Introduction to Biochemistry

Scope and Importance of Biochemistry

• Biochemistry deals with molecules in living cells and organisms, and their chemical reactions
• Carl Alexander Neuberg (1877-1956) coined the term biochemistry
• Metabolism is the chemical processes in living organisms
• Enzymes catalyze metabolic reactions
• Metabolism involves catabolism (large to small molecules, producing ATP) and anabolism (small to large molecules, utilizing ATP)
• The basic principles of biochemistry are common to all living organisms
• Bacteria and humans share the same chemical compounds and metabolic processes
• Key aspects of biochemistry: molecule synthesis, structure, function, interaction with other molecules, and metabolism regulation

Levels of Organization in Biology and Medicine

• The levels of organization are: Subatomic particles, Atom, Molecule, Macromolecule, Organelle, Cell, Organ/Tissue, Whole animal, Population
• Biochemistry focuses on molecules, macromolecules, organelles, cells, tissues, and whole animals

Knowledge of Biochemistry

• Biochemistry is a fundamental science that aids in the understanding of other fields like cell biology, microbiology, nutrition, pharmacology, and physiology

• Biochemistry of nucleic acids is the basis of genetics

• Physiology and biochemistry overlap

• Immunology uses biochemical techniques

• Biochemistry forms the basis of pharmacology and pharmacy

• Toxicology studies poisons interacting with biochemical reactions

• Disease processes (pathology) are elucidated biochemically

• Understanding nutrition requires biochemical knowledge

• Molecular biology, which studies gene structure, function, and regulation, is a major branch of biochemistry

• Biochemistry is essential for biotechnology

• Clinical biochemistry is directly associated with clinical medicine

• Clinical biochemistry is valuable for disease prevention, diagnosis, and treatment, and monitoring treatment success

• Biochemistry technologies apply to any aspect of biology such as humans, mammals, insects, plants, bacteria, and viruses

Cell and Sub Cellular Components

• The cell is the basic structural, functional, and biological unit of life
• A cell is the smallest unit that can replicate independently
• Cells are the building blocks of life
• The study of cells is called cell biology
• Eukaryotic cells contain a nucleus
• Prokaryotic cells do not
• Prokaryotes are single-celled
• Eukaryotes can be single-celled or multicellular

Plasma Membrane

• The cell membrane, or plasma membrane, surrounds the cytoplasm of a cell
• In animals, it's the outer boundary, while in plants and prokaryotes it's covered by a cell wall
• The membrane separates and protects the cell
• It is primarily composed of a phospholipid bilayer, which is amphiphilic (partly hydrophobic and partly hydrophilic)
• The fluid mosaic membrane contains channels and pumps that transport molecules
• The membrane is semi-permeable, controlling substance passage
• Cell surface membranes have receptors for external signaling molecules like hormones

Cell Nucleus

• The cell nucleus, found in eukaryotic cells, is the information center
• It houses chromosomes and is the site of DNA replication and RNA synthesis (transcription)
• It is spherical, separated from the cytoplasm by a double membrane nuclear envelope
• The nuclear envelope protects DNA from molecules that could damage its structure or interfere with processing
• DNA is transcribed into mRNA, which is transported out of the nucleus and translated it into a specific protein molecule
• The nucleolus has ribosome subunits assembled
• In prokaryotes, DNA processing happens in the cytoplasm

Mitochondria and Chloroplasts

• They generate energy for the cell
• Mitochondria are self-replicating organelles in all eukaryotic cells, occurring in various numbers, shapes, and sizes
• Respiration occurs in cell mitochondria, using oxidative phosphorylation to generate ATP
• Mitochondria multiply by binary fission, like prokaryotes
• Chloroplasts are only in plants and algae
• Chloroplasts capture the sun's energy to make carbohydrates through photosynthesis

Endoplasmic Reticulum

• The endoplasmic reticulum (ER) transports molecules molecules targeted for certain modifications and specific destinations
• There are two forms of ER: rough ER with ribosomes for protein secretion, and smooth ER without ribosomes
• The smooth ER is vital for calcium sequestration and release

