BASIC CHEMISTRY AND CHEMICAL COMPOSITION

• living organisms are made up of chemicals continuously interacting to drive physiologic

processes in maintenance of life

Basic chemical terms

1. Matter

1. anything that occupies space and has mass

2. Energy

1. Has no mass but can be measured.

2. drives all the chemical reactions in the body

3. the sun is the ultimate source of energy in the planet

4. Energy is captured by plants and stored in high energy bonds in the process of
photosynthesis.

3. Elements - fundamental substance composing of matter

• 4. Atoms

• Building block of elements.

• a particular element has a unique physical and chemical property.

• Contains a dense inner core called nucleus.

The nucleus contains protons (positively(charged particles and neutrons ( with no charge ). Surrounding
the nucleus is a region containing negatively charged particles called electron.

5. Molecule - Combination of two or more atoms of the same element

held together by chemical bonds

6. Compound - Two or more atoms of different elements bound together.

7. Mixtures - Substance composed of two or more compounds physically intermixed together.

Has 3 types

1. Solution - Homogeneous mixture of two or more components.

- Composed of the solvent and solute.

- The substance present in greatest quantity is called solvent.

- Water is the body’s chief solvent.

- On the other hand, the substance present in smaller amount is the solute.

2. Colloids - heterogeneous mixture that appear milky or translucent.

Example : gelatin, cytosol

3. Suspension- heterogeneous mixture with large, often visible solutes.

Example: blood

8. Ions - charged particles.

- called Cationswhen positively charged.

- Anionswhen negatively charged

- Ions dissolved in solution are called electrolytes

9. Bonds - Chemical union of two or more atoms. Can be ionic, covalent or hydrogen bond.
Types of bonds

1. Ionic bond - electrons are completely transferred from one

atom to another.

An electron rich atom ( negatively charged ) transfers electrons to electron defi cient atom ( positively
charged )

Ex. Na+ + Cl- → NaCl

2. Covalent bond - Electrons are shared by the atoms.

Example: O2

3. Hydrogen bond - Hydrogen atoms already linked covalently to one electronegative atom is
attracted by another electronegative atom.

PATTERNS OF CHEMICAL REACTION

1 . synthesis : A + B → AB.

- A bigger compound is formed by the union of two or more atoms.

- In terms of metabolism, synthetic reactions are called anabolic.

- Synthetic reactions require energy

2. Decomposition: AB→A+B.

- A large molecule is broken down into constituent parts

- In the body, these types of reactions are called catabolic.

- These reactions release energy stored in the bonds between the atoms.

3. Exchange or displacement: AB+C→AC+B / AB+CD→AD+CB.

-Involves simultaneous synthesis and decomposition reactions wherein bonds are both broken and
made

CHEMICAL CONSTITUENTS OF LIVING MATTER

Compounds in the body are classifi ed as proteins, carbohydrates, lipids and nucleic acids.

A. CARBOHYDRATES-- Hydrates of carbon.

- Contain hydrogen, oxygen and carbon.

- Can be monosaccharides, disaccharides or polysaccharide

Some functions of carbohydrates

1. Structural

Ex. Cellulose, chitin

2. Energy storage

Ex. Starch, glycogen

3.Transport function

Ex. Glycoproteins in plasma like transferrin and thyroglobulin

4.Regulatory function

Ex. Some glycoproteins such as FSH, LH, TSH

5.Catalytic function

Ex. Some glycoproteins such as ribonuclease, deoxyribonuclease

6.Antigen-antibody interactions

Ex. Interferon, Rh factor

7. Cell lubrication and supportive function

Ex. Sialoglycoproteins

8. Components of cellular membrane

Ex. prothrombin, fi brinogen

9. Components of protective cellular coats

B. LIPIDS
Group of compounds with diverse chemical structure and composition, sharing the common property of
being insoluble in water but soluble in other lipids and organic compounds such as ether, chloroform
and alcohol.

- Usually classified according to their solubility

- Can be classified as simple lipids, complex lipid and precursor or derived lipids

Functions of lipids

1. As membrane structural components

2. Intracellular storage depot of metabolic fuel

3. Transport form of metabolic fuel

4. Receptors in nerve ending membranes

5. Determinants of immunologic specific city

6. Enzyme cofactors

C. PROTEINS

polymer of amino acids

CLASSIFICATION ACCORDING TO:

A. Composition

1. Simple protein – contain amino acids only

2. Compound protein - complex or conjugated with non-amino acid

e.g. Lipoproteins, Glycoproteins

B. Conformation

1. Fibrous

e.g. Collagen, Elastin, Keratin

2. Globular

e.g. Enzymes, Albumin

C. PROTEINS

polymer of amino acids

CLASSIFICATION ACCORDING TO:

