Biochemistry

- study of the structure, organizations, chemical compositions, functions and processes in a living organisms. - Chemistry of life

Suggested Reading: Pace, N. R. 2000. The universal nature of biochemistry. Proc. Natl. Acad. Sci. USA 98:805-808.

What makes a living thing 'alive'?

exhibit high degree of complexity & organization ability to extract, transform & utilize energy capacity to precisely self-replicate and/or self-assemble
all three attributes are ultimately due to biomolecular structure and function, which is the essence of Biochemistry

A brief overview of organic chemical principles

You should already be familiar with the following concepts from organic chemistry:
- functional groups (names & how to draw) - electronegativity & partial charges - chirality (assigning R vs S stereochemistry), enantiomers & diastereomers - acids & bases (pH values); protonation & pKa values

The types of reactions most frequently encountered in living systems are:

1. Oxidation-reduction reactions involving carbonoxygen, carbon-carbon, or carbonnitrogen bonds. 2. Intramolecular or intermolecular functional grouptransfer reactions. 3. hydrolysis of esters, ethers, and amides. 4. Elimination or addition reactions. 5. Isomerization reactions. 6. Formation of ester, thiol ester, and amide linkages.

An Overview of Biochemical Structures and Reactions that Occur in Living Organisms

Biochemical reactions utilize a limited number of elements, most prominently carbon, hydrogen, oxygen, nitrogen, sulfur, and phosphorus. Many biochemical reactions are simple organic reactions. Biochemical reactions of different types are localized to different parts in the cell. Biochemical reactions are carried out under very mild conditions in aqueous solvent.

An Overview of Biochemical Structures and Reactions that Occur in Living Organisms Biochemical reactions are frequently organized into multistep pathways. Biochemical reactions are regulated according to need by controlling the amount and activity of enzymes in the system. Most organisms depend on other organisms for their survival.

Essential Elements in Living Systems

H, O, C and N make up 99+% of atoms in the human body

Structural Heirarchy of Living Systems

Biochemistry focuses on these levels in the hierarchy of biological structure

THE CELL
- structural and functional unit of living organisms
smallest organisms (unicellular)
larger organisms (multicellular) human contains ~1014 cells

Types of Cell
1) Prokaryotic cell
- small, simple in structure, lacks some organelles and contains only one single chromosome

ex. Bacteria and blue-green algae

Eubacteria = commonly encountered in soil,water and living in or on larger organisms Archaebacteria = grows in unusual environment like salt brines, hot acid springs and ocean depths

2) Eukaryotic cell
- has complex structure composed of several organelle and a membrane-enclosed nucleus which contain the genetic information within multiple chromosomes.
cell components of higher plants and animals 1,000 10,000 larger than prokaryotic cell ex. fungi, protozoa, algae

CELLS

Major differences? Size and complexity

Parts of the Cell

Parts Functions
- bound the cell and made up of lipids and proteins - regulates the transport of molecules in and out of the cell - site for the manufacture of nucleic acids - within the nucleus - center for RNA and proteins biosynthesis

membranes

nucleus nucleolus

ribosomes
lysosomes

- tiny particles in the cell - site for manufacture of proteins

- storage of catalytic proteins

endoplasmic reticulum

- central part for the biosynthesis of macromolecules

Parts of the Cell

Parts Golgi apparatus mitochondria Functions
- storage house of the cell - involved in packaging, transport and synthesis of carbohydrates - Powerhouse of the cell - its inner membrane is the site for oxidative phosphorylation and electron transport

All cellular life has the following characteristics in common:

All cells have a CELL MEMBRANE that separates the CHAOS outside a cell from the high degree of organization within the cell. A cell without a cell membrane is NOT A CELL.

All cellular life CONTAINS DNA as its genetic material. All cells contain several varieties of RNA molecules and PROTEINS, most of the latter are enzymes.
All cells are composed of the same BASIC CHEMICALS: carbohydrates, proteins, nucleic acids, lipids

All cellular life has the following characteristics in common:

All cells REGULATE the flow of nutrients and wastes that enter and leave the cell. All cells REPRODUCE and are the result of reproduction. All cells require a SUPPLY OF ENERGY. The most common source of chemical energy used.

