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Notes in Biochemistry
Notes in Biochemistry
What Is Biochemistry?
Biochemistry is the study of the chemistry of living things. This includes organic molecules and their chemical
reactions. Most people consider biochemistry to be synonymous with molecular biology.
• carbohydrates
• lipids
• proteins
• nucleic acids
Many of these molecules are complex molecules called polymers, which are made up of monomer subunits.
Biochemical molecules are based on carbon.
The a carbon is chiral or asymmetric ( 4 different groups are attached to the carbon; exception is glycine.)
Amino acids exist as stereoisomers (same molecular formula, but differ in arrangement of groups).
Designated D(right) or L(left).
Amino acids used in nature are of L configuration.
carboxylate group at top --> points awayside chain at bottom a amino group orientation determines
NH3+ on left = L
NH3+ on right = D
Can also use RS system of nomenclature.
Amino acids are grouped based upon the properties and structures of side chains.
3) sulfur-containing R groups
methionine - sulfur is internal (hydrophobic)
cysteine - sulfur is terminal --> highly reactive; can form disulfide bonds
4) side chains with alcohols
serine - b-hydroxyl groups --> hydrophilicthreonine - “
5) basic R groups
histidine - hydrophilic side chains - + charged at neutral pHlysine - “
arginine - strong base
asparagine - amide of aspartate - side groups uncharged --> polarglutamine - amide of glutamat- “
Amide groups can form H bonds with atoms of other polar amino acids.
Ionization of Amino Acids
All amino acids are have a neutral net charge at physiological pH (7.4).
The a carboxyl and a amino groups and any other ionizable groups determine charge.
Each amino acid has 2 or 3 pKa values (7 amino acids have side chains that are ionizable) (see Table 3.2). This
complicates the basic titration curve, so that there are 3 inflectionpoints rather than 2.
Can use titration curves for amino acids to show ionizable groups.
The isoelectric point (pI) is the pH at which the amino acid has no net charge = zwitterion.
If pH > pI, amino acid would be negatively charged.If pH < pI, amino acid would be
positively charged.If pH = pI, amino acid would have no charge.
1.Nonpolar, Aliphatic amino acids: The R groups in this class of amino acids are nonpolar and hydrophobic.
Glycine, Alanine, Valine, leucine, Isoleucine, Methionine, Proline.
2.Aromatic amino acids: Phenylalanine, tyrosine, and tryptophan, with their aromatic side chains, are relatively
nonpolar (hydrophobic). All can participate in hydrophobic interactions.
3.Polar, Uncharged amino acids: The R groups of these amino acids are more soluble in water, or more
hydrophilic, than those of the nonpolar amino acids, because they contain functional groups that form hydrogen
bonds with water. This class of amino acids includes serine, threonine, cysteine, asparagine, and glutamine.
4.Acidic amino acids: Amino acids in which R-group is acidic or negatively charged. Glutamic acid and Aspartic acid
5.Basic amino acids: Amino acids in which R-group is basic or positively charged. Lysine, Arginine, Histidine
Classification of amino acids on the basis of nutrition
• Essential amino acids (Nine)
Nine amino acids cannot be synthesized in the body and, therefore, must be present in the diet in order for protein
synthesis to occur.
These essential amino acids are histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine,
tryptophan, and valine.
• Non-essential amino acids (Eleven)
These amino acids can be synthesized in the body itself and hence do not necessarily need to be acquired
through diet.
These non-essential amino acids are Arginine, glutamine, tyrosine, cysteine, glycine, proline, serine, ornithine,
alanine, asparagine, and aspartate.
Classification of amino acids on the basis of the metabolic fate
1.Glucogenic amino acids: These amino acids serve as precursors of gluconeogenesis for glucose formation.
Glycine, alanine, serine, aspartic acid, asparagine, glutamic acid, glutamine, proline, valine, methionine, cysteine,
histidine, and arginine.
2.Ketogenic amino acids: These amino acids break down to form ketone bodies. Leucine and Lysine.
3.Both glucogenic and ketogenic amino acids: These amino acids break down to form precursors for both ketone
bodies and glucose. Isoleucine, Phenylalanine, Tryptophan, and tyrosine
Enzymes
Enzymes Definition
An enzyme is a protein biomolecule that acts as a biocatalyst by regulating the rate of various metabolic reactions
without itself being altered in the process.
• The name ‘enzyme’ literally means ‘in yeast’, and this
was referred to denote one of the most important
reactions involved in the production of ethyl alcohol
and carbon dioxide through the agency of an
enzyme zymase, present in yeast.
• Enzymes are biological catalysts that catalyze more
than 5000 different biochemical reactions taking
place in all living organisms.
• However, these are different from other catalysts
which are chemical and can last indefinitely.
Enzymes are proteins that are prone to damage and inactivation.
• Enzymes are also highly specific and usually act on a specific substrate of specific reactions.
Enzymes are much larger than the substrate they act on, and thus there are some
specific regions or sites on the enzyme for binding with the substrate, called active
sites. Even in enzymes that differ widely in their properties, the active site present in
their molecule possesses some common features;
1. The active site of an enzyme is a relatively small portion within an enzyme
molecule.
