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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
+
+ +