A. Composition

1. Simple protein – contain amino acids only

2. Compound protein - complex or conjugated with non-amino acid

e.g. Lipoproteins, Glycoproteins

B. Conformation

1. Fibrous

e.g. Collagen, Elastin, Keratin

2. Globular

e.g. Enzymes, Albumin

Biologic functions of proteins

1. Catalytic role

Ex. Enzymes

2. Contraction

Ex. Actin and myosin

3. Gene regulation

Ex. Histones, non-histone nuclear proteins

4. Transport

Ex. Transferring

5. Protection

Ex. fi brin, immunoglobulin

6. Regulatory

Ex. Protein hormones

7. Structural

Ex. Collagen

NUCLEIC ACIDS

- made up of nucleotides, a molecule composed of a nitrogenous base, phosphate and pentose sugar

DNA - central information storage molecules

- Carry the hereditary message of the organism

RNA - Needed in the synthesis of cell protein

Ex. tRNA,mRNA,rRNA

Central dogma

Lesson Number 3
CELLULAR STRUCTURES AND FUNCTIONS

The cell is the smallest unit of living structure capable of independent existence, composed of a
membrane-enclosed mass of protoplasm and containing a nucleus. Within these cells, are specialized
structures called organelles each performing specific function.

TWO MAJOR CLASSES OF CELLS

1. Prokaryotic cells

- are the simplest and smallest cells

- first to arise in biological evolution, some 3 billion years ago

- generally solitary with the nuclear material unenclosed in a membrane

2. Eukaryotic cell

- much larger, more complex, with a wider range of diversity and differentiation

- arose perhaps a billion years after the prokaryotes

- multicellular and provided with a nuclear membrane

Functions of the Cell

1.Basic unit of life

2.Protection and support

3.Movement

4.Communication

5.Cell metabolism and energy release

6.Inheritance

Physiologic Properties of the Cell

1. Irritability/Excitability

2. Conductivity

3. Contractility

4. Absorption and secretion

5. Excretion

6. Respiration

7. Growth and reproduction

8. Organization

Principal Parts of the Cell

1. Cell membrane

2. Cytoplasm

3. Nucleus

CELL MEMBRANE(Plasma membrane/ Plasmalemma

- defines the extent of the cell

- appears as a trilaminar structure under the electron microscope formed of an inner and outer protein
layer and a middle lipid layer

- membrane lipids (mostly phospholipids) have a hydrophilic phosphate (polar) end and a hydrophobic
(non-polar) end

- the hydrophilic phosphate heads are exposed on the outer and inner surfaces and the hydrophobic
tails apposed to each other in the center of the membrane

- proteins make up more than 50% of the membrane weight and maybe an integral membrane protein
or a peripheral membrane protein

- integral membrane proteins are firmly inserted in the lipid bilayer and are mainly involved in transport
functions

- peripheral membrane proteins are not embedded in the lipid at all, some functions as enzymes; others
serve mechanical functions

- carbohydrate components are usually in the form of branching oligosaccharide chains forming the
glycocalyx which are necessary for cell recognition and adhesion
 • Membrane Functions

• 1. Gives shape to the cell

• 2. Separates the cell from its environment

• 3. Serves as recognition sites acting as antigenic determinants which render the cell surface its
immunological properties

• 4. Serves as a selective barrier to prevent harmful substances to disperse freely

• it allows some substances to pass while excluding other

Transport Mechanisms in the Selective Passage of Particles Inside the Cells

1. Passive processes

- movement of substances from an area with a higher concentration to an area with a lower
concentration without energy expenditure.

Energy source: Kinetic energy

a. Simple diffusion

- net movement of particles from an area of higher concentration to an area with a lower concentration,
that is, along their concentration gradient.

b. Osmosis

- simple diffusion of water through a selectively permeable membrane

c. Facilitated diffusion

- same as simple diffusion, but the diffusing substance is attached to a lipid soluble carrier protein

d. Filtration

- movement of water and solutes through a semi-permeable membrane from an area with higher
hydrostatic pressure to an area with a lower hydrostatic pressure, that is, along a pressure gradient

2. Active processes

- movement of substances with or against the concentration gradient which requires the expenditure of
energy

Energy source: Hydrolysis of ATP

a. Active transport (solute pumping)