2. The active site is a 3-dimensional entity made up of groups that come from different parts of the linear amino
acid sequence.
3. The arrangement and orientation of atoms in the active site are well defined and highly specific, which is the
cause of the marked specificity of the enzymes. However, in some cases, the active site changes its
configuration in order to bind a substance.
4. The interactions or forces between the active site and the substrate molecule are relatively weak.
5. The active sites in the enzyme molecules are mostly present in grooves or crevices from where large
quantities of water are excluded.
Enzyme-substrate complex
• The enzyme-substrate complex is a transitional molecule formed after the substrate binds with the enzyme.
• The formation of the enzyme-substrate complex is important for several reasons. The most important and notable
reason is that the substrate binds with the enzyme temporarily and the enzyme is set free once the reaction is
complete.
• This allows a single enzyme molecule to be used millions of times, and thus, only a small amount of enzyme is
required in each cell.
• Another advantage of an enzyme-substrate complex is the reduction in the free energy (activation energy) required
for the substrate to rise into the high-energy transition state.
Enzyme specificity
Most enzymes are highly specific towards the substrate they act on. Enzyme specificity exists in a way that they may act on
one specific type of substrate molecule or on a group of structurally related compounds or on only one of the two optical
isomers of a compound or only one of the two geometrical isomers. Based on this, four patterns of enzyme specificity have
been recognized;
1. Absolute specificity
• Some enzymes are capable of acting on only one substrate, and an example of this is the enzyme urease that acts
only on urea to produce ammonia and carbon dioxide.
2. Group specificity
• Other enzymes catalyze all reactions of a structurally related group of compounds.
• It is observed in lactic dehydrogenase (LDH) that catalyzes the interconversion of pyruvic acid and lactic acid along
with a number of other structurally related compounds.
3. Optical specificity
• Another important form of specificity is seen in some enzymes where a certain enzyme will react with only one of
the two optical isomers of a compound.
• The oxidation of the D-amino acids to the corresponding keto acids by amino acid oxidase is an example of optical
specificity.
• Among the enzymes that exhibit optical specificity, some might interconvert the two optical isomers of a compound.
An example of this is alanine racemase that catalyzes the interconversion between L- and D-alanine.
4. Geometrical specificity
• Geometrical specificity is observed in some enzymes exhibit specificity towards the cis and trans forms.
• An example of this is the enzyme fumarase that catalyzes the interconversion of fumaric and malic acids
Functions/ Biological roles of Enzymes
Enzymes are vital for all biological processes, aiding in digestion, and metabolism. Besides, these are also involved in
several other processes;
1. Enzymes like kinases and phosphatases are important for cell regulation and signal transmission.
2. Different enzymes are produced throughout the body for the regulation of reactions involved in various
metabolic pathways.
3. The activation and inhibition of enzymes resulting in a negative feedback mechanism adjust the rate of
synthesis of intermediate metabolites according to the demands of the cells.
4. They also catalyze Post-translational modifications involving phosphorylation, glycosylation, and cleavage of
the polypeptide chain.
5. Some enzymes are also involved in the regulation of enzyme levels by changing the rate of
enzyme degradation.
6. Since a tight regulation of enzymes is essential for homeostasis, any changes in the enzyme structure and
production might result in diseases.
7. Enzymes synthesized in various organisms are also utilized in various industries for wine production, cheese
production, bread whitening, and designing fabrics.
Carbohydrates
In biochemical perspective, a carbohydrate is defined as polyhydroxy aldehyde
or ketone.
Aldehyde: H-C=O
Ketone: O=C-CH2OH
The number of carbons may also be indicated by adding syllables in the carbohydrate’s name:
ALDOHEXOSE- Aldo(aldehyde) HEX (Six) Ose (Carb group)
Glyceraldehyde – aldotriose
Dihydroxyacetone – ketotriose
• Same molecular formula but different functional groups = Tautomers
Sugars only differ in only one chiral carbon such as the case of D-mannose and D-glucose at C2.
These are called epimers.
Cyclization (Making into haworth or chair conformation) results to formation of a NEW chiral center in carbon 1, hence
leading to formation of ANOMERS designated as alpha (OH below the ring) or beta (OH above the ring) conformation
which may interconvert through mutarotation
TYPES OF CYCLIC
CARBOHYDRATES
Sugars in ring conformation may adopt a six-membered or a five-membered closed structures which
resembles pyran and furan rings.
CLASSIFICATION OF CARBOHYDRATES
Carbohydrates are classified according to the number of sugar units (Monomers) they contain:
a.Monosaccharides
b.Disaccharides Carbohydrates composed of two sugar units joined by a glycosidic bond
c.Oligosaccharides
d.Polysaccharides
Glycosidic bond-
Can be 1 → 2 bond or 1 → 3 bond or 1 → 4 bond.
Oligosaccharides – are made up of 3-10 monomeric sugar units which are commonly attached to proteins or lipids such as
the ABO antigens.
Polysaccharides – Carbohydrates composed of long chains of sugar molecules, usually more than ten residues.
