Biochemistry Lecture 1 October 24 2011

8/3/2019 Biochemistry Lecture 1 October 24 2011

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BIOCHEMISTRYand

MICROBIAL PHYSIOLOGY

MQT 1173


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BIOCHEMISTRY

Biochemists discuss chemistry with

biologists, and biology with

chemists, thereby confusing bothgroups. Among themselves, they

talk about baseball.

Credit: Anonymous


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Biochemistry is a hybrid science:

Biology is the science of living organisms and chemistry is the

science of atoms and molecules, so biochemistry is the

science of the atoms and molecules in living organisms.

Its domain encompass all the living world with the unifying

interest in the chemical structures and reactions that occur in

living systems.

Where can you find biochemistry? All through science, medicine,

and agriculture.


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Biochemistry underlies ordinary life in unseen ways:

For example, take a middle-aged man who:

Takes a drug to lower his serum cholesterol. That drug was

developed by a pharmaceutical company's biochemists to inhibit a

key enzyme involved in cholesterol biosynthesis.

Shaves with a cream containing compounds that soften his

beard. These active agents were developed after studies of thephysical properties of keratin, the protein in hair.

Eats a breakfast cereal fortified with vitamins identified

through nutritional biochemistry.

Wears a shirt made from pest-resistant cotton. The cotton

plants were bioengineered by biochemists through the transfer ofgenes from a bacterium into plants.

Drinks milk before bedtime. His sleep is helped by the amino

acids in the milk, which are converted by his brain into molecular

signals that lead to a resting state in other parts of his brain.


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Biochemistry has three main branches

Metabolism study of the conversion of biological molecules,

especially small molecules, from one to another

forexample, the conversion of sugar into carbon dioxide andwater, or the conversion of fats into cholesterol. Metabolicbiochemists are particularly interested in the individualenzyme-catalyzed steps of an overall sequence ofreactions (called a pathway) that leads from onesubstance to another.

Structural Biochemistry study of how molecules in livingcells work chemically. For example, structural biochemiststry to determine how the three-dimensional structure of

an enzyme contributes to its ability to catalyze a singlemetabolic reaction.

Molecular Genetics is concerned with the expression ofgenetic information and the way in which this informationcontributes to the regulation of cellular functions.


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Chemical elements and biomolecules

Around two dozen of the 94 naturally-occuring chemical

elements are essential to various kinds of biological life.Most rare elements on Earth are not needed by life (exceptions

being selenium and iodine), while a few common ones(aluminum and titanium) are not used.

Most organisms share element needs, but there are a fewdifferences between plants and animals.

For example ocean algae use bromine but land plants andanimals seem to need none.

All animals require sodium, but some plants do not.

Plants need boron and silicon, but animals may not (or mayneed ultra-small amounts).

Just six elementscarbon, hydrogen, nitrogen, oxygen,calcium, and phosphorusmake up almost 99% of the massof a human body and require smaller amounts of at least 16

more.


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The four main classes of molecules in biochemistryare carbohydrates, lipids (Fatty acids), amino

acids (proteins), and nucleic acids.Many biological molecules are polymers: in thisterminology, monomers are relatively smallmicromolecules that are linked together tocreate large macromolecules, which are knownaspolymers.

When monomers are linked together to synthesizea biological polymer, they undergo a processcalled dehydration synthesis.

Most of these are optically active, that is, they arefound in only one of the possible stereoisomers.

(Stereoisomers are compounds that have the same kinds andnumbers of atoms but have different molecular arrangements)


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Amino acids

Generally, amino acids found in nature are the L-stereoisomers.

Amino acids are the building blocks of proteins, and have an

important role in energy metabolism and in cellular signaling.

They are also a small but important part ofcell membranes.

are molecules containing an amine group, a carboxylic acid groupand a side-chain that varies between different amino acids.

The key elements of an amino acid are carbon, hydrogen, oxygen,and nitrogen.