- movement of a substance through a membrane against a concentration or electrochemical gradient

and requires a membrane carrier protein

b. Exocytosis

- secretion or ejection of substances enclosed in a membranous vesicle which fuses with the plasma
membrane and ruptures, releasing the substance to the exterior

c. Endocytosis

- engulfed extracellular substance are brought to the cytoplasm in a membrane-limited vesicle

d. Phagocytosis

- cell eating, insoluble substances are engulfed and are enclosed in a vesicle known as phagosome

e. Pinocytosis

- cell drinking, engulfment of small amount of fl uid enclosed in pinocytic vesicles

f. Receptor mediated endocytosis

- external substances binds to membrane receptors and are engulfed with their receptors
II. CYTOPLASM

- this is the protoplasm outside the nucleus which contains the different organelles and inclusions

- in the usual H and E stains, it is acidophilic or reddish in color and this is due to the presence of
proteins in the cytoplasm

- it is colloidal in nature ( dispersed particles larger than 1 millimicron not exceeding 100 millimicra)

- the clear fl uid portion in which the particles are dispersed is called cytosol

- divided into an outer gel-like ectoplasm and an inner more liquefied endoplasm

Formed Elements of the Cytoplasm

1. Organelles

2. Inclusions

3. Cytoskeleton

1. ORGANELLES

- considered to be metabolically active internal organs organs carrying out specific essential functions

- all are bounded by membranes except for the free ribosomes

1. ORGANELLES

- considered to be metabolically active internal organs organs carrying out specific essential functions

- all are bounded by membranes except for the free ribosomes

a. Mitochondria/ Chondriosomes

- under the EM appears as a double layered structure containing an outer and an inner layer thrown into
infoldings called cristae

- within the mitochondria are matrix granules containing oxidative enzymes and a circular DNA of its
own

- concerned primarily with the production of energy & are abundant in cells with high metabolic rates

- its primary function is to synthesize Adenosine Triphosphate (ATP) and is the source of energy of cells

- traditionally called the powerhouse of the cell

- additional functions includes accumulation of calcium, synthesis of nucleic acids and proteins, and
oxidation of fatty acids

b. Ribosomes

- are protein synthesizing organelles

- composed of protein and ribosomal RNA

- maybe found free or bound to the endoplasmic reticulum

- ribosomes attached to the ER synthesized proteins destined for extracellular use and those proteins
synthesized by the free ribosomes are destined for intracellular consumption

c. Endoplasmic reticulum

- a complex network of paired membranes, saccules vacuoles, and tubules with flattened cisternae

i.Rough or Granular ER –

contains bound ribosomes hence concerned with protein synthesis

ii.Smooth or Non-granular ER

does not contain ribosomes

necessary for lipid metabolism, steroid hormone synthesis, formation of HCL in the stomach, and drug
detoxification in striated muscles, it is concerned with the release and recapture of calcium ions

d. Golgi complex (Dictyosomes)

- consists of saccules, vesicles, and vacuoles arranged in parallel stacks

- presents with two surfaces, a convex (cis face) or immature surface and a concave (trans face) or
maturing surface

- functions to accumulate and concentrate the secretory products of the cell

- it also packages hydrolytic enzymes for delivery toward the lysosomes

- site of sulfation in cells

• e. Lysosomes

• - these are small, dense bodies of varying sizes and shapes limited by a membrane and contain
hydrolytic enzymes for intracellular digestion

• - these enzymes are called acid hydrolases

• - lacks oxidases and catalase

• - plays an important role in cellular defense against foreign substances

• - participates in the normal replacement of cell components

Types of Intracellular Digestion

1. Autophagy- controlled degradation of organelles in a healthy cell

2. Heterophagy- degradaf. Peroxisomes/Microbodies

- membrane limited bodies of lower density than lysosomes

- were found to lack hydrolases but contain oxidases and catalase

- oxidases are used for fatty acid oxidation and catalase breaks down hydrogen peroxide to water and
oxygen

- generates energy by oxidation but differ from mitochondria, in that, they are unable to store energy

- energy generated is dissipated as heat and may contribute to the maintenance of body
temperaturetion of exogenous material taken into the cell

g. Newly described organelles

i. Melanosomes

- pigment granules formerly considered to be inert, have now been found to have a highly organized
internal structure and to have enzymatic activities (tyrosinase)

ii. Secretory granules –

formerly considered to be simply stores of cell product, are now found to be bounded by an
enzymatically active membrane

II. INCLUSIONS

- metabolically inert accumulations of cell products, are dispensable and often temporary constituents
of cells

