Introduction to Biochemistry

• Main reference textbooks include Harper's Biochemistry and Lippincott's Biochemistry.

Definition of Biochemistry

• Biochemistry applies chemistry to the study of biological processes at the cellular and molecular levels. Biochemistry emerged as a distinct discipline around the beginning of the 20th century.
• In general Biochemistry studies chemical processes of life and focuses on studying various molecules, chemical compositions, reactions and processes that occur in living cells of organisms.
• Biochemistry deals with the chemical composition of the body and all biochemical reactions that occur inside living cells or the body.

Aim of Biochemistry

• Aim to achieve a detailed understanding at the molecular level of all chemical processes in living cells. Biochemistry is studied by isolation of molecules, determining structure and analyzing their function.
• It uses chemistry, physics, molecular biology, and immunology to study the structure and behavior of complex molecules in biological material and their interactions. It serves as the foundation for understanding all biological processes.
• Offers explanations for the causes of various diseases in humans, animals, and plants and suggests potential treatments.
• Biochemists investigate mechanisms of brain function, cellular multiplication and differentiation, communication within and between cells and organs, and the chemical bases of inheritance and disease.
• Seeks to determine how specific molecules like proteins, nucleic acids, lipids, vitamins, and hormones function. Emphasis is placed on the regulation of chemical reactions in living cells.

Health and Disease in Biochemistry

• Health depends on the balance of chemical molecules and reactions in living cells.
• Disease reflects abnormalities in chemical molecules and reactions within living cells.
• Prevention of disease, diagnosis of disease, and treatment of disease are important for medical biochemistry.
• All diseases have a chemical basis: Disturbance to cell chemistry can lead to dysfunction, which then leads to disease.
• The organization of life is hierarchical, from atoms and elements to the complete body: Atom, element, compound, micromolecules, macromolecules, supermolecules, organelles, cells → tissue → organs → systems → body.

Micromolecules and Macromolecules

• Micromolecules are small molecules or monomers that combine to form a macromolecule, the four main micromolecules are amino acids, fatty acids, monosaccharides, and nucleotides.
• Macromolecules are large molecules or polymers formed from combined micromolecules, the four main macromolecules are protein, lipid, carbohydrates, and nucleic acids. In addition to water and minerals like metal ions.
• These molecules are the main components of the human body.
• Dehydration synthesis is the process where two monomers combine to form a polymer, removing a water molecule, also known as a condensation reaction.

Chemical Composition of a normal man (weight 65 Kg)

• A normal man is composed of 61.6% water (equivalent to 40 kg), 17% protein (11 kg), 13.8% lipid (9 kg), 1.5% carbohydrate (1 kg), and 6.1% mineral (4 kg).
• Water is the main component, and protein is the main macromolecule of the human body.
• The two main types of body compounds are inorganic compounds that do not contain carbon (example: NaCl) and organic compounds that do contain carbon (example: CH4).
• The major elements found in the human body are; 65% Oxygen, 18% Carbon, 10% Hydrogen, 3% Nitrogen, 1.5% Calcium, and 1.2% Phosphorus.
• Oxygen, carbon, and hydrogen make up the largest percentage because they are the main elements in the structure of amino acids, proteins, sugars, and fatty acids (lipids).
• The remaining percentage is related to trace elements such as Fe, I, and Zn.

Chemical Bonds in Biochemistry

• Covalent bonds are formed between non-metal atoms by sharing electrons, they can be single, double, or triple bonds, are strong, resistant to denaturation, and are formed and hydrolyzed by enzymes.
• Types of covalent bonds in biochemistry are non-polar covalent bonds where atoms share electrons equally and polar covalent bonds where atoms share electrons unequally.
• Examples of covalent bonds in biochemistry include peptide bonds in proteins, glycosidic bonds in carbohydrates, ester bonds in lipids, and phosphodiester bonds in nucleic acids.
• Non-covalent bonds are formed between atoms and groups of molecules that carry a charge, they are weak, sensitive to denaturation, and formed and hydrolyzed without enzymes.
• Examples of non-covalent bonds in biochemistry:
• Ionic bonds are formed between oppositely charged ionized items, for example (Na+) + (Cl-) = NaCl.
• Electrostatic bonds are attraction between oppositely charged ionized groups, like between carboxyl groups (COO-) and amino groups (NH3+).
• Hydrogen bounds are attraction between electronegative atoms like F or O and a hydrogen atom (H2O).
• Van der Waals bonds are weak, temporary attractions between non-polar molecules in close proximity (CH4-CH4).
• Hydrophobic interactions occur between non-polar groups in an aqueous environment, which causes the groups to cluster to reduce surface area.

