CHEM 102 Exam 5 Study Guide: Proteins, Nucleic Acids, and Metabolism (Ch. 10-12)

Proteins: Structure, Function, and Enzymes

Structure of Amino Acids

Amino acids are the building blocks of proteins, each containing a central carbon atom (the alpha carbon) bonded to an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R group).

• General Structure: The general formula is $\mathrm{H_2N{-}CHR{-}COOH}$.

• Abbreviations: Amino acids are identified by their full name, three-letter, and one-letter abbreviations (e.g., Glycine: Gly, G).

• Polarity: Amino acids are classified as nonpolar, polar neutral, polar positive (basic), or polar negative (acidic) based on their side chains.

• Isoelectric Point (pI): The pI is the pH at which an amino acid has no net charge. Below the pI, the amino acid is positively charged; above the pI, it is negatively charged.

Example: At pH 7, glycine (pI ≈ 6) is close to neutral, but at pH 2, it is positively charged.

Peptide Bond Formation

Peptide bonds link amino acids via a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water.

• Condensation Reaction: $\mathrm{Amino\ acid_1 + Amino\ acid_2 \rightarrow Dipeptide + H_2O}$

• Peptide Naming: Peptides are named from the N-terminus (amino end) to the C-terminus (carboxyl end) using one- or three-letter codes.

• Drawing Peptides: Given abbreviations, the sequence can be drawn by connecting the alpha carbons via peptide bonds.

Example: The tripeptide Ala-Gly-Ser is written as AGS (one-letter code).

Levels of Protein Structure

Proteins fold into specific shapes, stabilized by various interactions, which are described in four structural levels:

• Primary: Linear sequence of amino acids.

• Secondary: Local folding into alpha-helices and beta-sheets, stabilized by hydrogen bonds.

• Tertiary: Overall 3D shape, stabilized by hydrophobic interactions, hydrogen bonds, ionic bonds, and disulfide bridges.

• Quaternary: Association of multiple polypeptide chains.

Example: Hemoglobin has quaternary structure with four subunits.

Protein Denaturation and Hydrolysis

Denaturation is the loss of protein structure (and function) without breaking peptide bonds, while hydrolysis breaks peptide bonds.

• Causes of Denaturation: Heat, pH changes, detergents, heavy metals, and organic solvents.

• Forces Affected: Disruption of hydrogen bonds, hydrophobic interactions, and ionic bonds.

• Hydrolysis: Cleavage of peptide bonds, producing free amino acids.

Example: Cooking an egg denatures its proteins.

Functions of Proteins

Proteins perform diverse roles in biological systems:

• Enzymes: Catalyze biochemical reactions (e.g., amylase).

• Structural: Provide support (e.g., collagen).

• Transport: Carry molecules (e.g., hemoglobin).

• Defense: Antibodies in the immune system.

• Regulation: Hormones (e.g., insulin).

Example: The shape of an enzyme's active site determines its specificity.

Enzyme Catalysis

Enzymes are biological catalysts that speed up reactions by lowering activation energy.

• Active Site: The region where the substrate binds and the reaction occurs.

• Substrate: The molecule upon which the enzyme acts.

• Cofactor: Non-protein helper (metal ion).

• Coenzyme: Organic cofactor (e.g., NAD+).

• Prosthetic Group: Tightly bound cofactor.

• Lock-and-Key Model: Substrate fits exactly into the active site.

• Induced-Fit Model: Active site changes shape to fit the substrate.

• Activation Energy: Lowered by enzyme, increasing reaction speed.

Example: Sucrase catalyzes the hydrolysis of sucrose.

Enzyme Activity Regulation

Enzyme activity is influenced by several factors:

• Substrate Concentration: Activity increases with substrate up to a maximum (saturation).

• pH and Temperature: Each enzyme has optimal pH and temperature.

• Inhibition:

  • Competitive: Inhibitor competes with substrate for active site.

  • Noncompetitive: Inhibitor binds elsewhere, changing enzyme shape.

  • Irreversible: Inhibitor permanently inactivates enzyme.

Example: Penicillin irreversibly inhibits bacterial enzymes.

Nucleic Acids: Structure, Function, and Genetic Information

Structure of Nucleotides and Nucleic Acids

Nucleotides are the monomers of nucleic acids, each composed of a nitrogenous base, a five-carbon sugar, and a phosphate group.

• Nitrogenous Bases: Five types: adenine (A), guanine (G), cytosine (C), thymine (T), uracil (U).

• Purines: Adenine and guanine (double-ring).

• Pyrimidines: Cytosine, thymine, uracil (single-ring).

• Sugars: Ribose (RNA) and deoxyribose (DNA).

• Nucleoside: Base + sugar.

• Nucleotide: Nucleoside + phosphate.

Example: ATP is a nucleotide with adenine, ribose, and three phosphates.

Formation and Structure of Nucleic Acids

Nucleic acids (DNA and RNA) are formed by condensation reactions linking nucleotides via phosphodiester bonds.

• Condensation Reaction: $\mathrm{Nucleotide_1 + Nucleotide_2 \rightarrow Dinucleotide + H_2O}$

• Abbreviation: Sequences are written using one-letter base codes (e.g., AGCT).

