Biochemistry presentationBiochemistry presentationBiochemistry presentationBiochemistry...

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Biochemistry

Biochemistry aims to explain biological form and function in chemical terms.Biochemistry explains life in terms of atomic structures of biological molecules.


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Biochemistry of Carbohydrate

Originally thought to have the formula (CH2O)n.Now known that only simple monosaccharides obey this rule.

Carbohydrate- polyhydroxy aldehyde or ketone or a larger molecule whichcan be hydrolyzed to a polyhydroxy aldehyde or ketone.

Carbohydrates (CHO) are the most abundant biomolecules in nature

CHO are the photosynthesis productnCO2 +H2O (CH2O)n + nO2

light

1. Energy source for plants and animals

2. Source of carbon in metabolic processes3. Storage form of energy

4. Structural elements of cells and tissues

5. Some CHO participate in recognition and adhesion between cells and mediatesome forms of inter cellular communications

Functions of Carbohydrates


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Classes of Saccharides

Monosaccharides

= single polyhydroxy aldehyde or ketone unit,(eg. 6-carbon glucose, most abundant in nature)

Oligosaccharides= short chain of 2- ~20 monosaccharides joined by glycosidic bonds

(eg. disaccharide sucrose = glucose-fructose)- oligosaccharides > 3 residues are usually joined to protein or lipid

in glycoconjugates

Polysaccharides

- chains > ~ 20 to 1000s of monosaccharides in length- linear: eg. cellulose (glucose)n or chitin (N-acetylglucosamine)n

- branched: eg. glycogen & starch (glucose)

- depending on the sugar residues in a polysaccharide and the linkages

between them, polysaccharides can have very different biological roles


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- Backbone = unbranched carbon chains in which all C atoms are linked by single bonds

- Colorless, crystallin, solid freely soluble in water, insoluble in organic solvents

- If it has keto group as the most oxidized functional group = Ketose

- If it has aldehyde group as the most oxidized functional group = aldose

According to the number of carbon atoms

- 3 C = triose, 4 C = tetrose, 5 C = pentose, 6 C = hexose (eg. aldo- or ketohexoses)

Monosaccharides

Simplest monosaccharides are 3 carbon...Common monosaccharides are 6 carbon...

Aldotriose ketotriose...


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D and L configurations of monosaccharides

- Most of the hexoses in living organisms are D-isomers

- Stereoisomers of monosaccharides > 3 C divided into 2

groups:

differ in the configuration about the chiral center mostdistant from the carbonyl C

In biochemistry, we use the D-L system (similar principle to

the R-S system usually used in organic, but everything iscompared with glyceraldehyde


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Joining of sugars via glycosidic bonds

Non-reducing

reducing

reducing


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Polysacchs. usually dont have precisely defined molecular weights, unlike proteins

Polysaccharides:are polymers of monosaccharides units of medium to high molecular weight.Homopolysaccharides contain only a single type of monomers, as starch, glycogen, celluloseHeterpolysaccharides contain two or more different kinds monomers, asglycosaminoglycans

Polysaccharides could be branched or unbranchedFunction: storage of energy, structural elements, animal exoskeleton and provide support

- Important cell surface components, eg.in holding cells together in tissues

- Important in molecular recognition events


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Storage polysaccharides: glycogen and starch

Glycogen:polymer of (14) linked glucoses with (16) branches (one every 8-12 glucoses),

average mol. wt. = several millions. Can be 7 % wet wt. of liver

Starch:= mixture of amylose, a linear polymer of (14) linked glucoses, and amylopectin,

a linear polymer of (14) linked glucoses with (16) branches (one every 4-30glucoses)

Liver cells (hepatocytes) store glycogenequivalent to a [glucose] of 0.4 M

Storage polysaccharides are essentiallyinsoluble in the cell, so they dont raisethe intracellular [glucose], which wouldset up a very high [glucose] gradient.


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Defined on the basis of solubility.Lipids: heterogeneous group of water insoluble (hydrophobic) organic

molecules, they are chemically diverse compound but have one feature:water insoluble

Many distinct chemical species in a lipid fraction

Functions

-The biological functions of lipids are divers as their chemistryLipids perform three biological functions:

1. Lipids in form of a bilayer are essential components of biological

membranes.

