BIOCHEMISTRY NOTES.pptx

BME 1203: Biochemistry
By MULOOGI DERICK
dmuloogi@must.ac.ug
Wednesday, September 27,
2023
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Course Name Biochemistry
Course Code BME 1203
Contact Hours 45
Credit Units 3
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Course Description
• Chemical activity forms a large part of biological interactions
within the human body. Chemistry finds wide applications in
Biomedical engineering and this course is intended to
awaken students to the importance of chemistry in the
engineering field. This course builds on Applied Chemistry I.
Aims
• To provide an in-depth understanding of chemical process
analysis
• To introduce students to possible chemical processes within
the human body and their relation to chemical processes
within the physical environment.
• To educate students on the different kinds of energy fuels
and their use in engineering
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• Learning Outcomes
Knowledge
• Students will be able to explain the different chemical
processes in the human body
• Students will be able to explain the different characteristics
of energy fuels and their possible fields of application in
medical engineering
• Students will be able to explain the process of catalysis
Skills and competences
Students will develop:
• Experimental skills
• Problem solving skills
• Analytical skills
• Managing own learning
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Course content
No. TOPICS Contact hours
1. Biomolecules 10
2. Biochemical reactions 15
3. Molecular Genetics; DNA and
RNA
15
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Visual
Oral Written
Communication Skills
Characteristics Needed to excel in this
course
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Introduction to biochemistry
• Biochemistry is the chemistry of living things (life).
• To understand and control or modify (for disease prevention
or other purposes) chemical reactions of living organisms,
we must understand life on the molecular level.
• The study of chemical compounds and the reactions in
which they participate is called biochemistry
• Since living things are extremely complicated then the
chemical reactions and molecules must be very complex,
however we can get an overview by understanding the
types of biomolecules
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Biomolecules
• These are compounds needed to maintain life
of living organisms. They are divided into two
groups, i.e.
I. Inorganic compounds e.g. water, vitamins,
salts, acids and roughages.
II. Organic compounds e.g. carbohydrates,
lipids, proteins and nucleic acids.
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Compounds Approximate percentages
Water 65
Proteins 18
Fats 10
Carbohydrates 5
Other organic 1
Inorganic 1
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Carbohydrates
• Are polyhydroxy aldehydes or ketones, or substances
that yield such compounds on hydrolysis.
• They comprise of a large group of organic
compounds which contain C,H and O. They have a
general formula CX(H2O)Y though some do not
conform to it e.g. deoxyribose C5H10O4.
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Main functions of carbohydrates
• They are a primary source of energy being
oxidized in the body to release energy.
• They are structural components of cells e.g.
cellulose making up the cell wall.
• They are determinants of osmotic potential of
body fluids therefore maintain blood pressure.
• They are recognized units on the surface of body
cells, i.e. they are component structures of the
surface cell membranes recognized by
antibodies.
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Classification of carbohydrates
• They are classified according to;
i) Number of sugar units viz;
• Monosaccharides (single unit sugars)
• Disaccharides (double unit sugars)
• Oligosaccharides ( 3 to 10 units)
• Polysaccharides (several unit sugars- more than 10 units)
ii) number (n) of carbon atoms;
Example: Trioses, 3 carbon atoms, e.g. Glyceraldehyde;
Pentoses, 5 carbon atoms, e.g. Ribose, Deoxyribose; Hexoses, 6
carbon atoms e.g. Glucose, Fructose, Galactose.
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iii) Functional groups present (Aldoses or ketoses):
• In monosaccharides, all carbon atoms except one, have a
hydroxyl group attached. The other carbon has either an
aldehyde group or a ketone group attached.
• The monosaccharide with aldehyde group is called aldose or
aldo sugar, while the ones with a keto group, is called a
ketose or keto sugar.
• Aldoses include: Glyceraldehyde, Ribose, Glucose etc.
• And Ketoses include: Dihydroxyacetone, Ribulose, fructose
etc.
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Example
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Trioses Pentoses Hexoses
Aldoses Glyceraldehyde Ribose Glucose, galactose
Ketoses Dihydroxyacetone Ribulose Fructose

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iv) Open chain or ring forms.
• The open chain form can be straight.
• But because of bond angles between carbon atoms, hexoses
and pentoses, tend to bend to form a stable ring structures.
• In hexoses like glucose, First carbon atom combines with the
oxygen on carbon atom five to give a six – membered ring.
Note that oxygen is part of the ring and one carbon atom
(carbon atom number 6), sticks up out of the ring.
• In Pentoses, the first carbon atom combines with oxygen
atom on the fourth carbon atom forming a five – membered
ring. These ring structures are the forms used to make
disaccharides and polysaccharides.
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Fischer Projection structures of Sugars:
Steps Involved
1. Write the carbon chain vertically with the aldehyde or
ketone group toward the top of the chain.
