introduction wk 1 biochem

Prentice Hall c2002 Chapter 1 1

Chapter 1 Introduction to Biochemistry

• Adenovirus: Viruses consist of a nucleic acid molecule surrounded by a protein coat


1.1 Biochemistry Is a Modern Science

• Urea was synthesized by heating the inorganic compound ammonium cyanate (1828) by Friedrich Wohler

• This showed that compounds found exclusively in living organisms could be synthesized from common inorganic substances


Two notable breakthroughs in the history of biochemistry

(1) Discovery of the role of enzymes as catalysts

(2) Identification of nucleic acids as information molecules

Flow of information: from nucleic acids to proteins

DNA RNA Protein

History of Biochemistry

• Chromosomes were discovered in 1875 by Walter Flemming and identified as genetic elements by 1902

• Nucleic acids had been isolated in 1869 by Friedrich Miescher, but their chemical structures were poorly understood


History of Biochemistry

• The idea of the gene, a unit of hereditary information, was first proposed in the mid-nineteenth century by Gregor Mendel

• 1953, James Watson and Francis Crick described the double-helical structure of DNA



1.2 The Chemical Elements of Life

• Only six nonmetallic elements: oxygen, carbon, hydrogen, nitrogen, phosphorous, and sulfur account for >97% of the weight of most organisms

• These elements can form stable covalent bonds

• Water is a major component of cells

• Carbon is more abundant in living organisms than it is in the rest of the universe


Fig 1.1 Periodic Table of the elements

• Important elements found in living cells are shown in color

• The six abundant elements are in red (CHNOPS)

• Five essential ions are in purple

• Trace elements are in dark blue (more common) and light blue (less common)


Functional groups in biochemistry

• Functional groups - specific parts of molecules involved in biochemical reactions

• Figure 1.2 shows the general formulas of:

(a) Organic compounds

(b) Functional groups

(c) Linkages common in biochemistry

(R represents an alkyl group (CH3CH2)n-)


Fig 1.2 (a) General formulas


Fig 1.2(b) General Formulas


Fig 1.2 (c) General Formulas


1.3 Many Important Biomolecules are Polymers

• Biopolymers - macromolecules created by joining many smaller organic molecules (monomers)

• Condensation reactions join monomers (H2O is removed in the process)

• Residue - each monomer in a chain


A. Proteins

• Proteins are composed of 20 common amino acids

• Each amino acid contains:

(1) Carboxylate group (-COO-)

(2) Amino group (-NH2)

(3) Side chain (R) unique to each amino acid


Fig 1.3 Structure of an amino acid and a dipeptide

(a) Amino group (blue), carboxylate group (red)(b) Dipeptides are connected by peptide bonds


Polypeptides

• Polypeptides - amino acids joined end to end

• Conformation - the three dimensional shape of a protein which is determined by its sequence

• Active site - a cleft or groove in an enzyme that binds the substrates of a reaction


B. Polysaccharides

• Carbohydrates, or saccharides, are composed primarily of C,H and O

• Polysaccharides are composed of saccharide monomers

• Most sugar structures can be represented as either linear (Fischer projection) or cyclic


Fig 1.5 Representations of the structure of ribose


Fig 1.6 (a) Glucose, (b) Cellulose

Glycosidic bonds connecting glucose residues are in red


C. Nucleic Acids

• Polynucleotides - nucleic acid biopolymers are composed of nucleotide monomers

• Nucleotide monomers are composed of:

(1) A five-carbon sugar

(2) A heterocyclic nitrogenous base

(3) Phosphate group(s)


Fig 1.7 Deoxyribose

• Deoxyribose lacks a hydroxyl group at C-2. It is the sugar found in DNA.


Nitrogenous bases

• Major Purines:

Adenine (A)

Guanine (G)

• Major Pyrimidines

Cytosine (C)

Thymine (T)

Uracil (U)


Fig 1.8 Adenosine Triphosphate (ATP)

• Nitrogenous base (adenine), sugar (ribose)


Fig 1.9 Structure of a dinucleotide

• Residues are joined by a phosphodiester linkage


Fig 1.10 Short segment of a DNA molecule

• Two polynucleotides associate to form a double helix

• Genetic information is carried by the sequence of base pairs


D. Lipids and Membranes

• Lipids are rich in carbon and hydrogen, but contain little oxygen

• Lipids are not soluble in water

• Fatty acids are the simplest lipids: long chain hydrocarbons, a carboxylate group at one end

