BIOCHEMISTRY

Introduction

Organisms are made up of lifeless elements and molecules. When these substances are
considered individually they are inanimate. However, when put together in a particular
manner, they conform to the attributes of life.

The living cell is considered as the basic unit of life. It exhibits the attributes of life. It
feeds, respires, digests, excretes, moves, and reproduces.

In this unit, you will be acquainted with the characteristics and biochemical activities of
living cells.

Objectives:

At the end of the unit, you should be able to:

- define biochemistry
differentiate between prokaryotes and eukaryotes
identify the important organelles of the cell
describe the functions of these organelles
name the elements required by living organisms
discuss the importance of these elements in living organisms
describe the four classes of biopolymers

What is Biochemistry?

 - Biochemistry is simply defined as the “Chemistry of the living cell”.

 - Uses basic laws of chemistry, biology and physics to explain processes of living cells
 - Describes life processes at the molecular level
 - The study of life at the molecular level

Why study biochemistry?

Lead us to fundamental understanding of life

- Understand important issues in medicine, health, and nutrition

- Has led to greater molecular understanding of diseases such as

diabetes, sickle cell anemia, and cystic fibrosis.
 o Next frontier: AIDS, cancer, Alzheimer’s Disease

- Advance biotechnology industries

o Biotechnology is the application of biological cells, cell components, and biological properties
to technically and industrially useful operations

Three areas to study:

1. Structural and Functional Biochemistry: Chemical structures and 3D arrangements of

molecules.

2. Informational Biochemistry: Language for storing biological data and for transmitting

that data in cells and organisms.

3. Bioenergetics: The flow of energy in living organisms and how it is transferred from one

process to another.

Tools to study biochemistry:

Know chemical structures and reactivities of molecules that participate in cellular reactions
Know biological function of cellular molecules
Know how all of the pieces and different pathways fit together

LIVING SYSTEMS APPEAR COMPLEX BUT THERE IS AN UNDERLYING

SIMPLICITY AND ELEGANCE:

- Most biological compounds are made of only SIX elements: C, H, O, N, P, S

- Only 31 chemical elements occur naturally in plants and animals

- All organisms have similar biochemical pathways.

- All organisms use the same genetic code.

-Limited number of molecular building blocks make up larger macromolecules.

4 MAJOR CLASSES OF BIOMOLECULES SERVE AS BUILDING BLOCKS FOR

LARGER MACROMOLECULES:
 1. Carbohydrates: e.g. glucose, fructose, sucrose - mainly used as sources of cellular energy

2. Lipids: commonly known as fats

o - organic compounds that are not very water soluble
o - used as sources of cellular energy
o - components of cell membranes
3. Amino Acids:
o - 20 natural amino acids in total
o - Used as building blocks for proteins
4. Nucleotides:
o - 5 in total
o - Used as building blocks for DNA and RNA precursors

Building blocks are used to create macromolecules: polymer of several, hundreds, to

sometimes millions of building blocks

Examples:

Biomacromolecules:

 - self-assemble into cellular structures and complexes.

 - recognize and interact with one another in specific ways to perform essential cellular
 functions (e.g. membranes are complexes of lipids and proteins)

 - Interactions are weak and reversible

 - Molecules have three dimensions and shapes! Much of biochemistry relies on this
fact.

- Starch and Cellulose: polymers of glucose molecules that differ only by how the glucose
monomers are linked.

- Proteins/polypeptides: amino acid monomers linked together

- DNA:deoxyribonucleic acid o Heteropolymer of monomeric

nucleotides
o Storage of genetic information

- RNA: ribonucleic acid

o Heteropolymer of monomeric

nucleotides
o Involved in the TRANSFER of the genetic information encoded by DNA
Starch and Cellulose: polymers of glucose molecules that differ only by how the glucose
monomers are linked.

- Proteins/polypeptides: amino acid monomers linked together

- DNA:deoxyryribonucleic acd - Storage of genetic information

- RNA: ribonucleic acid - Heteropolymer of monomeric nucleotides

o Involved in the TRANSFER of the genetic information encoded by DNA

Biomacromolecules:

 - self-assemble into cellular structures and complexes.