They are particularly important in biochemistry, where the termusually refers to alpha-amino acids.
http://en.wikipedia.org/wiki/Moleculehttp://en.wikipedia.org/wiki/Aminehttp://en.wikipedia.org/wiki/Carboxylic_acidhttp://en.wikipedia.org/wiki/Side_chainhttp://en.wikipedia.org/wiki/Carbonhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Nitrogenhttp://upload.wikimedia.org/wikipedia/commons/c/ce/AminoAcidball.svghttp://en.wikipedia.org/wiki/Nitrogenhttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Carbonhttp://en.wikipedia.org/wiki/Side_chainhttp://en.wikipedia.org/wiki/Side_chainhttp://en.wikipedia.org/wiki/Side_chainhttp://en.wikipedia.org/wiki/Carboxylic_acidhttp://en.wikipedia.org/wiki/Aminehttp://en.wikipedia.org/wiki/Molecule


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Carbohydrates

are molecules of the empirical formula Cm

(H2O)

nwhere n usually

ranges from 3

7 (where m could be different from n).

They are found in sugars and starches and make up parts ofnucleotides (the energy currency of a cell, and the building blocksfor genetic information).

They are also present in some components of all cell membranes.

They are the central components of energy-producing pathways inbiology.

Carbohydrates are made from monomers called monosaccharides.

Monosaccharides include glucose , fructose, and deoxyribose

When two monosaccharides undergo dehydration synthesis,water is produced, as two hydrogen atoms and one oxygen atomare lost from the two monosaccharides' hydroxyl group.
http://en.wikipedia.org/wiki/Monosaccharideshttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Fructosehttp://en.wikipedia.org/wiki/Deoxyribosehttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Hydroxyl_grouphttp://en.wikipedia.org/wiki/Hydroxyl_grouphttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Hydroxyl_grouphttp://en.wikipedia.org/wiki/Hydroxyl_grouphttp://en.wikipedia.org/wiki/Hydroxyl_grouphttp://en.wikipedia.org/wiki/Hydroxyl_grouphttp://en.wikipedia.org/wiki/Oxygenhttp://en.wikipedia.org/wiki/Hydrogenhttp://en.wikipedia.org/wiki/Deoxyribosehttp://en.wikipedia.org/wiki/Fructosehttp://en.wikipedia.org/wiki/Glucosehttp://en.wikipedia.org/wiki/Monosaccharides


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Properties of GlucoseMolecular formula C6H12O6

Molar mass 180.16 g/mol

Melting point -D-glucose: 46 C,

-D-glucose: 150 C

Solubility in water Very soluble

Properties of FructoseMolecular formula C6H12O6

Molar mass 180.16 g/mol

Melting point 103 C

http://en.wikipedia.org/wiki/Molar_masshttp://en.wikipedia.org/wiki/Melting_pointhttp://en.wikipedia.org/wiki/Solubilityhttp://en.wikipedia.org/wiki/Waterhttp://en.wikipedia.org/wiki/Molar_masshttp://en.wikipedia.org/wiki/Melting_pointhttp://en.wikipedia.org/wiki/Solubilityhttp://en.wikipedia.org/wiki/Waterhttp://upload.wikimedia.org/wikipedia/commons/e/e5/D-Fructose.svghttp://en.wikipedia.org/wiki/Waterhttp://en.wikipedia.org/wiki/Solubilityhttp://en.wikipedia.org/wiki/Melting_pointhttp://en.wikipedia.org/wiki/Molar_masshttp://upload.wikimedia.org/wikipedia/commons/1/14/DGlucose_Fischer.svghttp://en.wikipedia.org/wiki/Waterhttp://en.wikipedia.org/wiki/Solubilityhttp://en.wikipedia.org/wiki/Melting_pointhttp://en.wikipedia.org/wiki/Molar_mass


