Introduction to Biochemistry

Introduction to Biochemistry

• Organisms consist of lifeless elements and molecules.
• Individually, these components are inanimate, but together they exhibit attributes of life.
• The living cell is the basic unit of life, capable of feeding, respiring, digesting, excreting, moving, and reproducing.
• The course will cover characteristics and biochemical activities of living cells.

Objectives of Biochemistry

• Define biochemistry
• Differentiate between prokaryotes and eukaryotes
• Identify important organelles of the cell
• Describe the functions of cell organelles
• Name the elements required by living organisms
• Discuss the importance of these elements in living organisms
• Describe the four classes of biopolymers

What Biochemistry Is

• Biochemistry is the "Chemistry of the living cell."
• It uses chemistry, biology, and physics to explain processes in living cells at the molecular level.
• Biochemistry enhances the fundamental understanding of life.
• It addresses important issues in medicine, health, and nutrition.
• Biochemistry has led to a greater molecular understanding of diseases like AIDS, cancer, diabetes, sickle cell anemia, and cystic fibrosis.
• Biochemistry advances biotechnology industries using biological cells, cell components, and biological properties in technically and industrially useful operations.

Three Areas of Study in Biochemistry

• Structural and Functional Biochemistry: Deals with the chemical structures and 3D arrangements of molecules.
• Informational Biochemistry: Focuses on the language for storing and transmitting biological data in cells and organisms.
• Bioenergetics: Studies the flow of energy in living organisms and its transfer between processes.

Tools for Biochemistry Studies

• Requires knowledge of chemical structures and reactivities of molecules in cellular reactions.
• Understanding the biological functions of cellular molecules is crucial
• Understanding how all the pieces and different pathways fit together

Simplicity and Elegance in Living Systems

• 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 and use the same genetic code.
• A limited number of molecular building blocks make up larger macromolecules.

Major Classes of Biomolecules

• Serve as building blocks for larger macromolecules:
  • Carbohydrates (e.g., glucose, fructose, sucrose): mainly used as sources of cellular energy
  • Lipids (fats): organic compounds not very water soluble, used as energy sources and cell membrane components
  • Amino Acids: 20 total natural amino acids used as building blocks for proteins
  • Nucleotides: 5 in total used as building blocks for DNA and RNA precursors

Macromolecules

• Building blocks are used to create macromolecules- polymer of several, hundreds, to sometimes millions of building blocks
• Macromolecules self-assemble into cellular structures and complexes
• They interact in specific ways to perform essential cellular functions like membranes (complexes of lipids and proteins).
• Interactions are weak and reversible.
• Molecules have three dimensions and shapes
• Starch and Cellulose: polymers of glucose molecules differing in how glucose monomers are linked
• Proteins/polypeptides: amino acid monomers linked together
• DNA (deoxyribonucleic acid): heteropolymer of monomeric nucleotides storing genetic information
• RNA (ribonucleic acid): heteropolymer of monomeric nucleotides involved in the transfer of genetic information encoded by DNA

Organisms

• There are two basic classes of organisms: prokaryotes (e.g., E. coli) and eukaryotes
• Eukaryotic cells will be the primary focus
• Similar processes occur in all cells, including prokaryotes, and much of our understanding of biochemistry comes from prokaryotic systems.
• Class includes plants, animals, fungi, protozoans, yeasts and some algae
• Large cells (10-100 (mu) m in diameter), 10X bigger than prokaryotes
• Surrounded by plasma membrane
  • Composed of lipids and proteins
  • Serves as chemical barrier to the outside environment
• Contain internal membranes and compartments which is a unique feature
  • Compartments = organelles
  • Organelles contain organized complexes of macromolecules that perform a certain biological function
  • Most enzymes are compartmentalized Compartmentalization results in separation of biological function
• No cell wall in animal cells
• Plants, fungi, algae generally have a cell wall

Eukaryotic Cell Structures and Functions

• Cytoplasm/cytosol: viscous aqueous environment containing molecules, nutrients, salts, and soluble proteins (20-30% protein), major site of cellular metabolism
• Cytoskeleton: 3-dimensional matrix of protein fibers providing cell shape, movement, and guides internal organelle movement
• Nucleus: contains most DNA and RNA synthesis, storage of genetic information, enclosed by a double membrane, largest organelle in eukaryotic cells
• 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
  • Smooth ER: site of lipid synthesis
  • Rough ER: site of protein synthesis via ribosomes
• Ribosomes: made up of RNA and proteins, site of protein synthesis
• Lysosomes: internal sacs bound by a single membrane, responsible for degrading obsolete cell components (internal pH ~5), degrade polymers into individual building blocks
• Golgi Apparatus: flattened vesicles of lipid/protein/sugar near smooth ER and nucleus. It is involved in protein and fat processing/trafficking to other organelles as well as distribution and shipping dept for cell materials
• Mitochondria: have double membrane, oxidative energy production occurs here as well as the "powerhouse" of the cell, form ATP, contain a circular DNA molecule like that of bacteria (own genome), believed to be descendants of bacteria engulfed by a larger cell billions of years ago = endosymbiotic hypothesis, can have over 1000 mitochondria per cell