Internal Environment of Body

• Includes water, electrolytes and pH. Internal environment must maintain constant water distribution, electrolyte concentration & pH.
• Water is the main component of the body. 73% in muscle and 20% in fat tissue.
• An adult weighing 70 kg has approximately 40 liters of water in their body.
• Water is abundant in all tissues except adipose tissues.
• The amount of water in the body represents approximately 65-70% of body weight.
• Women generally have less water than men due to a higher percentage of adipose tissue.
• As people age they have lower amounts of body water (babies have more water than adults).
• Adults lose approximately 1.5-2 liters of water per day, depending on factors such as; exercise intensity and weather conditions.
• Dehydration is a factor that may lead to the formation of renal stones.
• Drinking water suppresses appetite and reduces weight.

Important Functions of Body Water

• Some molecules, such as sugar, enzymes, hormones, and salts, are only soluble in water.
• Water is necessary for transport to and from all the body's cells.
• Water acts as a solvent for waste products such as urea and minerals so they can be excreted via sweat and urine.
• Water is needed for some metabolic reactions and produced by others.
• Regulates the body temperatures via sweating.
• Involved in the composition of body fluids like ECF & ICF.
• Distribution of total body water is 2/3 intracellular fluid and 1/3 extracellular fluid.
• Extracellular fluid (ECF) is composed of 75% interstitial fluid and 25% blood plasma.

Molecules With Water

• Molecules can be hydrophilic, hydrophobic, or amphipathic.
• Hydrophilic Molecules are water-loving molecules, lipophobic molecules, able to form H-bonds in water, and soluble in water, like molecules with Hydroxy, Amine or Ester as well as ionic compounds like NaCl.
• Hydrophobic molecules are water-hating and lipophilic, they cannot form H-bonds and are insoluble in water, hydrocarbons for example.
• Amphipathic molecules have a polar head that is soluble in water and a non-polar tail that is insoluble, like phospholipids, fatty acids, and globular proteins.
• Bile salts are an example, such as glycocholic or taurocholic bile salts, made of cholic acid and deoxycholic acid. i.e. Bile salts = bile acids + glycine (protein amino acid) or taurine (non protein amino acid).
• Bile salts present in the bile juice aid in digestion of fats in the small intestines, because fats are non-polar substances.

Water Daily Requirements And Dehydration

• 2800 ml should be intake and output in a day.
• Water intake varies between men and women.
• Requirements increase when vomiting, having diarrhea, sweating, during exercise, and during fever.
• Low hydration is dehydration, which can lead to increased pulse, body temperature, and respiratory rate, thirst, loss of appetite, emotional instability, flushed skin, fatigue, headache, and nausea.
• In severe cases, dehydration can lead to kidney dysfunction and risk of death.
• Anions are negatively charged and move towards the anode, the major anions in body fluids are chloride (Cl-), bicarbonate (HCO3-), and phosphate (HPO4-).
• Cations are positively charged and move toward the cathode, the major cations in body fluids are sodium (Na+), potassium (K+), calcium (Ca++), and magnesium (Mg++).
• Na+ and Cl- are predominant in extracellular fluid (ECF).
• K+ and HPO4- are predominant in intracellular fluid (ICF).
• Ca++ and HPO4 are also present in teeth and bones.

Electrolyte Function

• Hormonal stimulation (Calcium)
• Nerve Conduction and Muscle Contraction (Calcium, magnesium, potassium).
• Needed for blood coagulation (calcium, magnesium).
• Maintaining osmotic pressure (sodium, chlorine, potassium).
• Production of energy ATP (phosphate, magnesium).
• Enzyme cofactor (magnesium, calcium, zinc).
• Regulation of ATPase pump (magnesium).
• Contribute to buffer system (bicarbonate).
• Heme synthesis (iron).

Solution

• Forms when a solute dissolves in a solvent i.e. (NaCl in water).
• Solution concentration refers to the percentage ratio between the solute and the solvent.
• Methods to measure solution concentration include Weight / Volume (ex; mg% & g%).
• Part / Million (ex; 1: 106 Used for Trace elements).
• Molarity; this is the number of moles of solute per liter or Kg of solution. Molecule is the weight of substance in gram equal to molecular wright.

Water Ionization

• Water dissociates into H+ and OH- ions, making it an amphoteric molecule, meaning it can act as both an acid and a base.

pH, pOH Of Water

• pH is the negative log of hydrogen ion (proton) concentration, pH= -log (H+), at 25°C pure water pH = 7.
• pOH is the negative log of OH ion concentration, pOH= -log (OH-), at 25°C pure water pOH = 7.
• The pH range is from 0 to 14; 7 is acidic (↑H+ & ↓pH). While above 7 is basic (↓H+ & ↑pH).
• In the lab acidic solution pH < 7, neutral is pH = 7, and basic pH > 7.
• In the blood pH, Acidosis is when pH < 7.35, physiological pH = 7.4 ± 0.05, and alkalosis is when pH > 7.45.
• Various body fluids have different pH levels, e.g., blood plasma pH is 7.4, gastric juice pH 1.5–3.0, urine pH 5.0–8.0, and saliva pH 6.4–7.0.
• The pH compatible with life is 6.8 -7.8.
• pH affects body functions, as each enzyme needs a certain optimum pH to act at maximum level.

