Introduction to Biochemistry

• Definition of Biochemistry

• science concerned with the chemical constituents of living cells and with reactions and processes
they undergo

• deals with cell biology, molecular biology and molecular genetics

Relevance of Biochemistry

• understanding of the chemical processes associated with living cells

• knowledge of biochemistry is essential to all life sciences

 biochem-genetics

 biochem-physiology

 biochem-immunology

 biochem-pharmacology

 biochem-toxicology

 biochem-pathology

 biochem-MEDICINE

• concerned with entire spectrum of life forms

• biochemical researches have impact on nutrition and preventive medicine

• Biochemical Evolution

• all living things make use of the same types of biomolecules; all use energy

• Biochemical Evolution

• “the fundamental similarity of cells of all types makes it interesting to speculate on the origins of
life”

 both cells and biomolecules must have arisen from very simple molecules, such as H 2O,
CH4, CO2, NH3, N2, and H2

• Biomolecules

Organic chemistry: the study of the compounds of carbon and hydrogen with their derivatives

• the cellular apparatus of living organisms is made up of carbon compounds

 • Biomolecules

• biomolecules are part of the subject matter of organic chemistry

• the reactions of biomolecules can be described by the methods of organic chemistry

• Biomolecules

• The experiment of Friedrich Wöhler in 1828

• Biomolecules

• living cells include very large molecules (proteins, nucleic acids, polysaccharides, lipids)

• these biomolecules are polymers (Greek: poly + meros, many + parts)

• What are Biomolecules?

• Biomolecules are molecules found in living matter.

• Two broad types: Small molecules and macromolecules

• Importance of Macromolecules:

a) Essential structures for the basis of life

b) Control and regulate these processes

c) Responsible for energy exchanges, irritability,

metabolism, mobility and reproduction

• Biomolecules

– they are derived from monomers (Greek: mono + meros, single + part)

--amino acids --> proteins

--nucleotides --> nucleic acids

--monosaccharides --> polysaccharides

--glycerol and 3 fatty acids --> lipids

• Informational Macromolecules

• Level of Organization of Human Organism

Functional group: an atom or group of atoms that shows characteristic physical and chemical properties

• Relative Abundance of Important Elements

• Gases present in the atmosphere of the early earth included NH 3, H2S, CO, CO2, CH4, N2, H2, and
H2O but not O2

Enzymes: a class of proteins that are biocatalysts

• the catalytic effectiveness of a given enzyme depends on its amino acid sequence

Genetic code: the relationship between the nucleotide sequence in nucleic acids and the amino acid
sequence in proteins

• theories of the origin of life consider how such a coding system might have arisen

The Bioorganic & Bioinorganic chemicals

• Water – 75%

• Inorganic elements

– Major elements – N, Na, Mg, P, S, Cl, K and Ca

– Trace elements – Fe, Zn, I

• Organic compounds

A. Nucleic acids

B. Proteins

C. Carbohydrates

D. Lipids

Prokaryotes vs Eukaryotes

• Prokaryote: “before the nucleus”

– single-celled organisms

– includes bacteria and cyanobacteria

• Eukaryote: “true nucleus”

• contains a well-defined nucleus

• single-celled (yeasts and Paramecium), multicellular (animals and plants)

 • Eukaryotic Versus Prokaryotic Cells

eukaryotic cell

a. The nuclear body is bounded by a nuclear membrane

b. It contains one or more paired, linear chromosomes composed of (DNA)

c. A nucleolus is present.
d. The nuclear body is called a nucleus.

prokaryotic cell
a. The nuclear body is not bounded by a nuclear membrane.
b. It usually contains one circular chromosome composed of deoxyribonucleic acid (DNA) associated with
histone-like proteins.
c. There is no nucleolus.
d. The nuclear body is called a nucleoid .

2.) cell division

eukaryotic cell
a. The nucleus divides by mitosis.
b. Haploid (1N) sex cells in diploid or 2N organisms are produced through meiosis

prokaryotic cell
a. The cell usually divides by binary fission. There is no mitosis.
b. Prokaryotic cells are haploid Meiosis is not needed.

Cell Parts and Their Functions

3 Basic Parts of a Cell

• Animal Cell

• Differences Between Plant and Animal Cell

• cell membrane - the thin layer of protein and fat that surrounds the cell. The cell membrane is
semipermeable, allowing some substances to pass into the cell and
blocking others.

centrosome - (also called the "microtubule organizing center") a small body located near the
nucleus The centrosomes is where microtubules are made.

cytoplasm - the jellylike material outside the cell nucleus in which the organelles are located.

• Golgi body - (also called the Golgi apparatus or golgi complex) a flattened, layered, sac-like
organelle that looks like a stack of pancakes and is located near the nucleus. The Golgi
 body packages proteins and carbohydrates into membrane-bound vesicles for "export" from the
cell.

lysosome - (also called cell vesicles) round organelles surrounded by a membrane and containing
digestive enzymes. This is where the digestion of cell nutrients takes place.

• nucleolus - an organelle within the nucleus - it is where ribosomal RNA is produced.

nucleus - The nucleus controls many of the functions Of the cell (by controlling protein synthesis)
and contains DNA (in chromosomes).

ribosome - small organelles composed of RNA-rich cytoplasmic granules that are sites of protein
synthesis.