Peroxisomes

• They have oxidative enzymes like catalase, D-amino acid oxidase, and uric acid oxidase
• Catalase decomposes hydrogen peroxide into water or to oxidize another organic compound
• A major function is the breakdown of very long chain fatty acids through beta-oxidation
• In animal cells, long fatty acids are converted to medium chain fatty acids, shuttled to mitochondria, and broken down to carbon dioxide and water
• In yeast and plant cells, this process takes place exclusively in peroxisomes

Golgi Apparatus

• The Golgi apparatus processes and packages macromolecules such as proteins and lipids synthesized by the cell

Lysosomes and Peroxisomes

• Lysosomes have digestive enzymes called acid hydrolases, and digests excess or worn-out organelles, food particles, and engulfed bacteria or viruses
• Peroxisomes have enzymes to remove toxic peroxides
• These destructive enzymes are contained in a membrane-bound system

Acids and Bases

• An acid is a proton donor, and a base is a proton acceptor
• On ionization, an acid donates a proton and a base accepts a proton, and that base becomes its conjugate acid
• Acids and bases are grouped by proton or hydroxyl group loss tendency
• Strong acids/bases are completely ionized
• Weak acids/bases dissociate to a limited extent
• An alkali yields OH ions when dissolved in water

Dissociation of Water

• Pure water mainly consists of H2O molecules

• H2O dissociates into H+ + OH (auto-ionization of water)

• The equilibrium expression for this is 1.8 x 10-16 moles/liter at 25°C

• The concentration of pure H2O is about 55M

• Its concentration is essentially unchanged during chemical reactions involving dilute aqueous solutions

• Kw, is the ion-product constant

• At 25°C, the value of Kŵ is 1 x 10-14

• Using this, if one knows the concentration of either H+ or OH ions in solution, the other ion's concentration can be derived

• A solution for which has [H+] = [OH] is said to be neutral, [H+][OH] = 1 x 10-14

pH

• The measurement of acidity and alkalinity

• biochemical processes are affected the concentration of H+ ion

• pH depends on the charge on the molecules (+ ve or -ve charge)

• Molecule charge relies on its ability to release or accept a proton, which in turn depends on the solution's pH

• H+ ion concentration of biological solutions is very low, so Sorenson introduced pH in 1909 to express the hydrogen ion concentration as pH = -log of [H+] or log 1 / [H+]

• For example, the [H+] concentration of 10-8 g/L will be pH 8.0

• pH is an abbreviation of power of hydrogen

• The pH scale is a useful way to express acidity, which in turn dependent on [H+]

• pH is generally in the range of 0–14, as the dissociation constant of water at 25°C is 10-14

• An acidic solution has a pH below 7, a basic solution has a pH above 7, and pure water is neutral

• pH is inversely related to hydrogen ion concentration - the lower the pH, the higher the H+ion concentration

• The pH scale is logarithmic (exponential), not arithmetic (linear)

• Changing from pH 7 to pH 6 increases H+ ion concentration by 10-fold, and from pH 7 to pH 5 it increases by 100-fold

• The pH of water is 7.0 containing 1x10-7 g of H+ ions/L

• pH can be found through certain dyes

• Accurate determination of pH in chemical and clinical laboratory is made with a glass electrode that is sensitive to H⁺ ion concentration

• The normal pH of human plasma is 7.4, referred to as physiological pH

• The blood of patients suffering from certain diseases such as diabetes can have a lower pH, a condition called acidosis

• The condition in which the pH of the blood is higher than 7 is called alkalosis

Buffer

• A buffer resists pH change on the addition of a small quantity of acid or alkali
• Body fluids must be protected against pH change, because most enzymes are pH sensitive
• Metabolism produces acids and bases, and in the long run, excess acids or base is eliminated via kidney and lungs
• Carbonic acid, sulfuric acid, and phosphoric acid are acids produced by the body
• Bicarbonate buffer is the major extracellular buffer, and phosphate buffer is the major intracellular buffer
• A buffer solution consists of a weak acid and its salt (the conjugate base)
• During buffering strong acid or base is replaced by a weaker one, with a consequent reduction in the number of free hydrogen or hydroxyl ion