Buffer Solution

• Defined as a solution that resists changes in pH when acids or bases are added in small amounts, that are formed of conjugate acid or base pairs.
• Can be a weak acid with its conjugate strong base (salt).
• Can be a weak base with its conjugate strong acid (salt).

Types of Body Buffers

• Chemical buffers: The first line of defense, act within a few minutes that include the bicarbonate system, phosphate system, glucose-6-phosphate, nucleotides, and plasma proteins, as well as hemoglobin.
• Organ buffers: Act within a few days by playing roles in pH regulation, like lungs (reduce pCO2 in blood), kidneys (generate more bicarbonate (HCO3-) by converting carbonic acid (dissolved CO2) H2CO3 to HCO3- & H+), and liver (synthesize neutral urea from alkaline ammonia and neutral glycogen from acidic lactic acid).

Acid-Base Balance Disturbances

• Disturbance in physiological pH (7.35-7.45) generally leads to acidosis or alkalosis.
• Acidosis and alkalosis can be respiratory or metabolic.
• Respiratory acidosis involves an increase in pCO2 which increase H2CO3 levels in the blood (hypercapnia).
• Main cause is by inadequate breathing or hypoventilation, breathing air containing high CO2, chronic lung disease such as asthma, respiratory centre depression by general anaesthesia, or morphine poisoning.
• Respiratory alkalosis involves a decrease in pCO2 and decreases H2CO3 levels in the blood (hypocapnia).
• Main cause is increased breathing or hyperventilation, from fever, hot atmosphere, or high altitude.
• Metabolic acidosis involves decrease HCO3- or increase H+ in blood.
• Causes such as shock (anoxia), heavy exercise and/or starvation.
• Bacterial infection as well large amount of acidity in diet.
• Diarrhea and diuretic drugs decrease levels of HCO3.
• Metabolic alkalosis involves increase HCO3- or decrease H+ in blood.
• Causes such as excess secretion of aldosterone.
• Vomiting can cause decrease in H+.

Cells

• Building blocks of life and the smallest living unit of an organism, unable to be seen by the naked eye.
• Unicellular organisms like bacteria are formed of only one cell. In contrast, multicellular organisms like animals are made up of billions of cells.
• Prokaryotes cells are before nucleus, smaller in size and posses both a cell membrane and a cell wall, they also lack membrane bound organelles, lack a membrane bound nucleus, and contain nucleiods, bacteria for example.
• Eukaryotes are cells that have a true nucleus, are larger in size, have a cell membrane but no cell wall, contain organelles that bound with membranes.

Organelles in Cells

• Plasma membrane has lipid bilayers. It functions as; a Cell boundary, provides a barrier, contains active transport systems for amino acids, facilitates glucose, Na and K, contains signaling. Includes Na-K ATPase and 5-Nucleotides.
• Cytoplasm is the liquid enclosed by the plasma membrane, functions as; a site for organelle housing, enzymes and a container of glycolysis and fatty acids synthesis enzymes. Lactate Dehydrogenase is a marker enzyme.
• The nucleus is surrounded by a double membrane and contains the chromosome.
• The nucleus works as a cellular center, site of replication, DNA synthesis, and contains DNA Marker. DNA is marker enzyme.
• The mitochondria is formed after surrounding a double membrane (outer & inner), contains cristae, DNA, muscle cells, contains food and produces energy . Succinate Dehydrogenase, Glutamate Dehydrogenase, cytochromes are marker enzymes.
• Ribosome- formed of protein + RNA, can be found in forms for protein synthesis and RNA Marker enzymes.
• Endoplasmic Reticulum (ER), smooth or rough, responsible for cytochrome P450.
  • SER F'ns as site of synthesis with P450 enzymes
  • Site of RER functions and proteins
• The Golgi device is stacked for packing the proteins of macromolcules.
• Galactosyl transferase Is the maker.
• Membrane-bound organelles of lysosomes have a single membrane.
  • Contains and digests the enzymes for protein degredation, destroying old and harmful debris
  • Marker enzyme has ẞ Galactsidase.
• Rich in enzymes; it Is smaller in its mitochondria.
• Beta-oxidation with marker enzymes are responsible for catalase and hydrolase with glycosidase

Subcellular Fractionation

• Molecules become fractioned to study concentration and composition. The organelle must be pure.
• The normal step is the fractional portion.
• Purity steps; Extraction and homogenization
• Separation is a way to clarify and evaluate molecules.
• With X-ray structure