che 214 lecture 01

CHE 214: Biochemistry

Lecture one

TODAYS TOPICS•INTRODUCTION AND COURSE OUTLINE•CARBOHYDRATES•LIPIDS

Lecturer: Dr. G. Kattam Maiyoh

February 14, 2013 1GKM/CHE 214/LEC 01/SEM 02/2013

CHE 214: BIOCHEMISTRY

Contact information

Dr. Geoffrey Kattam Maiyoh

E-mail: maiyoh07@yahoo.com / jeffkattam@gmail.com Tel: 0713-592879

Website: http://MAIYOH.1faculty.com

Recommended Textbooks/ Lecture Notes•L. Stryer, Biochemistry•Lehninger, Principles of Biochemistry•Any other textbook of Biochemistry •Power point lecture notes will be available after class (Class

representatives to collect on flash discs).

Examination–CAT s – 20%–Practical – 10%–Final Exam – 70%–Everyone is required to be present during CATs and Exams

•Examination / CATs Format•CAT Questions – Both CATs will comprise 30 questions each. There will be 3

sections in each CAT paper (Multiple choice, Structured i.e. “Filling in the blank spaces” and True/False sections)

• Examination Questions – All Exam questions will be in essay form

•Attendance –Exams will mostly be based on the material presented during

classes. –It is in your best interest to attend each lecture.

February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 3

TOPICS Title

1. Biological Molecules: Structure, Chemistry and Function of Carbohydrates and Lipids

2. Biological Molecules: Structure, Chemistry and Function of Proteins and Nucleic acids

3. Bioenergetics: Pathways of Glucose, Fat and Amino acid metabolism

CAT ONE

4. Biomembrane Chemistry

5. Introduction to Enzymology

6. Biochemistry Techniques: Preparation of buffers and PH measurement

7. Biochemistry Techniques: Chromatography, Column, Paper, Gas-Liquid Chromatography

CAT TWO

8. Biochemistry Techniques: Electrophoresis, Precipitation, Colorimetry, Spectrophotometry, Flame Photometry

EXAMINATIONS

PROTEIN

Cells as chemical reactors• Living organisms obey the laws of chemistry and

physics– Can think of cells as complex chemical reactors in

which many different chemical reactions are proceeding at the same time

• All cells are more similar than different if looked at on the inside!– Strip away the exterior and we see that all cells need

to accomplish similar tasks and in a broad sense they use the same mechanisms (chemical reactions)

– This MAY reflects a singular origin of all living things!

LUCA (Last Universal Common Ancestor)

Some key similarities among all types of cells• All cells use nucleic acids (DNA) to store

information– RNA viruses, but not true cells

(incapable of autonomous replication) – All cells use nucleic acids (RNA) to access

stored information• All cells use proteins as catalysts

(enzymes) for chemical reactions– A few examples of RNA based enzymes, which

may reflect primordial use of RNA • All cells use lipids for membrane

components– Different types of lipids in different types of

cells • All cells use carbohydrates for cell walls (if

present), recognition, and energy generation

• Biologically important macromolecules are “polymers” of smaller subunits

• Created through condensation reactions

Carbohydrates : simple sugarsLipids : CH2 units

Proteins : amino acidsNucleic acids : nucleotides (Base,

Sugar and Phosahate)

Macromolecule Subunit

Where do the subunits come from? • All cells need a source of the atomic components of the

subunits – (C, O, H, N, P, and a few other trace elements )

There are several possibilities to acquire them. They include;i. Some cells can synthesize all of the subunits given these

atomic components and an energy sourceii. Some cells can obtain these subunits from external sourcesiii. Some cells can convert other compounds into these

subunits

• We will discuss further in section on Bioenergetics

Carbohydrates• All have general formula CnH2nOn (hydrates

(H2O) of carbon) • A variety of functions in the cell

– Large cross-linked carbohydrates make up the rigid cell wall of plants, bacteria, and insects

– In animal cells, carbohydrates on the exterior surface of the cell serve a recognition and identification function

– A central function is energy storage and energy production !

Carbohydrates – Cell structure:

– Cellulose, LPS, chitin

Cellulose in plant cell walls Lipopolysaccharides (LPS) in bacterial cell wall

Chitin in exoskeleton

Carbohydrate Structure

Monosaccharides may also form part of other biologically important molecules

• Complex carbohydrates are built from simple sugars – Most often five (pentose) or six (hexose) carbon

sugars – Numerous –OH (hydroxyl) groups can form many

types of “cross links” – Can result in very complex and highly cross linked

structures ( cellulose, chitin, starch, etc.)

Carbohydrate StructureA Few Examples

• Triose (3 carbon)– Glyceraldehyde

• Pentose (5 carbon)– Ribose

Carbohydrate StructureExample of two hexoses

– Glucose Galactose

– What’s the difference? Both are C6H12O6

• They are isomers of one another!• Same molecular formula, but different structure (3D-

shape).February 14, 2013 15GKM/CHE 214/LEC 01/SEM 02/2013

Carbohydrate Structure • Monosacharides can be joined to one another to form

disaccharides, trisaccharides, ……..polysaccharides

– Saccharide is a term derived from the Latin for sugar (origin = "sweet sand")

• Carbohydrates classified according to the number of saccharide units they contain. – A monosaccharide contains a single carbohydrate, over

200 different monosaccharides are known. – A disaccharide gives two carbohydrate units on hydrolysis. – An oligosaccharide gives a "few" carbohydrate units on

hydrolysis, usually 3 to 10. – A polysaccharide gives many carbohydrates on hydrolysis,

examples are starch and cellulose.