Polysaccharides play significant roles in organisms as they serve as energy storage (glycogen and starch), provide
structure (cellulose and chitin) as well as protection to host (bacterial cell wall of Gram positive bacteria).
Functions of Carbohydrates:
1.Energy Source
2.Structural Support
3.Cell-mediated recognition
• Starch, the primary carbohydrate storage molecule in plants and Glycogen in animal liver and skeletal muscles both
contain amylose and amylopectin but differ in the frequency of branching points.
•Starch has branch points every 24-30 residues.
•Glycogen has branch points every 8-12 residues
Glycosaminoglycans
Unbranched polysaccharides that consists of alternating uronic acid and hexosamine residue
Hyaluronic acid – component of connective tissue, synovial fluid, and vitreous humor. Serves as shock absorbers and
lubricants
Heparin – not a constituent of connective tissue; occurs in the intracellular granules of mast cells in arterial walls.
Heparan sulfate – ubiquitous cell surface component; extracellular substance in blood vessels and brain
Plants don’t produce glycosaminoglycans
Glycoproteins
The polypeptide chains of glycoprotein are synthesized under genetic control
Carbohydrate chains are enzymatically added and covalently linked to the polypeptide chain without the guidance of the
nucleic acid template --- microheterogeneity
Types:
◦Proteoglycan
◦Peptidoglycan
◦Glycosylated protein
Proteoglycan
The brushlike structure of proteoglycans, together with the polyanionic character of keratan sulfate and chondroitin
sulfate cause these complexes to be highly hydrated.
Peptidoglycans
Gram positive bacteria have peptidoglycan layers in their surface which contains carbohydrates. Since
carbohydrates have polyhydroxyl groups that form hydrdogen bond with water, Gram positive bacteria can be stained by
dyes dissolved in water
Inborn Diseases
• Hartnup’s disease- Inability to absorb neutral amino acids including tryptophan, thus, leading to pellagra-like
condition.
• Albinism- Skin depigmentation due to tyrosinase deficiency.
• Alkaptonuria- Darkening of urine on standing due to oxidation of homogentisic acid into brownish-black pigment
caused by deficiency in homogentisate oxidase.
• Phenylketonuria- Caused by deficiency of phenylalanine hydroxylase.
• Maple syrup disease- Genetic deficiency of branched-chain alpha-ketodehydrogenase
Creatinine kinase
Enzymes Diseases
•Troponin I- increased with enzymes suddenly experienced nausea, chest pain that may feel like pressure,
tightness, pain, squeezing or aching, and pain or discomfort that spreads to the shoulder, arm, back, neck, jaw,
teeth or sometimes the upper belly.
• Tarui’s disease- Deficiency in Phosphofructokinase (PFK)
• Her - Deficiency in Liver glycogen phosphorylase
• McArdle’s- Muscle glycogen phosphorylase
WATER SOLUBLE VITAMINS DEFICIENCIES
1. B1 Thiamine: Wernicke-korsakoff, Beri-Beri
2. B2 Ribloflavin - Seborrheic Dermatitis, Glossitis, Cheilosis, Photophobia, Decrease ability of mitochondria to
generate ATP and Growth retardation
3. B3 Niacin - Pellagra: Dermatitis, Dementia, Diarrhea
4. B5 Pantothenic acid: Dermatitis in chicks, Burning foot disease
Folic acid: Spina bifida
5. B6 Pyridoxine- Peripheral neuropathy
6. B7 Biotin, Vitamin H- Dermatitis, Impaired Fat and carbohydrate metabolism
7. B9 Tetrahydrofolate, Folic acid, Pteroylglutamic acid- Megaloblastic anemia, Spina bifida
8. B12 Cyanocolamin, Hydroxocabalamin- Pernicious Anemia and Megablastic Anemia
Vitamin C – Scurvy
FAT SOLUBLE VITAMINS DEFICIENCIES
• Vitamin A - Nyctalopia, Xeropthalmia
• Vitamin D- Rickets, Osteomalacia
• Vitamin E-
• VITAMIN K- Bleeding (Decrease microflora in the intestines)
CARBOHYDRATES DISEASES
• Obesity. Non-insulin dependent diabetes mellitus (NIDDM) Cardiovascular disease.
Galactosemia- usually is caused by a defective component of the second major step in the metabolism of the
sugar galactose.
• Lactose Intolerance- unable to fully digest the sugar (lactose) in milk. As a result, they have diarrhea, gas and
bloating after eating or drinking dairy products.
• Hypoglycemia is a condition in which your blood sugar (glucose) level is lower than the standard range.
• Diabetes- A metabolic disorder in which the body has high sugar levels for prolonged periods of time.
• Type 1 diabetes juvenile diabetes- A chronic condition where the pancreas produces little or no insulin.
Autoimmune disease and insulin dependent.
• Type 2 diabetes mellitus, formerly known as adult-onset diabetes, is a form of diabetes mellitus that is
characterized by high blood sugar, insulin resistance, and relative lack of insulin.
• Gestational diabetes- A condition in which women develop diabetes (high blood sugar) during pregnancy.