Buffer Pair

• Example: acetic acid and sodium acetate

• In that system, when an acid like HCL is added, the weak salt binds with H+ to form more weak acid, resisting pH change

• In that same system, when a base like NaOH is added, the H+ ions of the weak acid combine with OH- ions to form water, resisting pH change

Henderson-Hasselbalch Equation

• A weak acid (HA) ionizes as follows: HA->H+ + A-
• Kₐ = [H+][A-]/[HA], with Kₐ describing the the tendency of the acid to lose its proton (stronger acids have a greater tendency)
• Where [HA] = undissociated acid, [H+] = hydrogen ion, [A-] = conjugate base, then: [H+][A-] = Kₐ[HA]
• [H+] = Kₐ * ([HA] / [A-])
• -log [H+] = -log Kₐ -log ([HA] / [A-])
• pH = pKₐ -log ([HA] / [A-])
• pH = pKₐ + log ([A-] / [HA])
• When pH = pKₐ, the concentration of conjugate base is equal to concentration of undissociated acid

Factors determining a buffer’s effectiveness

• Effectiveness factors:

• Its pKa relative to pH of the solution

• Concentration

• A buffer works best within 1 pH unit above or below its pKa

• A buffer becomes more effective the more concentrated it is because the more concentrated solution contains more buffer molecules

• Buffering capacity is the efficiency of the buffer solution to resists the change in pH when acid or base is added, and is the # of gram equivalents of either hydrogen ion or hydroxyl ion required to change the pH of 1L of 1M solutions by 1 unit

Donnan's Membrane Equilibrium

• A semipermeable membrane permits the passage of small solutes (usually small molecules and solvent) but not colloids

• With two electrolyte solutions separated by a semipermeable membrane, non-diffusible ions lead to unequal diffusible ion distribution which is referred to as Donnan's Membrane Equilibrium

• Effect of non-diffusible solute

• Consider compartments A/B separated by semi-permeable membrane, freely permeable to Na+/Cl-, but impermeable to protein

Due to the Donnan effect: Cl- diffuses down its gradient from side B to A, going along with some Na+ because it is attracted to its opposite charge

• According to Donnan membrane theory, the diffusible ions will pass through the membrane, until the products of concentration of the diffusible ions products becomes the same on both sides: Na+ × Cl-
• At equilibrium, compartment A of this setup will have more osmotically active particles than compartment B because there is more ions present in compartment A than in compartment B.

Donnan's effects in the body:

Because proteisn are present inside the cells, there are more osmotically active particles than in interstitial fluid and Na+-K+-ATPase pump provides balance Due to differences in concentration of diffusible ions, electric differences are formed, because side A is more neagtive, which is balanced by opposite charges onthe memnbrane

• Due to the presence of more proteins in the blood, ionic movement occurs across the capillary walls

Biochemistry of Carbohydrates

• Carbohydrates are abundant bio molecules performing structural and functional roles, and are generally hydrated carbon molecules with a hydrogen and oxygen proportion 2:1
• Carbohydrates may be defined as poly hydroxy aldehydes or ketones, or any substances that yield one of these compounds upon hydrolysis
• Formula (CH2O) n , where n is 3 or larger
• Some carbohydrates contain nitrogen, phosphorous or sulphur

Biological importance of carbohydrates

• Carbohydrates provide the majority of energy for organisms
• Glucose is stored as glycogen in liver and muscle
• Carbohydrates give structure to cell walls and cell membranes
• Carbohydrates serve as metabolic intermediates
• Carbohydrates (e.g. Ribose, deoxyribose) comprise portions of nucleotides
• Carbohydrates play a role in lubrication, cellular intercommunication and immunity as well as protein and fatty acid metabolism