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Properties of Deoxyribose

Molecular formula C5H10O4

Molar mass 134.13 g mol1

Melting point 91 C


A molecule of sucrose (glucose + fructose), a disaccharide
http://en.wikipedia.org/wiki/Molar_masshttp://en.wikipedia.org/wiki/Melting_pointhttp://en.wikipedia.org/wiki/Solubilityhttp://en.wikipedia.org/wiki/Waterhttp://en.wikipedia.org/wiki/Sucrosehttp://en.wikipedia.org/wiki/Disaccharidehttp://en.wikipedia.org/wiki/Disaccharidehttp://en.wikipedia.org/wiki/Sucrosehttp://upload.wikimedia.org/wikipedia/commons/b/b3/Sucrose-inkscape.svghttp://en.wikipedia.org/wiki/Waterhttp://en.wikipedia.org/wiki/Solubilityhttp://en.wikipedia.org/wiki/Melting_pointhttp://en.wikipedia.org/wiki/Molar_mass


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LipidsClosely related to hydrocarbons (compounds containing

hydrogen and carbon atoms exclusively), although they usually haveother atoms beside C and H.

Constitute a broad group of naturally occurring molecules

which include fats, waxes, sterols, fat-soluble vitamins (such as

vitamins A, D, E and K), monoglycerides, diglycerides, phospholipids,and others.

Characterized by limited solubility in water, essential

components of membranes, important energy stores in plants and

animals and signaling molecules

May be broadly defined as hydrophobic or amphiphilic small

molecules; the amphiphilic nature of some lipids allows them to form

structures such as vesicles, liposomes, or membranes in an aqueous

environment.
http://en.wikipedia.org/wiki/Vesicle_%28biology%29http://en.wikipedia.org/wiki/Liposomehttp://en.wikipedia.org/wiki/Liposomehttp://en.wikipedia.org/wiki/Vesicle_%28biology%29


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Biological lipids originate entirely or in part from two

distinct types of biochemical subunits or "building blocks":

ketoacyl and isoprene groups.

Using this approach, lipids may be divided into eight

categories: fatty acyls, glycerolipids, glycerophospholipids,

sphingolipids, saccharolipids and polyketides (derived from

condensation of ketoacyl subunits); and sterol lipids and prenol

lipids (derived from condensation of isoprene subunits)

Palmitic acid (C16H32O2)
http://en.wikipedia.org/wiki/Fatty_acylshttp://en.wikipedia.org/wiki/Glycerolipidhttp://en.wikipedia.org/wiki/Glycerophospholipidhttp://en.wikipedia.org/wiki/Sphingolipidhttp://en.wikipedia.org/wiki/Saccharolipidhttp://en.wikipedia.org/wiki/Polyketidehttp://en.wikipedia.org/wiki/Polyketidehttp://en.wikipedia.org/wiki/Saccharolipidhttp://en.wikipedia.org/wiki/Sphingolipidhttp://en.wikipedia.org/wiki/Glycerophospholipidhttp://en.wikipedia.org/wiki/Glycerolipidhttp://en.wikipedia.org/wiki/Fatty_acyls


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A nucleic acid is a complex, high-molecular-weight biochemical

macromolecule composed of nucleotide chains that convey geneticinformation.

The most common nucleic acids are deoxyribonucleic acid (DNA) andribonucleic acid (RNA).

Nucleic acids are found in all living cells and viruses.

Aside from the genetic material of the cell, nucleic acids often play arole as second messengers, as well as forming the base molecule for

adenosine triphosphate, the primary energy-carrier molecule foundin all living organisms.

Nucleic acid, so called because of its prevalence in cellular nuclei, isthe generic name of the family ofbiopolymers.

Nucleosides and nucleotides
http://en.wikipedia.org/wiki/Second_messengerhttp://en.wikipedia.org/wiki/Adenosine_triphosphatehttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Biopolymerhttp://en.wikipedia.org/wiki/Biopolymerhttp://en.wikipedia.org/wiki/Cell_nucleushttp://en.wikipedia.org/wiki/Adenosine_triphosphatehttp://en.wikipedia.org/wiki/Second_messenger


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The monomers are called nucleotides, and each consists of threecomponents: a nitrogenous heterocyclic base(either a purine or apyrimidine), a pentosesugar, and a phosphate group.

Different nucleic acid types differ in the specific sugar found in their

chain (e.g. DNA or deoxyribonucleic acid contains 2-deoxyriboses).

