Biochemistry

INTRODUCTION TO BIOCHEMISTRY

  • Study of chemical substances found in living organisms and the chemical interactions of these substances with each other
  • Application of chemistry to the study of biological processes at the cellular and molecular level
  • Compounds, chemical reactions, and molecular interactions involved in production maintenance and reproduction of living organisms
  • Concerned with the physio-chemical processes underlying:

  ○ digestion, absorption, circulation, respiration, metabolism, growth, and reproduction

  • How cells manufacture the molecules needed for life and how the chemical reactions by which life is maintained occur
  • All living things make use of the same type of biomolecules and use energy, hence studied through methods of chemistry and biology
  • Fundamental similarity of cells and speculating on origin of life
  • Cells and biomolecules arisen from very simple molecules such as
  ○ H2O (Water), CH4 (Methane), NH3 (Ammonia), N2 (Nitrogen), H2 (Hydrogen)
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* Deals with the study of chemistry and living

  organisms
* Answers questions on molecular nature of life
* Both life and chemical science
* Foundation for understanding all biological processes ***Roots of Biochemistry***
* **Karl Scheele**
  * Swedish founder of Biochemistry
  * studied the chemical composition of matter in mid *1700*
* **Schleiden & Schwann**

        ○ *1840* - formulated cell theory **● Walter Flemming**

        ○ *1875* - discovered chromosomes

* **Carl Newberg**

      ○ German scientist who coined the word biochemistry
* **Hans Kreb**

      ○ *1937* - proposed Kreb cycle of the TCA (Tricarboxylic Acid)
* **Embden & Mayerhoff**

       ○ *1925* - described glycolytic pathway **● James Watson & Francis Crick**

       ○ *1953* - described double helical structure of DNA

\*Most diseases (in humans, animals, and plants) have a biochemical basis. Biochemical Research has an impact on nutrition and preventive medicine \n \*● Diagnose & Monitor Diseases

* ○  Transaminase levels
* ○  Hemoglobin breakdown product

■ Bilirubin (high levels of this can indicate liver problems)

○ Troponins (a protein complex involved in muscle contraction) in the blood to determine extent of myocardial infarctions (fancy way to say you had a heart attack due to high troponin levels)

* ●  Designer drugs
  * ○  New & improved Antibiotics
  * ○  New & improved chemotherapy agents
  * ○  Protein diseases
* ●  Health Maintenance (nutrition) \n ○ intake of vitamins, amino acids, fatty acids,

  various minerals, and water
* ●  Protein structure & function

○ Normal vs. Sickle Cell hemoglobin ● Alkaptonuria, Albinism, Pentosuria

○ Inborn errors of metabolism

* ●  Molecular mechanisms of Oncogenes, and tumor

  suppressing genes for normal cell growth
* ●  How cholesterol contribute to heart disease and why aspirin lower body temperature (how medicine and

  biochemistry are connected)
* **●  Major Causes of Diseases**

○ Physical Agents \n ■ mechanical trauma, temperature extremes,

radiation, electric shock ○ Chemical Agents

■ toxic compounds, drugs ○ Biologic Agents

■ viruses, bacteria, fungi, parasites

* ○  Genetic Disease
* ○  Oxygen Lack

  ■ loss of blood, decreased oxygen-carrying capacity of blood, mitochondrial poisoning
* ○  Immunologic Reactions

■ anaphylaxis, autoimmune disorders

○ Nutritional Imbalances \n ■ deficiencies, excesses

○ Endocrine Imbalances \n ■ hormonal deficiencies/excesses

*Career Opportunities for Biochemistry*

* ●  Agriculture Industry
* ●  Medicine
* ●  Research Science
* ●  Food & Cosmetic Industries
* ●  Patent Law
* ●  Pharmaceuticals
* ●  Publishing
* ●  Education
* ●  Forensic Science