• Fatty acids are often components of glycerophospholipids


Fig 1.11 Structures of (a) glycerol 3-phosphate, (b) a glycerophospholipid


Fig 1.12 Model of a membrane lipid

• Hydrophilic (water-loving) head interacts with H2O

• Hydrophobic (water-fearing) tail


Fig 1.13 Structure of a biological membrane

• A lipid bilayer with associated proteins


1.4 The Energetics of Life

• Photosynthetic organisms capture sunlight energy and use it to synthesize organic compounds

• Organic compounds provide energy for all organisms


Energy Flow


Metabolism and energy

• Metabolism - collection of reactions by which organic compounds are synthesized and degraded

• Bioenergetics - study of the changes in energy during metabolic reactions


1.5 Biochemistry and Evolution

• Prokaryotes - do not have a membrane-bounded nucleus

• Eukaryotes - possess nucleus and other complex internal structures

• Prokaryotes and eukaryotes appear to have evolved from a common ancestor over three billion years ago


1.6 The Cell is the Basic Unit of Life

• Plasma membrane - surrounds aqueous environment of the cell

• Cytoplasm - all materials enclosed by the plasma membrane (except the nucleus)

• Cytosol - aqueous portion of the cytoplasm minus subcellular structures

• Bacteriophage or phage - viruses that infect prokaryotic cells


1.7 Prokaryotic Cells: Structural Features

• Prokaryotes, or bacteria are usually single-celled organisms

• Prokaryotes lack a nucleus (their DNA is packed in a nucleoid region of the cytoplasm)

• Escherichia coli (E. coli) - one of the best studied of all living organisms

• E. coli cells are ~0.5m diameter, 1.5m long


Fig. 1.14 E. coli cell


1.8 Eukaryotic Cells: Structural Features

• Eukaryotes: plants, animals, fungi, protists

• Have a membrane-enclosed nucleus containing the chromosomes

• Are commonly 1000-fold greater in volume than prokaryotic cells

• Have an intracellular membrane network that subdivides the interior of the cell


Fig 1.15 (a) Eukaryotic cell (animal)


Fig 1.15(b) Eukaryotic cell (plant)


A. The Nucleus

Nuclear envelope and endoplasmic reticulum of a eukaryotic cell


B. Endoplasmic Reticulum and Golgi Apparatus

• Endoplasmic reticulum - network of membrane sheets and tubules extending from the nucleus

• Golgi apparatus - responsible for modification and sorting of some biomolecules.


Golgi apparatus


C. Mitochondria and Chloroplasts

• Mitochondria are the main sites of energy transduction in aerobic cells.


Chloroplasts - sites of photosynthesis in plants, green algae


D. Specialized Vesicles

• Lysosomes - contain specialized digestive enzymes

• Peroxisomes - carry out oxidative reactions in animal and plant cells

• Vacuoles - fluid-filled vesicles, used as storage sites for water, ions and nutrients such as glucose


E. The Cytoskeleton

• A protein scaffold is required for support, internal organization and movement of a cell

• Actin filaments form ropelike threads

• Microtubules are rigid fibers packed into bundles

- Serve as an internal skeleton

- Form the mitotic spindle during mitosis

- Form movement structures (e.g. cilia, flagella)


1.10 Biochemistry is Multidisciplinary

• Various disciplines contribute to understanding biochemistry:

Physics Genetics

Chemistry Physiology

Cell biology Evolution

Biochemistry draws its major themes from:

• Organic chemistry, which describes the properties of biomolecules

• Biophysics, which applies the techniques of physics to study the structures of biomolecules

• Medical research, which increasingly seeks to understand disease states in molecular terms


Biochemistry draws its major themes from

• Nutrition, which has illuminated metabolism by describing the dietary requirements for maintenance of health

• Microbiology, which has shown that single-celled organisms and viruses are ideally suited for the elucidation of many metabolic pathways and regulatory mechanisms


Biochemistry draws its major themes from

• Physiology, which investigates life processes at the tissue and organism levels

• Cell biology, which describes the biochemical division of labor within a cell

• Genetics, which describes mechanisms that give a particular cell or organism its biochemical identity.


Uses of Biochemistry

• In clinical chemistry, biochemical measurements on people help diagnose illnesses and monitor responses to treatment. Liver disease is now routinely diagnosed and monitored by measurements of blood levels of enzymes called transaminases and of a hemoglobin breakdown product called bilirubin.


Uses of Biochemistry• Pharmacology and toxicology are

concerned with the effects of external chemical substances on metabolism. Drugs and poisons usually act by interfering with specific metabolic pathways.

• The results of biochemical research are used extensively in the world outside the laboratory - in agriculture, medical sciences, nutrition, and many other fields.


introduction wk 1 biochem

Documents

organic compounds

amino acid

nucleic acids

amino group

functional

carboxylate

major themes

nucleotide