Biochemistry: Proteins, Nucleic Acids, and Enzymes (Lecture Notes)

Proteins

• Acidic proteins

  • At physiological pH, such proteins are referred to as acidic proteins. Most blood proteins are acidic.

• Classification of proteins (by structure)

  • On the basis of structure, proteins are classified into three categories. (Slide shows options like nucleoprotein, mucoprotein, chromoprotein, globulin as identifiers of structural classes.)

• Simple proteins

  • Simple proteins on hydrolysis yield only amino acids.
  • Properties:
  • Solubility: simple proteins are soluble in water in many cases.
  • Histones (protein component of nucleoproteins) are soluble in water.
  • Globular molecules are soluble; some—through heating—may coagulate. Histones do not coagulate by heating.
  • Albumins (a class of simple proteins) are widely distributed, e.g., egg albumin, serum albumin, legumin from pulses.
  • Associated terms:
  • Peptide chain and amino acids are the basic building blocks of these simple proteins.

• Conjugated proteins

  • Definition: Conjugated proteins consist of a simple protein united with a non-protein substance, called the prosthetic group.
  • Example: Hemoglobin — globin is the protein part, hem is the iron-containing prosthetic pigment.
  • Nucleoproteins contain nucleic acids coupled with histone proteins.
  • Other conjugated protein classes:
  • Glycoproteins and mucoproteins (carbohydrate-protein complexes).
  • Mucoproteins: e.g., mucin of saliva; heparin of blood.
  • Lipoproteins: lipid-protein complexes found in brain, plasma membranes, milk, etc.
  • Conjugated proteins examples emphasize how non-protein components modulate function (e.g., oxygen transport, signaling, membranes).

• Derived proteins

  • Derived proteins are not found in nature in their native form; they are produced from native proteins by hydrolysis.
  • Examples include metaproteins and peptones (derivatives).

• Practice questions (from transcript prompts)

  • 1) All proteins are made up of the same amino acids; then how do proteins in humans/animals differ from those in other organisms?
  • 2) What are conjugated proteins? How do they differ from simple proteins? Give one example of each.
  • 3) Which of the following is a simple protein: nucleoprotein, a simple protein example from options (the transcript lists a question about simple vs conjugated forms).

Nucleic Acids

• Historical context and scientists

  • Friedrich Miescher (1869) discovered and isolated nucleic acids from pus cells.
  • Fuelgen (1924) showed that chromosomes contain DNA.
  • By 1938, DNA and RNA were recognized as two types of nucleic acids.
  • Erwin Chargaff (1950) quantified base composition: pyrimidines and purines occur in pairs; A+T and G+C ratios vary among species, but A+T/G+C ratio is constant within a species.
  • Wilkins and colleagues helped establish the regular placement of bases along DNA.
  • Watson and Crick (1953) proposed the DNA structure (double helix) based on these data; Crick was skilled in physics and X-ray crystallography, Watson in genetics.
  • The model and experiments: Franklin and Wilkins contributed critical X-ray data; Watson and Crick derived the double-helix model without performing the original experiments.

• Basic components of nucleic acids

  • Three types of molecules in nucleic acids:
  • a) 5-carbon sugar (pentose sugar)
  • b) Phosphoric acid (phosphate)
  • c) Nitrogen-containing bases
  • Nucleotides are the units formed when a phosphate attaches to the sugar of a nucleoside.
  • Nucleoside = sugar + base (no phosphate).
  • Types of bases:
  • Purines: Adenine (A) and Guanine (G)
  • Pyrimidines: Cytosine (C), Thymine (T), and Uracil (U)
  • In DNA, bases are A, T, C, G; In RNA, thymine is replaced by uracil (U).

• Structure of DNA

  • DNA is a very long chain of alternating sugar (deoxyribose) and phosphate groups; the sugar-phosphate backbone is regular.
  • Each sugar carries a base; base attached to the 1' carbon of the sugar; phosphate links the 5' carbon of one sugar to the 3' carbon of the next sugar (phosphodiester bond).
  • Nucleotides form a polynucleotide chain; the nucleotide unit consists of a sugar, a phosphate, and a base.
  • Nucleoside vs nucleotide:
  • Nucleoside = sugar + base
  • Nucleotide = sugar + base + phosphate
  • DNA nucleic acid structure features:
  • A single strand is not straight; it is helical.
  • Double-stranded DNA consists of two polynucleotide chains that are antiparallel and complementary.
  • Length measurements in the transcript reference: base-pair distance of ~3.4 \,\text{\AA} between neighboring base pairs; diameter of the helix ~20 \,\text{\AA}; one full turn spans ~10 \,\text{bp} with a pitch of ~3.4 \,\text{nm} (which is 34 \,\text{\AA}).