Possibly nitrogenous bases are different in the two nucleic acids :adenine, cytosine, and guanine occur in both RNA and DNA,

while thymine occurs only in DNA and uracil occurs in RNA.
http://en.wikipedia.org/wiki/Nucleotidehttp://en.wikipedia.org/wiki/Base_%28chemistry%29http://en.wikipedia.org/wiki/Purinehttp://en.wikipedia.org/wiki/Pyrimidinehttp://en.wikipedia.org/wiki/Pentosehttp://en.wikipedia.org/wiki/Sugarhttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Deoxyribosehttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/Cytosinehttp://en.wikipedia.org/wiki/Guaninehttp://en.wikipedia.org/wiki/Guaninehttp://en.wikipedia.org/wiki/Cytosinehttp://en.wikipedia.org/wiki/Adeninehttp://en.wikipedia.org/wiki/Deoxyribosehttp://en.wikipedia.org/wiki/Phosphatehttp://en.wikipedia.org/wiki/Sugarhttp://en.wikipedia.org/wiki/Pentosehttp://en.wikipedia.org/wiki/Pyrimidinehttp://en.wikipedia.org/wiki/Purinehttp://en.wikipedia.org/wiki/Base_%28chemistry%29http://en.wikipedia.org/wiki/Nucleotide


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Adenosine, a nucleoside
http://upload.wikimedia.org/wikipedia/commons/e/e8/Adenosin.svghttp://upload.wikimedia.org/wikipedia/commons/e/e2/Nucleotides_1.svg


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General formulas of organic compoundsR represents an alkyl group (CH3(CH2)n)


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General formulas of functional groups

R represents an alkyl group (CH3(CH2)n)


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General formulas of linkages

common in biochemistry


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Representations of the structure of ribose.

(a) In the Fischer projection, ribose is drawn as a linear molecule.

(b) In its usual biochemical form, the ribose molecule is in a ring, shown

here as a Fischer projection.

(c) In a Haworth projection, the ring is depicted as lying perpendicular to

the page (as indicated by the thick lines, which represent the bonds closest

to the viewer).

(d) The ring of ribose is not actually planar but can adopt 20 possible

conformations in which certain ring atoms are out-of-plane. In the

conformation shown, C-2 lies above the plane formed by the rest of the

ring atoms.


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Types of Biochemical Reactions

Many possible biochemical reactions fall into only a few types to

consider:

Oxidation and reduction:For example, the interconversion of an alcohol and an aldehyde.

Movement of functional groups within/between moleculesFor example, the transfer of phosphate groups from one oxygen

to another.

Addition and removal of water:For example, hydrolysis of an amide linkage to an amine and a

carboxyl group.

Bond-breaking reactions:

For example, carbon-carbon bond breakage.


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All Organisms are Related

The classification and grouping of organisms, the science called

taxonomy, regards organisms as similar based on their visible

characteristics. Thus, plants and animals were regarded as the two

main kingdoms of life.

Later, cell biologists divided organisms into prokaryotes and

eukaryotes, that is, organisms without and with a nucleus.

Most recently, a new taxonomy has been developed, largely byCarl Woese and associates, based on the information in the

ribosomal RNA sequences.


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Remarkably, the most information-rich classifications of life shows

three main divisions, sometimes called domains, which aremore fundamental than the distinction between plants and

animals, or prokaryotes and eukaryotes. These domains are:

Eukarya: Includes organisms with a nucleus.This division includesplants, animals, and a large number of what are sometimes called

protists, or organisms that can be seen only under a microscope,

such as yeasts or paramecia.

Bacteria: The second domain includes microorganisms without anucleus, including many that are familiar, like Escherichia coli.

Archaea: The third groupis as different from bacteria as they arefrom eukarya on the molecular/biochemical level. These

remarkable microorganisms inhabit niches often thought of as

inhospitable to life for example, locations with high

temperature, low oxygen, or high salt. Their biochemistry is

unique and largely unexplored.


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Biochemistry Lecture 1 October 24 2011

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