Introduction to Biochemistrylibvolume2.xyz/biotechnology/semester4/biochemical...08/21/08...

08/21/08 Biochemistry: Introduction 1

Introduction to Biochemistry

Andy Howard

Biochemistry, Fall 2008

IIT

08/21/08 Biochemistry: Introduction p. 2 of 62

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.


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


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 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 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

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


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


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


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


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


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


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


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

concepts 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 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 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

concepts 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

Concepts V

� Chirality: The property of

a molecule under which it

cannot be superimposed

upon its mirror image.

Image courtesy DRECAM, France


Organic

Concepts 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

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.


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 with

HO-R3-X-H to form

R1-X-R2-X-R3-OH with elimination of another water molecule, and so on.


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 equilibriumsystems


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


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".


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 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 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 III

� Amino acids: Compounds containing an

amine (NH3+) group and a carboxyl (COO-)

group.

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

� H3N+ - CHR - COO-


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.


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


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.


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


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


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.


Categories 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 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 polar

� Charge is somewhat unequally shared

� Small positive charge on H’s (δδδδ+); small

negative charge on O (2δδδδ-) (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 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 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 properties

� High heat capacity:

stabilizes temperature in living

things

� High surface tension

� Nearly incompressible (density

almost independent of pressure)

� Density max at 3.98ºC


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


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


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


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 ∆∆∆∆Go = -RT ln Keq


Kinetics

� 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‡

Svante Arrhenius


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


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.


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.


The molecules of

molecular 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 is

NH-(CHR)-CO; side chains are 20

ribosomally encoded styles


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)


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


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.


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


Exponentials

� Many important biochemical equations are expressed in the formY = ef(x)

� O 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


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


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)


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!


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


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


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!


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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