• DNA structure details (base pairing and geometry)

  • Base pairing rules (Watson–Crick):
  • Adenine (A) pairs with Thymine (T) via two hydrogen bonds; Guanine (G) pairs with Cytosine (C) via three hydrogen bonds.
  • In RNA, Adenine pairs with Uracil (U) instead of Thymine.
  • DNA sequence information is encoded by the order of bases; the sequence of one strand determines the sequence of the other (complementary strand).
  • DNA ends and directions:
  • 5' end and 3' end refer to the sugar's carbon atoms to which phosphates are attached.
  • The two strands run antiparallel (one 5'→3', the other 3'→5').

• DNA in different organisms and forms

  • DNA is found in the nucleus; also present in chloroplasts and mitochondria in some organisms.
  • Some organisms (e.g., certain phages such as φX174) can have single-stranded DNA.

• Ribonucleic acid (RNA)

  • RNA uses ribose sugar (not deoxyribose) and contains Uracil (U) instead of Thymine (T).
  • RNA is typically single-stranded, but can fold into structures with intramolecular base pairing to gain stability.
  • Types of cellular RNA:
  • Messenger RNA (mRNA): carries genetic information to arrange amino acids in a specific sequence. It is linear and accounts for about 3\% of total cellular RNA; molecular weight is in the millions.
  • Ribosomal RNA (rRNA): a major structural and functional component of ribosomes; constitutes about 80\%–90\% of cellular RNA and about 50\–60\% of the ribosome mass; synthesized in the nucleus; base-paired regions contribute to structure.
  • Transfer RNA (tRNA): small RNAs (~70\–80 nucleotides) with a cloverleaf structure; carries specific amino acids; contains an anticodon loop that recognizes codons on mRNA; the amino acid attachment site is at the 3' end (acceptor stem).
  • Structural notes:
  • mRNA synthesis begins at the 5' end of the DNA template and proceeds toward the 3' end.
  • tRNA structure features: anticodon loop, D-loop, TψC loop, and acceptor stem; anticodon pairs with the codon on mRNA during translation.
  • Holley (1965) contributed to understanding tRNA structure as cloverleaf.

• Do you know? (concept checks from transcript)

  • Difference between DNA and RNA mostly due to sugar (deoxyribose vs ribose) and bases (T vs U).
  • DNA vs RNA differentiation questions, and nucleotide naming.

Enzymes

• What are enzymes?

  • Enzymes are biological catalysts that accelerate chemical reactions in living cells at body temperature.
  • Without enzymes, many cellular reactions would occur too slowly to sustain life.
  • Discovery: German chemist Eduard Buchner discovered enzymes by showing that living cells are not strictly necessary for fermentation; yeast extracts could catalyze fermentation processes. He coined the term "enzyme" (from Greek en zyma, meaning 'in yeast').

• Terms and concepts related to enzymes

  • Substrate: the substance upon which an enzyme acts.
  • Endo-enzymes: enzymes that act inside the cell in which they are synthesized (e.g., chloroplast or mitochondrial enzymes).
  • Exo-enzymes: enzymes that act outside the cell in which they are synthesized (e.g., enzymes released by fungi).
  • Enzymes retain their catalytic properties when extracted from cells (i.e., many enzymes are active outside their native cellular context).
  • Co-factors: inorganic ions or organic molecules necessary for enzyme activity (e.g., Mg2+, Fe2+, Mn2+; nicotinamide and flavin mononucleotide as coenzymes).

• Components and types of enzymes

  • Most enzymes have a protein component and, in some cases, a non-protein prosthetic group; such enzymes are called conjugated enzymes.
  • Holoenzyme: the whole active enzyme, including its protein portion and prosthetic group.
  • Apoenzyme: the protein portion without the prosthetic group; inactive by itself.
  • Co-factors and coenzymes can be tightly bound (as in prosthetic groups) or loosely associated.
  • Two broad categories by chemical composition:
  • (i) Purely proteinaceous enzymes (e.g., proteases that catalyze protein hydrolysis).
  • (ii) Conjugated enzymes with non-protein prosthetic groups (e.g., heme-containing peroxidases, metal-containing enzymes).

• Examples and practical notes

  • Renin (enzyme used in cheese-making to coagulate milk protein casein) is often supplied in tablet form and originates from the stomach of calves.
  • Enzymes are highly specific, typically catalyzing a small set of reactions.
  • The active site is the region of the enzyme where substrate binding occurs; the substrate binds to this site to form the enzyme–substrate complex and undergo catalysis to yield products.

• Enzyme activity and regulation

  • Enzymes have an optimal pH range; extreme pH values can denature enzymes and reduce activity.
  • Temperature and pH effects are critical for enzyme function; most human enzymes have a narrow activity window.
  • The structure of enzymes is three-dimensional and highly specific; changes in conformation can alter activity.

• Summary points

  • Enzymes are classified by their protein nature and by the presence of prosthetic groups (holoenzyme vs apoenzyme; conjugated vs purely proteinaceous).
  • They act as catalysts, forming transient enzyme–substrate complexes and returning to their original state after product release.
  • Co-factors and coenzymes extend enzyme functionality beyond the amino acid sequence alone.