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POLYPEPTIDE CHAIN

  • Polypeptides (proteins) are constructed from monomers known as amino acids.

AMINO ACIDS

  • Individual amino acids combine to form various polypeptide chains.

  • Examples of amino acids include:

    • Phenylalanine (Phe)

    • Leucine (Leu)

    • Serine (Ser)

    • Cysteine (Cys)

PEPTIDE BOND FORMATION

  • Peptides or proteins are assembled from amino acids during the process of translation in ribosomes.

  • The formation of a peptide bond occurs specifically between:

    • The amino group (NH2NH_2) of one amino acid and the carboxylic acid group (COOHCOOH) of another.

  • This bond formation releases a water molecule (dehydration reaction).

  • The formation of peptide bonds can be reversed by the action of protease enzymes.

AMINO ACID CHARGES

  • Charges and properties are based on the pKa of their side chains:

    • Arginine (Arg, R) - Positively charged, pKa approximately 12.1.

    • Histidine (His, H) - Positively charged, pKa approximately 6.0.

    • Lysine (Lys, K) - Positively charged.

    • Aspartic Acid (Asp, D) - Negatively charged.

    • Glutamic Acid (Glu, E) - Negatively charged.

    • Glycine (Gly, G) - Non-polar, small side chain.

    • Cysteine (Cys, C) - Contains sulfur, capable of forming disulfide bridges.

    • Selenocysteine (Sec, U) - Contains selenium.

  • Proteinogenic amino acids include such amino acids vital for protein synthesis.

THE CENTRAL DOGMA OF MOLECULAR BIOLOGY

  • Describes the flow of genetic information from DNA to mRNA to polypeptides:

    • DNA -> mRNA: Transcription

    • mRNA -> Polypeptides: Translation

    • Example sequence: DNA ATGATCTCGTAA translates to mRNA AUGAUCUCGUAA, which results in the polypeptide sequence Methionine (Met) - Isoleucine (Ile) - Serine (Ser) - STOP.

TYPES OF RNA INVOLVED IN PROTEIN SYNTHESIS

  • Messenger RNA (mRNA): carries the genetic code.

  • Ribosomal RNA (rRNA): forms the core of ribosome's structure and catalyzes protein synthesis.

  • Transfer RNA (tRNA): transports amino acids to the ribosome and matches them to the coded mRNA message.

LEVELS OF PROTEIN ORGANIZATION

  • Primary Structure: Sequence of amino acids (peptide chain).

  • Secondary Structure: Local folding into structures such as alpha helices and beta pleated sheets.

  • Tertiary Structure: Full three-dimensional configuration of a polypeptide chain.

  • Quaternary Structure: Assembly of multiple polypeptide subunits into a single functional unit.

HUMAN PROTEINS IN NUMBERS

  • Estimates suggest approximately 100,000 to 400,000 distinct proteins in the human body.

  • A typical human cell may contain about 42 million protein molecules.

  • Within a human body with approximately 30 trillion cells, this equates to roughly 10^21 total proteins.

  • Remarkably, around 20% of these proteins experience turnover (degradation and synthesis) daily.

TYPES OF PROTEINS AND THEIR FUNCTIONS

  • Transport proteins: e.g., Hemoglobin - Transports oxygen in the blood.

  • Hormonal proteins: e.g., Insulin - Regulates blood glucose levels.

  • Structural proteins: e.g., Collagen - Provides structural support in tissues.

  • Enzymes: e.g., Amylase - Catalyzes the breakdown of starch into sugars.

  • Motor proteins: e.g., Actin and Myosin - Facilitate muscle contraction.

  • Defense proteins: e.g., Antibodies - Protect against pathogens.

  • Regulatory proteins: e.g., Transcription factors - Control gene expression.

  • Various classes serve in distinct cellular functions, enhancing homeostasis and metabolic processes.

ENZYME FUNCTION: CATALYSIS

  • Enzymes function to catalyze biochemical reactions, which can include breakdown (catabolism) or synthesis (anabolism).

  • Classic example: Sucrose converted via an enzyme into glucose and fructose.

TYPES OF ENZYME REACTIONS

  • Oxidoreductases: Catalyze electron transfer reactions.

  • Transferases: Move functional groups between molecules.

  • Hydrolases: Use water to break chemical bonds.

  • Lyases: Add groups to, or remove groups from double-bonded molecules.

  • Isomerases: Rearrange molecules into isomers.

  • Ligases: Join two molecules with the use of ATP.

ENZYME CLASSIFICATION (EC NUMBERS)

  • Enzymes are classified by their reactions:

    • e.g., Amylase is classified EC 3.2.1.1 (hydrolase, glycosylase, acting on glycosyl compounds, amylase).

ENERGY FLOW IN METABOLISM

  • Catabolism - breaks down larger molecules and releases energy.

  • Anabolism - builds larger molecules, requiring energy.

  • Energy transfer in biochemical reactions depends on the formation and breaking of chemical bonds, described through concepts like activation energy and Gibb’s free energy.

GIBB'S FREE ENERGY AND REACTION THRESHOLDS

  • Activation energy (EaE_a): Minimum energy required to initiate a reaction.

  • Exothermic reactions release energy; endothermic reactions absorb energy.

  • The overall energy of a biochemical reaction depends on the energy of reactants versus products.

ENZYME KINETICS

  • Michaelis-Menten equation: Describes the rate of enzyme-mediated reactions.

  • Terms to note:

    • VmaxV_{max}: Maximum reaction rate.

    • K<em>mK<em>m: Michaelis constant, substrate concentration at which reaction rate is half of V</em>maxV</em>{max}.

    • The Lineweaver-Burk equation is a linear double-reciprocal plot of the Michaelis-Menten equation, aiding in the determination of enzyme kinetics.