2. Number the carbons.
3. Place the aldehyde or ketone group.
4. Place H and OH groups.
5. Identify the chiral centers.
6. Note the highest numbered chiral center to
distinguish D and L sugars.
7. Write the correct common name for the sugar.
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Examples
Glyceraldehyde Dihydroxyacetone
Linear- fischer projection structures of trioses
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Fischer Projection Structures of Hexoses
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Glucose(aldose)
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….CTD
Note: Fischer projection formula – is a method for giving
molecular chirality specifications in two dimensions.
• In general, a molecule with n chiral centers can have 2n
stereoisomers.
• So, a Fischer projection formula is a two-dimensional
structural notation for showing the spatial arrangement
of groups about chiral centers in molecules..
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Chirality
• Chiral molecules have the same relationship to each other
that your left and right hands have when reflected in a
mirror.
• Any carbon atom which is connected to four different
groups will be chiral, and will have two nonsuperimposable
mirror images; it is a chiral carbon or a center of chirality.
– if any of the two groups on the carbon are the same, the
carbon atom cannot be chiral.
• Many organic compounds, including carbohydrates, contain
more than one chiral carbon.
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• Enantiomers are stereoisomers whose molecules are
nonsuperimposable mirror images of each other. Molecules
with chiral center.
• Diastereomers are stereoisomers whose molecules are not
mirror images of each other. They have more than one chiral
centers.
• Diastereomers (or diastereoisomers) are stereoisomers that
are not enantiomers (non-superimposable mirror images of
each other). Diastereomers can have different physical
properties and different reactivity.
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• Enantiomers have same boiling points, melting points and
densities - all these are dependent upon intermolecular
forces and chirality doesn’t depend on them.
• Enantiomers are optically active: Compounds that rotate
plane polarized light.
• Our body responds differently to different enantiomers: One
may give higher rate or one may be inactive Example: Body
response to D form of hormone epinephrine is 20 times
greater than its L isomer.
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Ring form/Haworth Structures
Example:
Considering Glucose;
• In ring structure, it has two isomers namely; Alpha and Beta
isomers.
• The hydroxyl group on carbon atom 1 can project below the
ring forming Alpha glucose or above the ring forming the
Beta glucose. These play different biological roles.
• Alpha glucose is used in making polysaccharide starch, Beta
glucose is used in making polysaccharide cellulose.
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• C-1 in the new ring structure is the new chiral centre or
the anomeric carbon.
• Anomeric carbon- is the new chiral center created when
the sugar ring is formed.
• The two new sugar stereoisomers (alpha and beta
glucose units)created by ring closure are the called the
Anomers.
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Fructose haworth structure vs glucose haworth structure
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Structure of Pentose sugars
• They have 5 carbon atoms. They are found in nature as
ribose and deoxyribose. They exist in straight and ring
forms.
• Deoxyribose
Ring form
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Illustration
open chain vs ring membered

CTD
v) Classification of the molecule based on the rotation of
plane-polarized light.
• Dextrorotatory - rotate clockwise shown using (+) symbol or
- usually D isomers
• Levorotatory - rotate anti-clockwise shown using (-) symbol
or - usually L isomers
• Molecules which rotate the plane of polarized light are
optically active.
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..Examples
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Sugar Units and their Reactions
The five important reactions of monosaccharides are;
1. Oxidation to acidic sugars.
2. Reduction to sugar alcohols.
3. Glycoside formation.
4. Phosphate ester formation.
5. Amino sugar formation.
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a) Monosaccharides

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1. Oxidation to acidic sugars
• They are reducing sugars (a sugar aldehyde or ketone which
can be oxidised to an acid and drive the reduction of a
metal ion).
• Oxidation can yield three different types of acidic sugars
depending on the type of oxidizing agent used.
• Weak oxidizing agents such as Tollens and Benedict’s
solutions oxidize the aldehyde to give an aldonic acid.
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2. Reduction to sugar alcohols: The carbonyl group in a
monosaccharide (either an aldose or a ketose) is reduced
to a hydroxyl group using hydrogen as the reducing agent.
• The product is the corresponding polyhydroxy alcohol -
sugar alcohol.
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3. Glycoside formation
• The hemiacetal and hemiketal forms of monosaccharides
can react with alcohols to form acetal and ketal structures
called glycosides. The new carbon-oxygen bond is called
the glycosidic linkage.
• Simple carbohydrates: Glycoside- compound is formed
when a sugar in the cyclic form is bonded to an alcohol
through a glycosidic bond. For example reaction of
pyranose glucose with methanol.
-- write the equation of reaction
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ctd
4. Formation of phosphate esters
• Phosphate esters can form at the 6-carbon of
aldohexoses and aldoketoses.
• Phosphate esters of monosaccharides are found in the
sugar-phosphate backbone of DNA and RNA, in ATP, and
as intermediates in the metabolism of carbohydrates in
the body.
• Illustrate with an equation of reaction!!
