MB207 Molecular Cell Biology

2. Cell Chemistry and Biosynthesis

Chemistry of life:

- based majority on carbon compounds, organized into macromolecules that are require for cells growth and function. - cells are 70% water (life depends almost exclusively on chemical reactions that take place in aqueous solution) - cell chemistry is enormously complex: even the simplest cell is vastly more complicated in its

chemistry than any other chemical system known.

Cell Chemistry and Biosynthesis

Chemical component of a cell

• Matter is made of combinations of elements.

Substances that cannot be broken down or converted into other substances by chemical means ie. Hydrogen or carbon

• Smallest particle of an element is an atom

• A molecule may consist of atoms of a single element or of different elements.

• These elements are connected by chemical bonds that hold atoms together.

Cell are made from a few types of atoms

Cells are made from atoms. Cells are made from atoms. - Atom is the smallest particle of an - Atom is the smallest particle of an elementelement - consisting of a +ve charged - consisting of a +ve charged nucleus (protons and neutrons), nucleus (protons and neutrons), surrounded by a cloud of surrounded by a cloud of -ve charged electrons. -ve charged electrons. - There are 92 naturally occurring - There are 92 naturally occurring elements, differing in protons elements, differing in protons and electrons in its atoms. and electrons in its atoms. AtomAtom - electron (held in a series of orbitals - electron (held in a series of orbitals electrostatic attraction to the electrostatic attraction to the nucleus)nucleus) - protons (positively charged, gives - protons (positively charged, gives the atomic number)the atomic number) - neutron (uncharged)- neutron (uncharged)

Atomic nucleus

Living organisms are made up of 4 main elements: C, H, Living organisms are made up of 4 main elements: C, H, N & O. This composition differs markedly from that of N & O. This composition differs markedly from that of the nonliving inorganic environment.the nonliving inorganic environment.

Chemical bonds : Chemical bonds : 1) 1) Covalent bondsCovalent bonds (sharing of electrons) - strongly bonding (sharing of electrons) - strongly bonding 2) 2) Non-covalent bondsNon-covalent bonds: ionic, hydrogen bond, Van der : ionic, hydrogen bond, Van der

Waals attraction and hydrophobic strengthWaals attraction and hydrophobic strength

70% of a cell’s weight is water

Representations of a water molecule

Covalent bond and ionic bond

2 types of chemical bonds between atoms:

a. Covalent bond: formed when 2 atoms have a pair of electrons

b. Ionic bond: formed when electrons are donated by 1 atom to another

Chlorine molecule formed by 2 atoms sharing 1 pair of electrons

Carbon dioxide molecule formed from 2 oxygen atom each sharing 2 pairs of electrons with a carbon atom

Cl2 & CO2 : examples of covalent bonds formation

Sodium Chloride: ionic bond formation

Four types of noncovalent interactions help to bring molecules together in cells

Ionic bond

• Interactions between two oppositely charged ions.

Van der Waals interactions

• interactions between two atoms that occur only if the atoms are very close to one another and are oriented appropriately.

Hydrogen bond

• polar interactions of a electropositive hydrogen that is shared by two neighboring electronegative atoms.

Hydrophobic forces

• Pushing of non-polar surfaces out of the hydrogen-bonded water network.

Covalent Hydrogen IonicVan der Waals

Hydrophobic forces

~100 kcal/mole ~3 kcal/mole ~ 5 kcal/mole ~1 kcal/mole ~3 kcal/mole

electrons shared water-water full charge

transfer fluctuating not a bond per se

organic-water can attract H-bond induced dipole entropy driven

organic-organic

strong in dry crystal

at close range only

only works in water

strongweak, orientation sensitive

weak in water weak weak

Strong Weak

Covalent > ionic > hydrogen > van der Waals

Cells contain 4 major families of small organic molecules

Are carbon-based compounds having molecular weights in the range 100 to 1000 and contain up to 30 or so carbon atoms.

Function:

monomer subunits - to construct polymeric macromolecules eg. proteins, nucleic acids, and large polysaccharides of the cell.

energy sources - are broken down and transformed small molecules in intracellular metabolic pathways.