**BIOCHEMISTRY: A RESEARCH DISCIPLINE APPLICABLE TO THE REAL WORLD**

**ATTRIBUTES OF LIFE**

* ●  Polymers (Greek: *poly + meros,* many + parts); derived from monomers (Greek: *mono + meros,* single + parts)
* **●  Primordial Biomolecules**

○ Amino acids \n ■ glycine, alanine, serine

○ Nitrogenous bases \n ■ pyrimidines, purines

○ Sugars \n ■ glucose, galactose, mannose

○ Sugar alcohol ■ glycerol

○ Nitrogenous alcohol ■ choline

○ Fatty acids \n ■ palmitic acid, linoleic acid, linolenic acid,

arachidonic acid

**● 2 Broad Types**

***Micromolecules (small molecules)***

○ Biological Micromolecules

* Lipids
* Amino Acids
* Sugar
* Nucleotides

● a link to nucleotide codes, amino acid codes, and genetic codes

***Macromolecules***

* ○  Importance
  * Essential structures for the basis of life
  * Control and regulate these processes
  * Responsible for energy exchanges,

    irritability, metabolism, mobility, and

    reproduction
* ○  Biological Macromolecules
  * Protein
  * Carbohydrates
  * Nucleic Acid

● Directionality in Nucleic Acid

* ○  3’-OH of the ribose ring of 1

  nucleotide forms a bond with the 5’-OH of the ribose ring of the neighboring nucleotide
* ○  all these polymerization are accompanied by the elimination of water

○ Informational Macromolecules

* A strand of DNA (nucleotide bases)

  ● T (Thymine) ● A (Adenine) ● C (Cytosine) ● G (Guanine)
* A polypeptide segment \n ● made up of amino acids \n ● Directionality in Polypeptides

  ○ amino acids build proteins by connecting the carboxyl group of one amino acid with the amino group of the next amino acid
* A polysaccharide chain \n ● made up of sugar molecules bonded

  together \n ● Directionality in Polysaccharides

○ built by linking the first carbon of 1 sugar with the 4th carbon of the next sugar

**● Adaptation**

○ Body structures (physiology/morphology) that make living things fit to live in its habitat

* **●  Growth & Repair**

  ○ Ability to add new tissue and repair/replace damaged parts
* **●  Metabolism**
  * ○  Biological & chemical activities that provide energy
  * ○  Catabolism vs. Anabolism
* **●  Reproduction**

  ○ Produce offsprings, ensuring propagation and continuance of species
* **●  Complexity & Organization**
  * ○  Complexity - elaborate structures needed to carry out specific function
  * ○  Organization - to put structures in order to function efficiently
* **●  Regulation**

○ Keeping functions under control ■ Hormones, enzymes

**● Characteristic Size & Shape**

○ Unique morphology \n ■ i.e. ants can never become as big as

elephants

* **●  Response to Stimuli**

  ○ Respond favorably or unfavorably to its environment
* **●  Locomotion**

○ Movement by initiative, under own control

**● Variation & Change**

○ No 2 organisms are alike and no organism remains unchanged

*Review on* Levels of Structural Organization *(also part of the AnaPhy orientation)*

*Biochemistry seeks to describe the structure, organization, and function of living organisms in molecular terms* Understanding life on molecular level requires:

* ●  Knowledge of chemical structures of biological

  molecules
* ●  Understanding of the biological functions of the

  molecules
* ●  Understanding of **Bioenergetics**

○ The study of energy flow in cells

* ●  Cellular apparatus of living organisms made up of carbon

  **BIOMOLECULES**
* ●  molecules found in living matter
* ●  its reactions can be described by organic chemistry

  methods
* **●  4 Major Classes**
  * ○  Proteins
  * ○  Nucleic Acids
  * ○  Polysaccharides
  * ○  Lipids