2. Lipids containing hydrocarbon side chains serve as energy stores.

3. Many intra-and intercellular signaling events involve lipid molecules.

Lipids


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1. Storage lipids

Triglycerides, Waxes and Fatty acids.Fats and oils are stored forms of energy and are derivatives of fatty acids.

2. Structural lipids in membranes

Glycerophospholipids, Sphingolipids, Sterols.

are major structural elements in biological membranes

3. Lipids as signals, cofactors and pigments.

These lipids presents in small quantities but play crucial roles

-Phosphatidylinositols,

Eicosanoids

- Prostaglandins.- Thromboxanes.- Leukotrienes.- Steroid hormones carry messages between tissues.- Vitamins A and D are hormone precursors.- Vitamins E and K are oxidation-reduction cofactors.

Lipid Classification


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Fats and oils are derivatives of Fatty acids.

Fatty acids (F.A) are carboxylic acids with long hydrocarbon chain ranging from 4-36

carbon atom 16- and 18-C long are most abundant.-Even number of carbons, 16, 18 the odd are also present but rare.

-the hydrocarbon chain can be fully saturated (without double bonds), or with one, two orthree double bonds (cis-configuration only)- usually they are unbranched, some cases have methyl, hydroxyl, or three-carbon ring as

branch

Storage Lipids


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Triacylglycerols or Triglycerides

triglycerides are non-polar and

hydrophobic molecules (the polar groups

of both glycerol and F. A are linked in

ester linkage

non-polar molecule )

Fatty acid triesters of glycerolMost contain two or three different types

of fatty acid residues


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Fats and oils* Plant oils are usually richer in unsaturated fatty acids residues than animal fats

* Fats and oils are complex mixtures of triacylglycerols

*Triacylglycerols can be found in most eukaryotic cell as oily droplets in the aqueous

cytosol serving as metabolic fuel

*In vertebrates specialized cells called Adipocytes (fat cell) store amounts of

triglycerides as fat droplets that fill the cell.

Triglycerides also stored as oil in the seeds of many types of plants .

*Adipocytes contain lipasescatalysis the hydrolysis of stored triglycerides releasingF.A for export to sites where they can be used as fuel.

*Two advantages for using the triglycerides as stored fuel rather than

polysaccharides as glycogen and starch:

1- the carbon atoms of F.A are more reduced than that of carbohydrates

oxidation of triglycerides yields more than twice as much energy (gm/gm) as theoxidation of CHO

2- triglycerides are hydrophobic unhydrated, the organism that carries fat as

fuel does not have to carry the extra weight of water of hydration that is

associated with stored polysaccharides (2gm water/1gm polysaccharides


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Polar vs. NonpolarlipidsNon-Polar Lipids Energy storage

Polar lipids are the basis of Bilayers

Biological membranes

feature: double layer of lipid

act as barrier to the passage

of polar molecules and ions.

Amphipathic: one end of themolecule is hydrophobic and

the other is hydrophilic

The hydrophobic interactions

between molecules and thehydrophilic interactions with

water direct their packing

into sheets called membrane

bilayer


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Glycerophospholipidsare the major lipid component of biological membranes

-amphiphilicmolecules with non-polaraliphatic tails and polar phosphoryl-X

heads

Glycerophospholipids

Phosphoglycerides: two F. A are attached in ester linkage to the first and

decond carbons of glycerol and a highly charged group is attached through a

phosphodiester linkage to the thrid carbon


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SphingolipidsSphingolipids are major membrane components, with polar head and non-polar tail)

They are derivatives of the C18 amino alcohol sphingosine

The double bond in sphingosine is trans

C1, C2, C3 of sphingosine molecule are structurally similar to the three carbons ofglycerol in phospholipids

N-acyl fatty acid derivatives of sphingosine are known as ceramides

Ceramides are the parent compounds of the more abundant sphingolipids

. Sphingolipids are major lipids in mylene sheath and CNS lipids

General structure of Sphingolipids, if X is H, the compound is Ceramide


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3-SterolsStructural lipids present in the

membranes of some eukaryotic cells.

