction

classes of small molecules
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".

Biochemistry: Introduction

iclicker quiz for attendance
iClicker quiz (for attendance)
  • How many midterms will we have?
  • (a) 1
  • (b) 2
  • (c ) 3
  • (d) 4
  • (e) I don’t care.

Biochemistry: Introduction

biological small molecules i
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.

Biochemistry: Introduction

biological small molecules ii
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 < n < 9,
    • but usually n = 5 or 6.

Biochemistry: Introduction

biological small molecules iii
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-

Biochemistry: Introduction

biological small molecules iv
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.

Biochemistry: Introduction

small molecules v
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+, Mg+2, Mn+2, I-, Ca+2, 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

Biochemistry: Introduction

biological small molecules vi
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.

Biochemistry: Introduction

biological macromolecules
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

Biochemistry: Introduction

categories of biological polymers
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 C’s

Biochemistry: Introduction

polymers and oligomers
Polymers and oligomers
  • These are distinguished only by the number of building-blocks contained within the multimer
  • Oligomers: typically < 50 building blocks
  • Polymers  50 building blocks.

Biochemistry: Introduction

categories of biopolymers
Categories of biopolymers

Biochemistry: Introduction

water a complex substance
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 O=C=O (angle=180º) or urea ((NH2)2-C=O) (angles=120º)
  • Two lone pairs available per oxygen:these are available as H-bond acceptors

Biochemistry: Introduction

water is polar
Water is polar
  • Charge is somewhat unequally shared
  • Small positive charge on H’s (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.

Biochemistry: Introduction

liquid water is mobile
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

Biochemistry: Introduction

water in reactions
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 H’s better electrophiles
  • Therefore water is a direct participant in reactions that wouldn’t work in a nonenzymatic lab setting!

Biochemistry: Introduction

water s physical properties
Water’s physical properties
  • High heat capacity:stabilizes temperature in living things
  • High surface tension
  • Nearly incompressible (density almost independent of pressure)
  • Density max at 3.98ºC

Biochemistry: Introduction

catalysis
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

Biochemistry: Introduction

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

Biochemistry: Introduction

energy in biological systems
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

Biochemistry: Introduction

thermodynamics
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
  • They’re related by DGo = -RT ln Keq

Biochemistry: Introduction

kinetics
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

Biochemistry: Introduction

regulation
Regulation
  • Biological reactions are regulated in the sense that they’re 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

Biochemistry: Introduction

typical enzymatic regulation
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 can’t bind A.
  • This feedback inhibition helps to prevent overproduction of F—homeostasis.

Biochemistry: Introduction

molecular biology
Molecular biology
  • This phrase means something much more specific than biochemistry:
  • It’s 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; we’ll review some of the contents of that course here, mostly near the end of the semester.

Biochemistry: Introduction

the molecules of molecular biology
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

Biochemistry: Introduction

steps in molecular biology the central dogma
Steps in molecular biology:the 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)

Biochemistry: Introduction

evolution and taxonomy
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

Biochemistry: Introduction

quantitation
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.

Biochemistry: Introduction

mathematics in biochemistry
Mathematics in biochemistry
  • Ooo: I went into biology rather than physics because I don’t like math
  • Too bad. You need some here:but not much.
  • Biggest problem in past years:exponentials and logarithms

Biochemistry: Introduction

exponentials
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., it’s 2.7 1828 1828 45 90 45

Biochemistry: Introduction

logarithms
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

Biochemistry: Introduction

algebra of logarithms
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)

Biochemistry: Introduction

course structure
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: what’s on the help sheet doesn’t need to be memorized
  • My exams tend to be long but easy:budget your time carefully!

Biochemistry: Introduction

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

Biochemistry: Introduction

textbook and lecture notes
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 I’ve already posted to the Internet
  • Be prepared for the lecture notes themselves to evolve during the course

Biochemistry: Introduction

office hours
Office Hours
  • I should be available 3:30-5pm Tuesdays and Thursdays in most cases
  • If that doesn’t work, make an appointment
  • The discussion board is another good way to reach me and the rest of the class as well!

Biochemistry: Introduction

assignments
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

Biochemistry: Introduction