**CHEMICAL FOUNDATIONS OF BIOCHEMISTRY**

**ORGANIC CHEMISTRY:**

study of compounds of carbon

**INTRODUCTION TO BIOCHEMISTRY**

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ORGANIC COMPOUNDS

● Naming the organic compounds ○ counting the carbon atoms

  • ●  Types of carbon-carbon bonds
  • ●  Types of compounds
    • ○  alkanes, alkenes, and alkynes
    • ○  complex organic compounds
  • ●  2 General Classifications of Organic Compounds

○ Hydrocarbons

■ contain only carbon and hydrogen ● Aliphatic hydrocarbons

  • ○  no benzene rings or derivative of the benzene ring
  • ○  Saturated (contain single C-H bond)

■ Alkanes (ethane) - single bond

○ Unsaturated (contain 2 or more C-H bond)

  • Alkenes (ethene) - at least 1 double bond
  • Alkynes (ethyne) - at least 1 triple bond

● Aromatic hydrocarbons \n ○ contain a benzene ring or a

derivative of the benzene ring

○ Substituted Hydrocarbons

  • one or more hydrogen atoms is replaced by another atom or group of atoms
  • Functional Groups
    • ●  an atom or group of atoms arranged in a particular way that is primarily responsible for the chemical and physical properties of the molecule which it is found
    • ●  Common Functional Groups

○ Carbon-Oxygen Group

  • Alcohol - ******Methanol (Methyl alcohol)
  • Aldehyde - Ethanal (Acetaldehyde)
  • Ketone - Propanone (Acetone)
  • Carboxylic Acid - Ethanoic acid

  (Acetic Acid)

  • Acid Anhydride
  • Ether - Dimethyl ether
  • ○  Carbon-Sulfur Group
    • Sulfhydryl
    • Disulfide
  • ○  Carbon-Nitrogen Group
    • Amino
    • Quaternary
  • ○  Ester and Amines
    • Thioester
    • Phosphoester
    • Ester - Methyl ethanoate

    (Methyl acetate)

  • Amide - Ethanamide

    (Acetamide)

    ********Systematic Name (common name)

CHEMICAL REACTIONS OCCURRING IN LIVING MATTER (IN VIVO)

● Oxidation

  • ○  process wherein most of the energy liberated by living matter is derived from the oxidation of organic substances such as carbohydrates, fats, and protein
  • ○  2 Kinds
    • Aerobic Oxidation

    ● takes place in the presence of free oxygen

  • Anaerobic Oxidation
    • ●  takes place in the absence of free oxygen
    • ●  substance undergoes oxidation by loss of hydrogen (lactic acid fermentation or alcohol fermentation)
    • ●  Reduction
  • ○  reverse of oxidation
  • ○  maybe brought by either the loss of oxygen or the

    gain of hydrogen/electrons

  • ○  occurs simultaneously with oxidation
  • ○  all food and organic substances have the

    property of taking up oxygen, hence they are

    reducing agents

  • ●  Hydrolysis
    • ○  chemical process in which molecule of water is added to a substance \n ■ sometimes this addition causes both

    substance and water molecule to split into

    two parts

  • ○  large molecules are broken down into smaller

    and simpler forms

  • ●  Condensation
    • ○  reaction wherein simple fragments unite with one another to form more complex compound
    • ○  synthesis of complex substances like glycogen and tissue protein is accomplished through this process
  • ●  Tautomerism
    • ○  also called isometric transformation
    • ○  intramolecular rearrangement of atoms within a

    molecule leading to the formation of a new substance having distinctive properties of its own

■ e.g transformation of glucose into galactose

and galactose to mannose

● Hydrophobicity vs. Hydrophilicity

○ Hydrophobic

■ refers to a physical property of a molecule that is repelled from a mass of water \n ● Alkanes, oils, and fats

○ Hydrophilic

■ refers to a physical property of a molecule that can transiently bond with water through hydrogen bonding

● Chemical Bonds

○ Ionic bonding

■ transfer of one or more electrons from one atom to another, forming an ionic bond

○ Covalent bonding

■ sharing pairs of electrons between atoms

○ Hydrogen bonding

■ hydrogen atom is bonded to a small, highly electronegative atom