Introduction to Biochemistry and Biotechnology in Nursing - Study Guide (copy)

Characteristics of Life

• Organization: Living things are highly organized, ranging from the smallest microscopic parts to the largest structural components.
• Energy Acquisition: All living organisms possess the ability to acquire materials and energy from their environment.
• Responsiveness: Living things have the ability to respond to environmental stimuli.
• Reproduction: All living organisms have the capacity to reproduce.
• Adaptation: Living things possess the ability to adapt to their environment over time.
• Genetic Information: All living things contain genetic information that governs their biological processes.

Definition and Scope of Biochemistry

• Bio-Chemical Study: Biochemistry is the study of chemical substances and vital processes occurring in living organisms.
• Molecular Basis of Life: It examines the molecular basis of life and the chemical reactions required to sustain living processes, all of which are included in the organism's metabolism.
• Interdisciplinary Nature: Biochemistry combines biology and chemistry to study living matter. It serves as the foundation for scientific and medical discovery in fields such as pharmaceuticals, forensics, and nutrition.
• Metabolism: This includes the study of all chemical processes within living things, allowing for an understanding of how to harness these processes for advancements in health and science.

Biochemistry in the Nursing Profession

• Clinical Diagnosis and Treatment: Understanding biochemistry is crucial for nurses to effectively diagnose and treat patients by comprehending internal chemical reactions.
• Assessing Patient States: Nurses use biochemistry to recognize alterations in normal biochemical processes that occur during various disease states.
• Diagnostic Interpretation: It provides the framework for interpreting diagnostic tests and understanding drug actions and electrolyte balance.
• Nutrition and Health: A nurse's understanding of nutrition depends heavily on biochemistry, focusing on the chemicals required for maintaining health.

Biological Molecules (Biomolecules)

Biomolecules are divided into four main categories:

1. Macromolecules
2. Monomers
3. Miscellaneous functional molecules
4. Metabolic intermediates

1. Macromolecules

• Carbohydrates:
  • General Formula: $(CH_2O)_n$ where $n \ge 3$.
  • Synonym: Saccharide.
  • Functions: Acts as an energy source, helps control blood glucose and insulin metabolism, participates in cholesterol and triglyceride metabolism, and assists in fermentation.
• Proteins:
  • Structure: Consists of one or more polypeptide chains.
  • Functions: Provides structural support; acts as biochemical catalysts, hormones, enzymes, building blocks; and initiates cellular death.
  • Structural Levels: Primary, secondary, tertiary, and quaternary.
• Lipids:
  • Characteristics: Largely or wholly hydrophobic biomolecules.
  • Functions: Components of cell membranes; control cellular entry and exit; move and store energy; absorb vitamins; and produce hormones.
• Nucleic Acids:
  • Structure: A polymer of nucleotide residues (polynucleotide).
  • Major Types: Deoxyribonucleic acid (DNA) and Ribonucleic acid (RNA).
  • Functions: Storage and expression of genomic information. DNA specifically encodes the information needed for protein synthesis.

2. Monomers

• Sugar: The building block of carbohydrates with the general formula $C_n(H_2O)_n$. Used to supply glucose to the brain and provide energy to body cells.
• Amino Acids: The building blocks of proteins, linked by peptide bonds. Every protein has a unique sequence of amino acids determining its shape and function.
• Fatty Acids: The building blocks of fat. During digestion, fats break down into fatty acids to be absorbed into the blood. They often join in groups of three to form triglycerides.
• Nucleotides: Basic building block of DNA and RNA. Each consists of a sugar (ribose or deoxyribose), a phosphate group, and a nitrogenous base. DNA bases include Adenine (A), Cytosine (C), Guanine (G), and Thymine (T).

3. Metabolic Intermediates

• Catabolic Reactions: Reactions that break down large organic molecules into smaller ones, releasing chemical bond energy.
• Anabolic Reactions: Reactions involved in synthesis and building processes.
• Regulation: Involves hormonal regulation of metabolism and oxidation-reduction reactions.