- usually not membrane bound

1. Glycogen

storage form of carbohydrate in animal cells

polymer of D-glucose

stored principally in the liver and skeletal muscles

2. Lipid

serves as an energy source

used by the cell for the synthesis of membranes

mostly stored in the adipose tissues

3. Pigments

Exogenous-Carbon or coal dust

Endogenous

i. Lipofuscin

ii. Melanin

iii. Hemoglobin

iv. Bilirubin

4. Crystals

- least common among the inclusions eg. crystals of Reinke ( found in the interstitial cells of the testis)
and crystals of Charcot-Bottcher (found in the Sertoli cells of the testis

III. CYTOSKELETON
neither organelles nor inclusions - responsible for the gel-like consistency of the cytoplasm

- forms the structural support or framework of the cell

Principal Components

1. Microfilaments

- thinnest cytoskeleton (7-8nm dia)

- composed of actin proteins that interact with myosin to produce contraction

- plays a role in cellular movements endocytosis, cytoplasmic streaming constriction of dividing cells and
maintenance of cell shape

2. Intermediate fi laments

- about 10nm in diameter

Examples:

Keratin- found in epithelial cells

Vimentin- found in mesenchymal cells

Desmin- found in muscle cells

Glial fibrillary protein- found in glial cells of the nervous system

Neurofilaments- found in neurons

3. Microtubules

- thickest cytoskeleton (25nm in dia)

- composed of 13 protofi laments

Forms of Microtubules

a. Centrioles

- cylindrical groups of 9 triplet microtubules

- form the mitotic spindle during mitosis

- determine the polarity of the cell

- give rise to basal bodies

- capable of self duplication

b. Basal bodies

- anchoring points for cilia and flagella

c. Cilia

- a membrane modification composed of 9 doublet microtubules

- motile projections from cell surfaces characterized by a rapid forward stroke and a slow backward
movement

- found in the cells lining the upper respiratory tract

d. Flagella

- another cell membrane modification composed of 9 doublet microtubules

- found on the tail of the spermatozoa

Nucleus
is the control center of the cell

- repository of genes which are the carriers of hereditary traits for an Individual

- contains irregular clumps of chromatin scattered throughout the nucleoplasm

- chromatin consists of nucleic acids and associated histone proteins

- deoxyribonucleic acid (DNA) is the principal nucleic acid of chromatin

- a portion of the DNA that is inactive is condensed and are called heterochromatin, whereas other
portions that are being transcribed are in an extended state called euchromatin

- DNA contains the information that directs protein synthesis. It influences the structural and functional
characteristics of the entire organism because it directs protein synthesis.

- in eukaryotes, are provided with an envelope or nuclear membrane which appears as a double
membrane perforated with pores which provides a channel for movement of molecules between the
cytoplasm and the nucleoplasm

- contains one or two nucleoli that consist mainly of Ribonucleo-proteins

Cell Cycle

Interphase cycle (18-24 hours)

a. inactive or resting phase

b. the entire sequence of events transpiring from the close of one nuclear division to the beginning of
the next

Phases of cell cycle

1. G1 (gap1) phase

- follows telophase of mitosis

- no DNA synthesis but RNA and protein synthesis occurs

- longest phase but with the most variable length (may occupy 30-50% of the total time of interphase)

2. G0 phase

- cells that pull out of the cycle

- preparation for mitosis are suspended

- some cells re-enter the cycle while some are unable to because they are terminally differentiated

3. S (Synthesis) phase
- DNA synthesis/replication occurs

- DNA doubles in roughly occupy 35-45% of interphase

4. G2 phase

- final preparation before cell division

- new DNA is rapidly complexed with chromosomal proteins

- may occupy about 10-20% of interphase

Cell Division

- shortest period of the cell cycle

- division of nucleate cells consists of two distinct but integrated activities, nuclear division (karyokinesis)
and cytoplasmic division (cytokinesis)

- in general, cytokinesis begins after nuclear division but in many instances it may be deferred or entirely
lacking

Types of Nuclear Division

1. Mitosis

- nuclear division of vegetative or somatic cells ( contains diploid number of chromosomes = 46 )

2. Meiosis- occurs in conjunction with formation of reproductive cells/gametes (contains haploid

number of chromosomes = 23 )

Mitosis

• 4 Phases

• 1. Prophase

• i. chromosomes progressively shorten and thicken to form double structures

• ii. nucleolus gradually disappears

• iii. mitotic apparatus begins to form

• iv. degeneration of the nuclear membrane

• 2. Metaphase

• i. double chromosomes occupy the plane of the equator of the centromere

3. Anaphase

i. separation of sister chromatids and passage as daughter chromosomes to the opposite poles

4. Telophase

i. new nuclear membranes constructed

ii. mitotic apparatus gradually disappears

iii. nucleoli are reformed

Significance of Mitosis

a. precise and equal distribution of chromosomes can be carried through cell generation after cell
generation