 - recognize and interact with one another in specific ways to perform essential cellular

functions (e.g. membranes are complexes of lipids and proteins)

 - Interactions are weak and reversible

 - Molecules have three dimensions and shapes! Much of biochemistry relies on this

fact.

ORGANISMS:

2 basic classes of organisms

-Prokaryotes (e.g. E.coli) -Eukaryotes

We will focus on eukaryotic cells and the biochemistry that occurs in these cells.

Similar processes occur in ALL cells, including prokaryotes. In fact, much of the biochemistry
that we understand was first uncovered in prokaryotic systems.
EUKARYOTES: Typical Eukaryotic Cell – Animal

1. Class includes plants, animals, fungi, protozoans, yeasts and some algae.
2. Large cells (10-100 m in diameter). 10X bigger than prokaryotes.
3. Surrounded by a membrane called plasma membrane
i. Composed of lipids and proteins
ii. Serves as chemical barrier to the outside environment
4. Contain INTERNAL membranes and compartments. (Unique feature) i. Compartments
= organelles

ii. Organelles contain organized complexes of macromolecules that perform a certain

biological function.

iii. Most enzymes are compartmentalized

iv. Compartmentalization results in separation of biological function!! We’ll see a lot of

this phenomenon throughout the course.

5. No cell wall in animal cells.

6. Plants, fungi, algae generally have a cell wall.
7.
1. Cytoplasm/cytosol

- Viscous aqueous environment (NOT free flowing)

- Contains small molecules, nutrients, salts, soluble proteins

- 20-30% of cytosol is protein – Very concentrated

- Highly organized environment **

- A major site of cellular metabolism (e.g. glycolysis)

- Contains cytoskeleton

2. Cytoskeleton

- 3-dimensional matrix made of protein fibers

- Functions to give cells shape, allows cells to move, guides internal organelle movement.

3. Nucleus

 - Site of most DNA and RNA synthesis

 - Storage of genetic information
 - Bound by a double membrane
 - Largest organelle in eukaryotic cells
 cells

4. Endoplasmic Reticulum (ER)

 - Network of interconnected, closed, membrane-bounded vesicles

 - Attached to cell and nuclear membrane
 - Used for manufacturing, modification and transport of cellular materials
 - Two types:

* Smooth ER = site of lipid synthesis

* Rough ER = site of protein synthesis via ribosomes

 - Ribosomes are made up of RNA and proteins not bound by a membrane

5. Lysosomes

 - Internal sacs bound by a single membrane

  - Responsible for degrading cell components that have become obsolete for the cell or
organism.
 - Internal pH ~5 (very acidic)
 - Compartmentalization ESSENTIAL! Sequesters this biological activity from the rest of
the cell.
 - Enzymes in lysosomes degrade polymers into their individual building blocks.

6. Golgi Apparatus

 - Flattened vesicles of lipid/protein/sugar

 - Usually found near smooth ER and nucleus
 - Involved in protein and fat processing and trafficking to other organelles (e.g.
lysosomes, plasma membranes) – Distribution and shipping department for cell materials.

7. Mitochondria

 - Have double membrane (inner and outer)

 - Place where most oxidative energy production occurs = “powerhouse” of the cell
 - Form ATP – Convert oxygen and nutrients to energy
 - Small, typically the size of a bacterium
 - Contain a circular DNA molecule like that of bacteria (own genome)
 - Because of the double membrane, size and presence of own genome, mitochondria are
believed to be descendants of a bacteria that was engulfed by a larger cell billions of
years ago = endosymbiotic hypothesis.
 - A cell can have over 1000 mitochondria.This depends on need for energy---muscle
cells have a lot of mitochondria.

Learning Task:

1. Discuss the similarities and differences between:

a. eukaryotic and prokaryotic cells

b. animal and plant cells

2. Draw an animal cell and a plant cell. Label each part. Discuss the function of

each cell organelle.

3.What are the six major elements found in living organisms? Discuss the reasons why

only these six major elements are present in all organisms.

4.List down the monoatomic ions found in all organisms. What are the significant
 roles of these monoatomic ions in living organisms?

5. List down four noncovalent bonds of importance in biological structures. Discuss each.

6. What are the four macromolecules of life? Give the properties and functions of each.

References:

Biochemistry by: Campbell

Lehninger’s Principles of Biochemistry by; Cox, et al.

On-Line references