Introduction to BiochemistryIntroduction to Biochemistry

Andy Howard

Biochemistry, Spring 2008IIT

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.

PlansPlans

What is biochemistry? 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

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:

Topics in biochemistryTopics 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.

Organic and biological chemistryOrganic 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:

Why we use only a subset of Why we use only a subset of organic chemistry in biochemistryorganic chemistry in biochemistry

Biochemical reactions are almost 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.

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:

Organic Organic concepts Iconcepts I

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.

Image courtesy Michigan State U.

Organic concepts IIOrganic concepts II

Ionic bond: a strong attractive interaction between atoms in which one atom or group is positively charged, and another is negatively charged.

Organic concepts IIIOrganic 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

Organic Organic concepts IVconcepts IV

Van der Waals interaction:A weak attractive interaction between nonpolar atoms, arising from transient induced dipoles in the two atoms. Image courtesy

Columbia U. Biology Dept.

Organic Organic Concepts VConcepts V

Chirality: The property of a molecule under which it cannot be superimposed upon its mirror image.

Image courtesy DRECAM, France

Organic Organic Concepts VIConcepts VI

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.

acetonepropen-2-ol

Organic Concepts Organic Concepts VIIVII

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.

Organic Concepts VIIIOrganic 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, and so on.

Organic Concepts IXOrganic 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.

Organic Concepts XOrganic 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

Classes of small moleculesClasses 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".

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.

Biological small molecules IBiological 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.

Biological small molecules IIBiological 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.

Biological small molecules IIIBiological small molecules III

Amino acids: Compounds containing an amine (NH3

+) group and a carboxyl (COO-) group.

The most important biological amino acids are -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 -amino acid is

H3N+ - CHR - COO-

Biological small Biological small molecules IVmolecules 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.

Small molecules VSmall 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 include

Cl-, 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)

Biological Small Molecules VIBiological 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.

Biological macromoleculesBiological 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)

Categories of biological Categories of biological polymerspolymersProteinsNucleic acidsPolysaccharidesLipids (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

Polymers and oligomersPolymers 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.

Categories of biopolymersCategories of biopolymers

Category # mono-mers

<mol wt/monomer>

# mono-mers

Branch-ing?

Protein 20 110 65-5000 no

RNA 4-10 220-400 50-15K no

DNA 4 200-400 50-106 no

Polysac-charide

~10 180 2-105 Some-times

Water: a complex substanceWater: 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

Water is polarWater is polar

Charge is somewhat unequally shared Small positive charge on H’s (+); small

negative charge on O (2-) (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.

Liquid water is mobileLiquid 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

Water in reactionsWater 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!

Water’s physical propertiesWater’s physical properties

High heat capacity:stabilizes temperature in living things

High surface tensionNearly incompressible (density

almost independent of pressure)Density max at 3.98ºC

CatalysisCatalysis

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

Biological catalystsBiological 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 for the 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

Energy in biological systemsEnergy 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

ThermodynamicsThermodynamics

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 Go = -RT ln Keq

KineticsKinetics

Rate of reaction is dependent on Kelvin temperature T and on activation barrier G‡ preventing conversion from one site to the other

Rate = Qexp(-G‡/RT)Job of an enzyme is to reduce G‡

RegulationRegulation

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

Typical enzymatic regulationTypical 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.

Molecular biologyMolecular 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.

The molecules ofThe molecules ofmolecular biologymolecular 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

Steps in molecular biology:Steps in molecular biology:the the Central DogmaCentral 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 rotein)

Evolution and TaxonomyEvolution 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

QuantitationQuantitation

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.

Mathematics in biochemistryMathematics 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

ExponentialsExponentials

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

LogarithmsLogarithms

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) = ealnY = loge(Y) = a

Algebra of logarithmsAlgebra 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)