Characterized by the steroid nucleus

consisting of four fused rings threerings with 6 C atoms and one ring with 5

C atoms, the steroid nucleus is relatively

rigid and planar

Cholesterol is the major sterol in animal

tissues and it is amphipathic with a polar

head (the OH group), and the non-polarbody is the steroid nucleus

Similar sterols are present in

eukaryotes: Stigmasterol plants

Ergosterol fungi

Functions-membrane constituents

-precursors of different product with vital biological activities (steroidalhormones that regulate the gene expression)

-bile acids are derivatives of cholesterol that act as emulsifying agent in the

intestine

A i A id


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Side chain isdistinctivefor eachamino acid

Amino Acids

Amino acids are building blocks of proteins.

- There are more than 300 a. a. found in the nature, only 20 are found in

mammalian proteins and these are coded for by DNA

-The nature of the side chain decides the role of an amino acids in aprotein

- Amino acids can be classified according to the properties of their side

chains

All the amino acids found in the proteins are L-configuration

At physiologicpH

All the amino acids found in the proteins are L-configuration

H d h bi ( l ) R


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Hydrophobic (nonpolar) R groups

-Non polar side chains don't

bind or give off protons or

participate in hydrogen or ionbonds. So they are oily or

lipid like material

H d h bi ( l ) R G


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Hydrophobic (nonpolar) R Group

- Proline: the side chain of

proline and -amino group

form a ring structure and

it differs from other

amino acids that itcontains an imino group


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-Location of amino acids in proteins:proteins found at the aqueous

solutions, the side chain of non-polar amino acids tend to cluster

together in the interior of the protein. The hydrophobic interaction is

important in stabilizing protein structure.HydrophobicAmino acids

HydrophilicAmino acids


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Hydrophilic (polar) R Group

Uncharged side chains. These amino acids havezero net charge at neutral pH


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Some side chains act as sites of attachment for the compounds: serine,

threonine and tyrosine contain polar hydroxyl group that can serve as site

of attachment: phosphorylation. Side chain of serine residue is an

important component of the active sites of many enzymes. The OH ofserine and threonine can be linked to oligosaccharide in glycoprotein


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Uncharged side

chains. These amino

acids have zero netcharge at neutral pH


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Hydrophilic R Groups with Formal ChargeBasic R Groups Acidic R Groups


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These amino acids

have positive

charge at neutral

pH

H+

These amino acids are proton acceptor at neutral pH


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Disulfide bond: the cysteine contains a sulfhydryl group (-SH), which is

also an important component of the active site at many enzymes. The two

SH become oxidized to form a dimer cystine which contain a covalent

cross-link disulfide bond

Disulfide bond formation

Amino acid Abbreviated One letter


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Amino acid Abbreviatedname

One-lettersymbol

Nonpolar R groups:GlycineAlanine

ValineLeucineIsolecinePhenylalanineTryptophanMethionineProline

GlyAla

ValLeuIlePheTrpMetPro

GA

VLIFWMP

Polar, uncharged R:SerineThreonineTyrosineCysteineAsparagine

Glutamine

SerThrTyrCysAsn

Gln

STYCN

QAcidic R groups:AspartateGlutamate

AspGlu

DE

Basic R groups:Lysine

HistidineArginine

Lys

HisArg

K

HR

Essential Amino Acids

10 amino acids not

synthesized by the bodyarg, his, ile, leu, lys,met, phe, thr, trp, valMust obtain from thediet


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Amino Acids as Acids and Bases

Ionization of the NH2 and the COOH group

Zwitterion has both +ve and ve charge

Zwitterion is neutral overall

NH2CH2COOH H3NCH2COO

glycine Zwitterion of glycine

H

+

OH

H3NCH2COOH H3NCH2COO H2NCH2COO

Positive ion zwitterion Negative ion

Low pH neutral pH High pH

pH and ionization of amino acids

+

+ +

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