Ring (cyclic) form

Pentoses and hexoses are capable of forming ring (cyclic) structures. An equilibrium exists between the ring and open form.

Linear form

Fructose

Glucose

The carbonyl group reacts with the –OH group on the second to the last carbon

Condensation reaction

Two simple sugars can polymerize to form a disaccharide. For example, galactose reacts with glucose to form lactose, which is the sugar found in milk. Lactose on the other hand can be hydrolyzed to form the two monosaccharodesthe enzyme by lactase

Glycosidic bond

•The type of chemical linkage between the monosaccharide units of disaccharides, oligosaccharides, and polysaccharides, which is formed by the removal of a molecule of water (i.e. a condensation reaction).

•The bond is normally formed between the carbon-1 on one sugar and the carbon-4 on the other.

•An α-glycosidic bond is formed when the –OH group on carbon-1 is below the plane of the glucose ring and a β-glycosidic bond is formed when it is above the plane.

•Cellulose is formed of glucose molecules linked by 1-4 β-glycosidic bonds, whereas starch is composed of 1-4 α-glycosidic bonds.

They are a special type of isomers of one another. Called anomers

α-isomer β-isomer

Two common small carbohydrates

Glyceraldehyde Ribose

Complex Carbohydrates

• CelluloseMost abundant carbohydrate on the planet!

– Component of plant cell walls– Indigestible by animals

• β 1-4 bonds

• Starch– Energy storage molecule in plants – Can be digested by animals

• α 1-4 bondsFebruary 14, 2013 22GKM/CHE 214/LEC 01/SEM 02/2013

February 14, 2013 GKM/CHE 214/LEC 01/SEM 02/2013 23

Complex Carbohydrates

• Glycogen– Branched chain polymer of glucose– Animal energy reserve– Found primarily in liver and muscle

• α 1-4 & α 1-6 bonds

• Glycogen

Cellulose• Cellulose is a linear polysaccharide

in which some 1500 glucose rings link together. It is the chief constituent of cell walls in plants.

• Human digestion cannot break down cellulose for use as a food, animals such as cattle and termites rely on the energy content of cellulose.

• They have protozoa and bacteria with the necessary enzymes in their digestive systems.

Starches • Starches are carbohydrates in which 300 to

1000 glucose units join together. It is a polysaccharide used to store energy for later use.

• Starch forms in grains with an insoluble outer layer which remain in the cell where it is stored until the energy is needed. Then it can be broken down into soluble glucose units.

• Starches are smaller than cellulose units, and can be more readily used for energy. In animals, the equivalent of starch is glycogen, which can be stored in the muscles or in the liver for later use.

Has α-1,6 bonds glycosidic linkages

polysaccharides can be linked to other molecules to form glyco-proteins and glyco-lipids

GlycoproteinsSome examples

• Polysaccharide component of antibodies has major effect on antibody function

• Polysaccharides attached to proteins on surface of red blood cells (RBC) determine blood type (A,B,O) . See next slide

– Polysaccharides are attached to proteins in the Golgi apparatus through a process of post-translational modification

• Different types of cells do different post-tranlational modifications

April 12, 2023 29GKM/BMLS/SEM2/LEC 02/2012

GlycoproteinsMediate Cell Recognition

Your ABO bloodtype isdetermined by what sugarsyou have in a particularoligosaccharide side chainon one of the proteins thatlies on the surface of your red blood cells

Other Functions Of Glycoproteins

Contact Inhibition Cells stop growing when they contact neighbors This function is disrupted in some cancers

Protein Turnover Many glycoproteins have sialic acid residues at the end of the

carbohydrate chain. Loss of these sialic acid residues indicatesthe protein is old and ready to be turned over.

Antifreeze Some fish that live in cold water produce glycoproteins that lower

the freezing point of their body’s water, thereby enabling them to survive the cold water

Hiding Viruses Some viruses can modify their cell surface proteins to mimic the

native glycoproteins, thereby hiding from the host’s immune system

Glycolipids• Polysaccharides can be attached to lipid molecules

•An outer-membrane constituent of gram negative bacteria, LPS, which includes O-antigen, a core polysaccharide and a Lipid A, coats the cell surface and works to exclude large hydrophobic compounds such as bile salts and antibiotics from invading the cell.

•O-antigen are long hydrophilic carbohydrate chains (up to 50 sugars long) that extend out from the outer membrane •While Lipid A (and fatty acids) anchors the LPS to the outer membrane.

Lipids

• Lipids include the following;– Fatty acids (Polymers of CH2 units)– Glycerol– Triglycerides– Other subunits (phosphate, choline, etc) may be attached

to yield “phospholipids”• Charged phosphate groups will create a polar molecule with a

hydrophobic (nonpolar) end and a hydrophillic (polar) end

Lipids

Phospholipids

Function– Energy Storage

• Triglycerides

– Cell membranes and cell compartments– Bi-layer structure

• Outer or plasma membrane• Nuclear membrane• Internal structures

– ER, Golgi, Vesicles, etc.

Phospholipid bilayer

Hydrophillic heads

Hydrophobic tails

Steroids

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