4. Miscellaneous Functions of Molecules

• Vitamins: Organic molecules (or vitamers) essential in small quantities for metabolic function. They must be obtained through diet as they cannot be synthesized in sufficient amounts; deficiency can lead to death.
• Minerals: Required in the diet as macro minerals or trace minerals. They serve as electrolytes, structural components, and metabolic intermediates.
• Enzymes: Biological catalysts (usually proteins) that speed up reactions millions of times without being consumed.
• Steroids: Man-made versions of hormones produced by the adrenal glands. Used to treat inflammatory conditions like asthma and eczema by reducing redness and swelling.
• Hormones: Chemical messengers released by cells or organs (e.g., insulin produced by pancreas beta cells) that travel through the body to control cell/organ function.
• ATP (Adenosine-5'-triphosphate): A nucleoside triphosphate used as a coenzyme and primary cellular energy source. Consists of adenine, ribose, and three serially bonded phosphate groups.
• Cyclic AMP (cAMP): Derived from ATP; serves as a second messenger for intracellular signal transduction.
• Urea (Carbamide): Organic compound with the formula $CO(NH_2)_2$. It is the end-product of amino acid nitrogen conversion to dispose of toxic ammonia. It is soluble, non-toxic, and excreted by the kidneys.

Proteins and Amino Acids

Characteristics and Composition

• Definition: From Greek "proteios" (holding first rank). They are unbranched polymers of amino acids.
• Abundance: Constitute about $50\%$ of a cell's dry weight.
• Elemental Composition: Carbon (C), Hydrogen (H), Nitrogen (N), Oxygen (O), and often Sulfur (S).
• Amino Acid Structure: Contains an amino group ($-NH_2$), a carboxyl group ($-COOH$), and a unique side chain (R group) attached to the $\alpha$-carbon.

Medical and Biological Importance of Proteins

1. Transport: e.g., Hemoglobin.
2. Catalysis: All enzymes are proteins.
3. Defense: e.g., Immunoglobulins.
4. Regulation: e.g., Hormone insulin.
5. Motion: e.g., Muscle proteins.
6. Gene Expression: e.g., Histones.
7. Nutrient Storage: e.g., Casein in milk, Ferritin for iron.
8. Buffering: e.g., Plasma proteins.
9. Anti-vitamins: e.g., Avidin in eggs.
10. Infectious Agents: e.g., Mad Cow Disease (prions).
11. Toxins: e.g., Cholera enterotoxin.
12. Structure/Elasticity: e.g., Collagen and elastin in bone/ligaments.
13. Tissue Components: e.g., $\alpha$-keratin in hair and epidermis.

Classification of Proteins

According to Composition

• Simple Proteins: Yield only amino acids upon hydrolysis. Examples: Albumin, Insulin, Ribonuclease.
• Conjugated Proteins: Protein part attached to a non-protein prosthetic group. Examples: Hemoglobin (contains heme).
• Derived Proteins: Produced from simple or conjugated proteins.
  • Primary Derived: Denatured by heat or alcohol (e.g., cooked egg albumin).
  • Secondary Derived: Formed by partial hydrolysis (e.g., peptones, peptides).

According to Solubility

• Albumins: Soluble in water and salt solutions (e.g., egg albumin).
• Globulins: soluble in salt solutions; sparingly soluble in water (e.g., plasma globulins).
• Glutelins: Soluble in dilute acids/alkalies (e.g., Glutenin in wheat).
• Protamins: Soluble in ammonia and water (e.g., Salmine).
• Histones: Soluble in water and dilute acids (found in chromatin).
• Prolamines: Soluble in dilute alcohol (e.g., Gliadin in wheat).
• Scleroproteins: Insoluble in water and dilute acids (e.g., Keratin, Collagen).

Comparison of Fibrous vs. Globular Proteins

• Fibrous Proteins: Water-insoluble; extended along one axis; structural function (e.g., $\alpha$-keratin, collagen).
• Globular Proteins: Water-soluble; folded into spherical shapes; metabolic functions like catalysis and transport (e.g., Hemoglobin, Myoglobin).

Plasma Proteins and Immunoglobulins

• General Stats: Total plasma protein level is $6-7\,gm/dl$. The liver is the source for albumin, prothrombin, and fibrinogen.
• Albumin:
  • Accounts for $75\%$ of osmotic pressure ($25\,mmHg$) in blood.
  • Maintains blood volume and regulates fluid distribution; deficiency leads to edema.
  • Transports fatty acids, thyroxine, and calcium.
• Globulin Fractions:
  • $\alpha_1$-Globulin: Includes $\alpha_1$-antitrypsin (protease inhibitor); deficiency causes emphysema. Also $\alpha_1$-acid glycoprotein (increases during inflammation) and $\alpha$-Fetoprotein (tumor marker for liver carcinoma).
  • $\alpha_2$-Globulin: Haptoglobulin (removes hemoglobin from circulation).
  • $\beta$-Globulin: Transferrin (iron transport) and $\beta$-Lipoproteins (transports LDL cholesterol).
  • $\gamma$-Globulin: Contains immunoglobulins.
• Immunoglobulins (Antibodies):
  • $IgA$: Found in mucous, saliva, tears; protects against pathogens.
  • $IgD$: Part of B cell receptor; activates basophils.
  • $IgE$: Responsible for allergic reactions and protection against parasitic worms.
  • $IgG$: Secreted by plasma cells; able to cross the placenta.
  • $IgM$: Responsible for early stages of immunity.