ORGANELLES

PLASMA MEMBRANE

(CELL MEMBRANE)
-Separates cell from its environment

-Provides mechanical strength and shape to the cell -Vital function: transport
-Plays a role in communication between cells, responsiveness to extracellular signals, muscle contraction and nerve impulse conduction

ORGANELLES

NUCLEUS
-Contains the cells blueprint: the cells hereditary info -Exerts a profound influence over all cellular metabolic activities -Contains the nucleolus which plays a major role in the synthesis of ribosomal RNA

ORGANELLES

Endoplasmic reticulum
ROUGH ER -Primarily involved in the synthesis of membrane proteins & protein for export from the cell -Rough because of the ribosomes

SMOOTH ER
- Involved in lipid synthesis

ORGANELLES

Ribosomes
-20 nm in diameter -Biosynthesis of proteins -Composed of proteins and ribosomal RNA -Composed of 2 irregularly-shaped sub units

ORGANELLES

GOLGI COMPLEX
-Involved in the packaging & distribution of cell products to internal and external compartments

-In plants, its functions include transport of substances into the cell wall and expansion of plasma membrane during cell growth

ORGANELLES

LYSOSOMES
-Functions in intracellular and extracellular digestion -Suicide bag of the cell -Contains digestive enzymes -Capable of degrading most biomolecule - Typically spherical with a diameter of 500 nm

ORGANELLES

PEROXISOMES
-Small spherical membranous organelles that contain oxidative enzymes -Involved in the generation & breakdown of toxic molecules such as peroxides -In plants, it is found in leaves that is responsible for an oxygen-consuming process in which CO2 is produced

ORGANELLES
MITOCHONDRIA
-Powerhouse of the cell
-Aerobic respiration takes place here

-Usually sausage-shaped
-Has an inner membrane which is the site for oxidative phosphorylation & electron transport chain

ORGANELLES
CHLOROPLASTS
-Found only in plants, algae and some protists
-Type of chromoplasts that are specialized for the conversion of light energy into chemical energy THYLAKOID MEMBRANE

- Chlorophyll are bound to thylakoid membrane proteins

ORGANELLES

VACUOLE
-tend to be very large and are extremely important in providing structural support, as well as serving functions such as storage, waste disposal, protection, and growth. -Many plant cells have a large, single central vacuole that

- Smaller in animal cells and are more commonly used to temporarily store materials or to transport substances.

ORGANELLES

VACUOLE

-provides the cell with structural support, protection, and acts as a filtering mechanism -prevents over-expansion when water enters the cell - are found in plants, bacteria, archaea, fungi, and algae.

ORGANELLES
MITOCHONDRIA
-Powerhouse of the cell
-Aerobic respiration takes place here

-Usually sausage-shaped
-Has an inner membrane which is the site for oxidative phosphorylation & electron transport chain

ORGANELLES
CHLOROPLASTS
-Found only in plants, algae and some protists
-Type of chromoplasts that are specialized for the conversion of light energy into chemical energy THYLAKOID MEMBRANE

- Chlorophyll are bound to thylakoid membrane proteins

ORGANELLES

VACUOLE
-tend to be very large and are extremely important in providing structural support, as well as serving functions such as storage, waste disposal, protection, and growth. -Many plant cells have a large, single central vacuole that

- Smaller in animal cells and are more commonly used to temporarily store materials or to transport substances.

ORGANELLES

VACUOLE

-provides the cell with structural support, protection, and acts as a filtering mechanism -prevents over-expansion when water enters the cell - are found in plants, bacteria, archaea, fungi, and algae.

A Comparison of Prokaryotes and Eukaryotes

Organelle Nucleus Prokaryotes No definite nucleus; DNA present but not separate from rest of cell Eukaryotes Present

Cell membrane (plasma membrane)

Present

Present

Mitochondria

None; enzymes for oxidation reactions located on plasma membrane

Present

Endoplasmic reticulum Ribosomes Chloroplasts

None Present None; photosynthesis localized in chromatophores

Present Present Present in green plants

Summary of Organelles and Their Function

Organelle Function

Nucleus Mitochondrion Chloroplast Endoplasmic Reticulum

Location of main genome; site of most DNA and RNA synthesis Site of energy-yielding oxidation reactions; has its own DNA Site of photosynthesis in green plants and algae; has its own DNA Continuous membrane throughout the cell; rough part studded with ribosomes (the site of protein synthesis) Series of flattened membranes; involved in secretion of proteins from cells and in reactions that link sugars to other cellular components Membrane-bounded sacs containing hydrolytic enzymes Sacs that contain enzymes involved in the metabolism of hydrogen peroxide Separates the cell contents from the outside world; contents include organelles (held in place by the cytoskeleton) and the cytosol Rigid exterior layer of plant cells Membrane-bounded sac (plant cells)

Golgi apparatus

Lysosomes Peroxisomes Cell Membrane

Cell Wall Central Vacuole

(Principles of Biochemistry, Zubay,1995)

Carbohydrates/Sugars
-energy source -important components of genetic materials

-synthesized by photosynthesis in plants -a gram of digested carbohydrate gives about 4 kcal of energy

 Are biological catalysts (enzymes) Are antibodies that fight antigens (bacteria and viruses) Transport molecules and ions Regulate cell function Provide structural support and mechanical strength

- structural components of biological membranes - provide energy reserves, predominantly in the form of triacylglycerols - vitamins and hormones

NUCLEIC ACIDS
RNA (ribonucleic acid) & DNA (deoxyribonucleic acid)

- information molecules - into their primary structure is encoded a set of directions that ultimately governs the metabolic activities of the living cell