1) Sugar (2%) polysaccharides

2) Fatty acids (2%) Fats, lipids,

phospholipids (membrane)

3) Amino Acids (15%) polypeptides,

proteins

4) Nucleotides (7%) nucleic acids

Others (4%) + H2O (70%)

Cells contain four major families of small organic molecules

Sugars Simplest - monosaccharides. General formula [CH2O]n where n is a number between 3 – 8. Polysaccharides are large molecules composed of individual sugar units. Can exist in either 2 forms, D-form and L-form, which are mirror images of

each other. Exist in either a ring or and open-chain form. Open –chain form: aldosugars or ketosugars Main functions:

• Energy source• Mechanical support e.g. cellulose• Covalently linked to protein and lipid glycoprotein or glycolipids

Condensation and hydrolysis of disaccharide

Fatty Acids

Is a long, unbranched hydrocarbon chain with a carboxyl group at one end.

Amphipathic; carboxyl group renders one end polar whereas the hydrocarbon tail is nonpolar.

Variable but usually even number of carbon atoms ranging from 12 to 20 carbon atoms per chain.

Main functions:• long-term energy storage• Act as structural components e.g. the

major building block in cell membranes• as "messengers" (hormones) that play

roles in communications within and between cells

Saturated fatty acids

Unsaturated fatty acids

Phospholipid structure and the orientation of phospholipids in membranes

Nucleotides• Nitrogen-containing ring compound linked to a five-carbon sugar.• Ribose: ribonucleotides

Deoxyribose: deoxyribonuleotides• Pyrimidines: cytosine, thymine and uracil• Purines: guanine and adenine• Main functions:

• Subunits for DNA & RNA, storage of genetic information• Short term carriers of chemical energy, e.g. ATP• Coenzyme & specific signaling molecules in the cells e.g. cAMP

The assembly of macromolecules

Energy is needed for the assembly of macromolecules, where can cells

obtain such energy?

Catalysis & the use of energy by cells

A set of enzyme-catalyzed reactions generates a metabolic pathway

Chemical reactions:

(1)catabolic pathways;

(2)anabolic or biosynthetic pathways

Cell Metabolism- Organized by enzymes

Cell metabolism

Catabolism

Anabolism

Breaks large molecules into smaller molecules; usually releases energy.

Builds large molecules from smaller ones; usually consumes energy.

The Carbon Cycle

How cells obtain energy from food???- To produce ATP, NADH

Food Molecules Are Broken Down in 3 Stages:Food Molecules Are Broken Down in 3 Stages:

a.a. Digestion (enzymatic breakdown of food molecules into Digestion (enzymatic breakdown of food molecules into monomer subunits) monomer subunits)

b.b. Partial breakdown of simple molecules to provide some energy Partial breakdown of simple molecules to provide some energy in the cytoplasm (Different metabolism pathways)in the cytoplasm (Different metabolism pathways)

c.c. Complete oxidation through respiration at the mitochondria to Complete oxidation through respiration at the mitochondria to provide more energyprovide more energy

Metabolism of Food Metabolism of Food & Energy production& Energy production

1) Break down of large 1) Break down of large macromolecules to simple macromolecules to simple subunits (amino acids, subunits (amino acids, simple sugars, fatty acids & simple sugars, fatty acids & gylcerol)gylcerol)

2) Further breakdown to Acetyl 2) Further breakdown to Acetyl CoA, production of limited amount CoA, production of limited amount of ATP and NADH (Glycolysis and of ATP and NADH (Glycolysis and Kreb Cycle)Kreb Cycle)

3) Complete oxidation of Acetyl 3) Complete oxidation of Acetyl CoA to HCoA to H22O & COO & CO22, production of , production of

large amount of NADH and ATP in large amount of NADH and ATP in mitochondria.mitochondria.

The 3 stages of cellular metabolism from food to waste products in animal cells

1st stage: Breakdown of large macromolecules to simple subunits outside cells

Digestion

Cytosol 2nd stage : Oxidation begin

Outside cell

1st stage Outside cells

2nd stage: Breakdown of simple subunits to acetyl CoA accompanied by production of limited amounts of ATP and NADH

Cytosol

Mitochondrial

3rd stage Mitochondrial

Glycolysis

Glycolysis

Glucose Pyruvate

ATP NADP

Cytosol

Pyruvate dehydrogenase

CO2 + Carbon acetyl group + coenzyme A

Aceyl CoA

Citric acid cycle

CO2

ATP

ATPATP

Oxidation phosphorylation

mitochondrion

Waste products

O2 + H2O

3rd stage

2nd stage Cytosol + mitochondrial

Mitochondrial

3rd stage: Complete oxidation of acetyl CoA to H2O and CO2 accompanied by production of large amounts of NADH and ATP

Waste product