• rough endoplasmic reticulum - (rough ER) a vast system of Interconnected, membranous,

infolded and convoluted sacks. Rough ER transports materials through the cell and produces
proteins in sacks called cisternae (which are sent to the Golgi body, or inserted into the cell
membrane).

smooth endoplasmic reticulum - (smooth ER) a vast system of interconnected, membranous,

infolded and convoluted tubes. Smooth ER transports materials through the cell. It
contains enzymes and produces and digests lipids (fats) and membrane proteins.

• Plant Cell

 non living structure that surrounds the plant cell.

 protects + supports the cell.

 made up of a tough fiber called cellulose.

Mitochondria

Vacuoles
Chloroplasts (Plant cells only )

 contains a green pigment known as chlorophyll which is important for photosynthesis.

Chloroplasts

• Nucleus

• Contains nucleolus and chromatin

• Location of main genome

• Mitochondrion
 • Site of oxidation reactions for the production of energy

• Chloroplast

• Photosynthetic organelle

• Double-membrane

• Endoplasmic reticulum

• Attached to cell membrane and nuclear membrane

• Rough and smooth ER

• Golgi apparatus

• Involved in protein secretion from the cell

• Site in which sugars are linked to other cellular components

• Lysosomes

• Secretes hydrolytic enzymes

• Peroxisomes

• Contains the enzyme catalase

• Vacuole

• Isolate waste substances that are toxic to the plant

Chemical Composition of Living Matter

• Water – 70-90% (free and bound water)

• Solids – 10-30%

• Inorganic substances – 1% (Na, K, Ca, Mg, NH4, Cl-, SO4, PO4-3, CO3-2, etc.

• Traces of Fe, I2, Cu, Mn, Co, Zn are also present in combination with organic radicals

• Rest- organic substances

Water

• This is the major component of the cell and is often referred to as an inert space filter in a living
organism.

• It is a strong dipole and has a high dielectric constant.

• It is highly reactive with unusual properties different physically and chemically from other
common liquids.

• Water and its ionization products H+ and OH- are important factors in determining the structure
and biological properties of proteins, nucleic acids, lipids, and other cell components.

IMPORTANCE OF WATER

• Supports existence of plant and animal life

• Every activity of every cell in the body takes place in a water environment.

• Properties of Water

• It is a universal solvent

• It is an ideal biologic agent or medium for the ionization of substances and therefore hastens
chemical reactions

• It has a high specific heat, that is, it takes up more heat to raise its temperature through 1 oC,
thus allowing the body to store heat effectively without greatly raising its temperature.

• It possesses a high latent heat of evaporation

• It has the capacity to conduct heat readily

• Water as an ideal biologic agent

• Water is a dipole, a molecule with chemical charge distributed asymmetrically about its
structure.

• Hydrogen bonding enables water to dissolve many organic biomolecules that contain functional
groups which can participate in hydrogen bonding.

• Hydrogen bonds account for the surface tension, viscosity, liquid state at room temperature, and
solvent power of water.

• Compounds that contain O, N or S can serve as hydrogen bond donors or acceptors.

IMPORTANCE OF WATER

• Essential in the processes of digestion, circulation, elimination and the regulation of body
temperature.

• Acts as a solvent, it dissolves sugar, salt and alcohol.

• Water intake = water output

Water intake > water output = edema

Water intake < water output = dehydration

PROPERTIES OF WATER

• Pure water is colorless, odorless, tasteless

Tap water taste comes from dissolved gases and minerals.

Blue color of oceans, and lakes is due to reflection of the sky and presence of finely divided solid
materials .

• Water volume at room temperature contracts as it cools but further cooling (4 oC ) causes
volume expansion (ice), decreasing its density. (lighter).

• Density of water is 1g/mL; (mass at 4oC = 1g)

• Boiling point of pure water is 100oC at 1atm pressure.

• Freezing point of water is 0oC.

• Heat is necessary for water to evaporate. The amount of heat necessary so that evaporation to
take place is called heat of vaporization = 540 cal/g. (perspiration)

• For ice to melt, amount of heat required is 80cal/g.

• Calorie is the amount of heat required to change the temperature of 1g of water by 1 oC

• A WATER MOLECULE

• WHAT MAKES WATER POLAR

What is a polar bond:

• Electrons are unequally shared,more negative charge found closer to one atom.

• Due to difference in electronegativity of atoms involved in bond.

POLARITY OF WATER

• Polar nature of water molecule is responsible for its property of dissolving many materials

• The unsymmetrical distribution of electrons i.e., the bond or molecule contains (+) and (-) poles
resulting into a dipole.

• Water as Ideal Biologic Solvent

• Ionic compounds (KCl) and low molecular-weight polar covalent compounds (e.g.C 2H5OH and
CH3COCH3) dissolve in water

• Interesting and Unique Properties of Water

Each water molecule can be involved in 4 hydrogen bonds: 2 as donor, and 2 as acceptor

• Due to the tetrahedral arrangement of the water molecule

• Hydrogen Bond

• Hydrogen bonding: important in stabilization of 3-D structures of biological molecules (DNA,

RNA, proteins)

• Even though hydrogen bonds are weaker than covalent bonds, they have a significant effect on
the physical properties of hydrogen-bonded compounds