Carbohydrate classification

• Classified into four groups based on the sugar units they contain: Mono, Di, Oligo and Polysaccharides

• Monosaccharides exist as single units for basic sugars

• Monosaccharides are polyhydroxy aldehyde or ketone units that can not be hydrolyzed to basic sugars

• These can be sub-divided into trioses, tetroses, pentoses, hexoses, heptoses and octoses

• Carbohydrates with an aldehyde are called aldoses

• Carbohytrates with a ketone group are called ketoses

• Disaccharides Yield two basic sugars when hydrolyzed

• Oligosaccharides Yield 3–6 basic sugars when hydrolyzed

• Polysaccharides Yield more than 6 basic sugars when hydrolyzed

• The polysaccharides may be linear/branched and are named hexosans/pentosans, depending on type of sugar

Physiologically important monosaccharides - Pentoses

D-Ribose: nucleic acids, DNA, RNA, nucleotides, phosphates, and intermediates

• D-Ribulose: intermediates on HMP pathway
• D-Arabinose: Glycoproteins
• D-Xylose: Glycoproteins
• D-Lyxose: Isolated from the human heart muscle
• L- Xylulose: Uronic acid

Physiologically important monosaccharides - Hexoses:

D- Glucose: glycolisis, blood sugar D-Fructose: Seminal source of energy D- Galactose: Sythensizes Glycolipids D-Mannose: Constituents of many glycoprotiens

Isomerism in Carbohydrates

• Isomers are compounds having same molecular formulae but different structural forms.

• Asymmetric/chiral carbon atom (carbon w/4 different atoms) produce isomers

• Isomers are structural or stereoisomers

• Structural isomers: same molecular forula, but differ in chain length, position of other functional groups -Example: Glucose and fructose are structural (functional) isomers using (C6H1206)

• Stereoisomers: same molecular formulae, same structures but different spatial configuration -Number of isomers that may be formed depend on number of asymmetric/chiral carbons -A sugar containing nn asymmetric carbon atoms yields 2^n stereo isomers

Optical: Mirrors of each other

-Can rotate polarized light: right and d-dextrorotatory + or left - 1- levorotatory -Gluclose is dextrorotatory but fructose Levo rotatory; Dihydroxyacetone - no optical activity

Enantomers

-Non super imposed mirror images: D and L sugars -Arrangement of HH and OH determine if D or L using Glyceraldehyde as reference

Majority of human Monosaccharides

-Monosaccharides in the human body are mostly D - LArabinose may occur but D ussually utilized

Anomerism

-Ring instead of straight formation occurs

Anomeric carbom

-A molecule that differs at configuration 1 and configuration 2 - Aldoses/Ketoses known as anomers -Orientation about anomeric carbs leads to 2 isomers Alpa and betta sugars -If a hydroxyl group - low alpha -Or high, betta sugar is formed

Furanose: Ketas sugar

• Aldoose sugars: Mostly pyranose rings

• Mutarotation: Changes in the optical rotation without properities chainging otherwise -Mutarotation and change of equlilbrium between anonmers

Epimerism

-Stereosomers differ one chiral carbon or one chiral bond callled epimers - Glu and Gali are epimers: differing only at carbon 4

Rxns of monosaccharides

• Mild oxidation and forms aldonic acid
• Stronger oxidation and aldaric aicd
• Protectional - and a unitonic acid eg glu to glucuron

Reduction

• Aldehyde - forms -Alcohols Glcu - Srbit, Fruck/Mannil

Dehydration

Sugats lose water

Enolisation

Sugars in the presence of a base leads Sugar with 2 OH groups Eneidal Acti as a reducing sugar

Fischer

• Reaction with cynide leads to carbon production Wholls - Reverse

Osazone: Reacts with Phenyl hydrazine

• Forms crystals - glucose, fructose Glactose

Glycosides

When reaction forms, Glycosides are formed Ouabain is called a clyoside that inhibits atpose