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Functions of monosaccharides
Monosaccharides Examples Functions
Trioses Glyceraldehyde ,
Dihydroxyacetone
Intermediates in respiration (Glycolysis) ,
Photosynthesis (dark reactions) and other branches
of carbohydraye metabolism
Pentoses Ribose, Deoxyribose, Ribulose Synthesis of nucleic acids; Synthesis of some
coenzymes (Ribose is used in synthesis of NAD and
NADP); Synthesis of ATP requires ribose; Ribulose
bisphosphate is the CO2 acce[ptor in photosynthesis,
made from ribulose.
Hexoses Glucose; Fructose; Galactose Source of energy when oxidized in respiration;
Synthesis of disaccharides; Synthesis of
polysaccharides
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Disaccharides
• A disaccharide forms by reaction of the -OH group on the
anomeric carbon of one monosaccharide with an –OH group
of a second monosaccharide.
• The linkage between monosaccharides in a disaccharide is
referred to as a glycosidic linkage and is named according to
the number of the carbon at which the linkage begins and
the carbon on the second monosaccharide at which the
linkage ends.
• The glycosidic linkage is also designated α or β, depending
upon whether the conformation at the anomeric carbon is
up or down.
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Examples of Disaccharides
Disaccharide Monosaccharide Units
Maltose Alpha glucose units
Sucrose Alpha glucose unit and Beta
Fructose unit
Lactose Beta glucose unit and Beta
galactose Unit.
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Formation of maltose
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Formation of sucrose
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Formation of lactose
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Polysaccharides
• Many monosaccharides may combine by condensation
reactions to form polysaccharides.
• A number of monosaccharides which combine may be
variable and the chain can be branched or unbranched.
• The chains may be folded to make them compact which
are ideal for storage.
• They are often large in size which makes them insoluble
in water and suitable for storage as they exert no
osmotic influence and do not easily diffuse out of the
cell.
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Important polysaccharides
1. STARCH
• It is found in plant parts in form of granules. It is a reserve
food formed from any excess glucose during photosynthesis.
• It is common in seeds e.g. maize where it is the main food
supply during germination.
Structure:
• It is a polymer of α-glucose molecules which are held by
glycosidic bonds forming chains of α-glucose units which
get folded or coiled into a helix.
• Starch has two components i.e. amylose and amylopectin,
that is, 20% amylose, 79% amylopectin and 1% other
substances e.g. phosphates and fatty acids.
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• Amylose stains deep blue with iodine while amylopectin
stains red to purple with iodine.
• Amylose is structurally unbranched while amylopectin is
branched.
• Structures on Next Slide
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Amylopectin
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Pause a bit!
A) compare the structures of amylose and amylopectin.
B) How does the molecular structure of starch relate to its
biological roles?
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Glycogen
• It is a major polysaccharide storage material in
animals. It stored mainly in the liver and muscles. It
is also made up of α-glucose molecules and exists
as granules. However its chains are shorter (10-20
glucose units) and is more branched. Glycogen is
more soluble than starch.
• Glycogen is made up of α(1 4) and α(1 6)
glucose branched molecule open spiral molecule. It
is more water soluble and a non reducing sugar
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• structure
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CELLULOSE
Structure:
• It is a polymer with straight chains of β-glucose units
held by glycosidic bonds with the OH group projecting
out wards from each chain forming cross linkages of
hydrogen bonds with adjacent chains.
• The cross linking binds the chains together which
associate to form micro fibrils that are arranged in larger
bundles to form macro fibrils.
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• Note: starch lacks the structural properties possessed by
cellulose because it lacks cross linkages.
• The stability of cellulose makes it difficult to digest and
therefore not a good source of food to animals except
those which have cellulase producing microorganisms
which live in them in a symbiotic way e.g. in the rumen of
cattle, goats, sheep, etc.
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Chitin
• [A structural polysaccharide in fungi and animals].
• Chitin is similar to cellulose, but instead of consisting of
glucose monomers, the monosaccharide involved is one
called N-acetylglucosamine (NAG).
• These NAG monomers are joined by β-1, 4-glycosidic
linkages.
• As in cellulose, the geometry of these bonds results in every
other residue being flipped in orientation. Like the glucose
monomers in cellulose, the NAG subunits in chitin form
hydrogen bonds between adjacent strands.
• Chitin is a polysaccharide that stiffens the cell walls of fungi.
It is also found in a few types of protists and in many
component of the external skeletons of insects and
crustaceans.
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Others include;
Inulin
• It is a polymer of fructose and found as a storage
carbohydrate in some plants.
Mucopolysaccharides
• This group includes hyaruronic acid which forms part of
the matrix of vertebrae connecting tissue. It is found in
cartilage, bones, vitreaous humor of the eye, synovial fluid,
etc.
• Heparin, an anti-coagulant also contains
mucopolysaccharides.
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TASK
• Raffinose is an oligosaccharide of α-D- glucose,
β- D- galactose and β-D- fructose. Using
equations of reaction, show how raffinose is
formed.
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