Amino Acid Classification and Biological Roles

There are 20 standard amino acids used in proteins, classified by their R-group.

1. Nonpolar Amino Acids (Hydrophobic)

• Glycine (Gly, G): Precursor to heme and glutathione; inhibitory neurotransmitter.
• Alanine (Ala, A): Central in glucose-alanine cycle; major gluconeogenic substrate.
• Valine (Val, V): BCAA; stimulates muscle growth and regeneration.
• Leucine (Leu, L): Potent BCAA for mTOR activation and muscle protein synthesis.
• Isoleucine (Ile, I): Enhances glucose uptake and recovery from fatigue.
• Proline (Pro, P): Major collagen component; protects against free radicals.
• Phenylalanine (Phe, F): Precursor to tyrosine and catecholamines (dopamine).
• Methionine (Met, M): Sulfur-containing; involved in DNA methylation and detox.
• Tryptophan (Trp, W): Precursor to serotonin and melatonin.

2. Polar Neutral Amino Acids

Side chains are neutral at physiological pH ($7.4$).

• Serine (Ser, S): Precursor for brain tissue (sphingolipids) and neurotransmission.
• Cysteine (Cys, C): Precursor to the antioxidant glutathione; vital for keratin synthesis.
• Threonine (Thr, T): Required for collagen, elastin, and antibody production.
• Asparagine (Asn, N): Involved in protein glycosylation and brain development.
• Glutamine (Gln, Q): Major fuel for intestinal and immune cells; detoxifies ammonia.
• Tyrosine (Tyr, Y): Precursor to thyroid hormones and melanin; nootropic effects.

3. Polar Acidic Amino Acids

Bear a negative charge at pH $7.4$.

• Aspartic acid (Asp, D): Energy production via TCA cycle; excitatory neurotransmitter.
• Glutamic acid (Glu, E): Primary excitatory neurotransmitter in the CNS; brain ammonia detox.

4. Polar Basic Amino Acids

Bear a positive charge at pH $7.4$.

• Histidine (His, H): Precursor to histamine; vital for myelin sheath maintenance.
• Lysine (Lys, K): Essential for collagen cross-linking; enhances calcium absorption.
• Arginine (Arg, R): Precursor to Nitric Oxide (NO) for circulation; enhances Urea Cycle.

Peptides and Small Signaling Molecules

• Definition: Unbranched chain of amino acids linked covalently via peptide bonds (substituted amide linkage formed by condensation).
• Nomenclature: Dipeptide (2 AAs), Tripeptide (3 AAs), Oligopeptide ($10-20$ AAs), Polypeptide (long chain).
• Biologically Important Peptides:
  • Oxytocin: Regulates uterine contractions and lactation.
  • Vasopressin (Anti-diuretic Hormone): Regulates water excretion in kidneys.
  • Enkephalins: Brain peptides that reduce pain.
  • Glutathione: Regulates redox reactions; antioxidant.

Enzymes: Structure, Classification, and Kinetics

• Structure:
  • Simple Enzyme: Composed only of protein.
  • Conjugated Enzyme: $Apoenzyme (protein) + Cofactor (nonprotein) = Holoenzyme (active)$.
  • Coenzyme: An organic molecule serving as a cofactor.
• Classification:
  1. Oxidoreductase: Catalyzes oxidation-reduction (e.g., Lactate dehydrogenase).
  2. Transferase: Transfers functional groups (e.g., Kinases transfer phosphate).
  3. Hydrolase: Breaks bonds using water (e.g., Maltase).
  4. Lyase: Adds/removes groups to double bonds without hydrolysis.
  5. Isomerase: Rearranges atoms (e.g., Phosphoglyceromutase).
  6. Ligase: Bonds two molecules using ATP (e.g., Pyruvate carboxylase).
• Factors Affecting Activity:
  • Temperature: Increases collision rate; optimum is typically $37\,^{\circ}C$ for humans; over $40\,^{\circ}C$ causes denaturation.
  • pH: Affects charge at active site; physiological optimum is $7.0-7.5$ (Pepsin optimum is $2.0$).
  • Substrate Concentration: Rate increases until a saturation point (turnover number: substrate molecules transformed per minute).
  • Enzyme Concentration: Reaction rate increases proportionally with more enzyme molecules available.