• Structural Features: DNA is double-stranded and helical; RNA is usually single-stranded.

Example: The DNA sequence 5'-ATCG-3' pairs with 3'-TAGC-5'.

DNA Structure and Base Pairing

DNA consists of two antiparallel strands held together by complementary base pairing.

• Base Pairs: Adenine pairs with thymine (A-T), guanine with cytosine (G-C).

• Double Helix: The two strands wind around each other.

Example: If one strand is 5'-GATTACA-3', the complementary strand is 3'-CTAATGT-5'.

RNA Types and Protein Synthesis

RNA plays several roles in protein synthesis:

• mRNA (messenger RNA): Carries genetic code from DNA to ribosome.

• tRNA (transfer RNA): Brings amino acids to ribosome.

• rRNA (ribosomal RNA): Forms part of the ribosome's structure.

• Transcription: DNA is copied into mRNA.

• Translation: mRNA is decoded to synthesize proteins.

Example: DNA 5'-TAC-3' is transcribed to mRNA 5'-AUG-3', which codes for methionine.

Genetic Code and Mutations

The genetic code translates nucleotide sequences into amino acid sequences.

• Codon: Three-base sequence in mRNA coding for an amino acid.

• Mutation: Change in nucleotide sequence, which may alter protein sequence and function.

Example: A point mutation in hemoglobin gene causes sickle cell anemia.

Viruses and Nucleic Acids

Viruses use nucleic acids to infect cells and replicate.

• Virus vs. Cell: Viruses lack cellular structure and metabolism; they require host cells to reproduce.

• Structure: Genetic material (DNA or RNA), protein coat (capsid), sometimes an envelope.

• Infection: Virus attaches to cell, injects genetic material, hijacks cell machinery.

• Vaccines: Stimulate immune response to viral components.

Example: Influenza virus is an RNA virus with a lipid envelope.

DNA Technology

Modern biotechnology manipulates nucleic acids for various applications.

• Recombinant DNA: Combining DNA from different sources.

• CRISPR: Genome editing tool using RNA-guided nucleases.

Example: Insulin production using recombinant DNA in bacteria.

Metabolism: Energy and Biochemical Pathways

Metabolic Reactions

Metabolism encompasses all chemical reactions in a cell, divided into catabolism and anabolism.

• Catabolism: Breakdown of molecules to release energy.

• Anabolism: Synthesis of complex molecules from simpler ones.

• Cellular Locations: Mitochondria (energy production), cytoplasm (glycolysis), etc.

Example: Glycolysis is a catabolic pathway in the cytoplasm.

Metabolically Relevant Nucleotides

Certain nucleotides act as energy carriers in metabolism.

• ATP (adenosine triphosphate): Main energy currency.

• NAD+ / NADH: Electron carrier (oxidized/reduced forms).

• FAD / FADH2: Electron carrier (oxidized/reduced forms).

Example: NADH is produced during glycolysis and the citric acid cycle.

Digestion of Food Molecules

Macromolecules are hydrolyzed into monomers during digestion.

• Carbohydrates: Broken down to monosaccharides (e.g., glucose).

• Lipids: Hydrolyzed to fatty acids and glycerol.

• Proteins: Hydrolyzed to amino acids.

Example: Starch is digested to glucose by amylase.

Glycolysis

Glycolysis is a ten-step pathway converting glucose to pyruvate, generating ATP and NADH.

• Net Reaction: $\mathrm{Glucose + 2\ ADP + 2\ NAD^+ + 2\ P_i \rightarrow 2\ Pyruvate + 2\ ATP + 2\ NADH + 2\ H_2O}$

• Anaerobic Fate: Pyruvate is reduced to lactate (in animals) or ethanol (in yeast).

• Aerobic Fate: Pyruvate enters mitochondria for further oxidation.

• Fructose: Enters glycolysis after conversion to intermediates.

Example: In muscle, anaerobic glycolysis produces lactate during intense exercise.

Citric Acid Cycle (Krebs Cycle)

The citric acid cycle oxidizes acetyl-CoA to CO2, generating NADH, FADH2, and GTP/ATP.

• Main Reactions: Eight steps, starting with acetyl-CoA and oxaloacetate forming citrate.

• Energy Output (per turn): 3 NADH, 1 FADH2, 1 GTP/ATP, 2 CO2.

Example: Each glucose yields two turns of the cycle.

Electron Transport Chain and ATP Production

Reduced nucleotides donate electrons to the electron transport chain (ETC), driving ATP synthesis.

• Complexes I-IV: Transfer electrons, pump protons to create a gradient.

• Coenzyme Q and Cytochrome c: Mobile electron carriers.

• Complex V (ATP Synthase): Uses proton gradient to synthesize ATP (chemiosmotic model).

Example: NADH donates electrons at Complex I; FADH2 at Complex II.

ATP Yield from Oxidative Catabolism

The total ATP produced from glucose oxidation can be calculated from the number of reduced nucleotides.

• ATP Equivalents: Each NADH yields about 2.5 ATP; each FADH2 about 1.5 ATP.

• Glucose Oxidation: $\mathrm{C_6H_{12}O_6 + 6\ O_2 \rightarrow 6\ CO_2 + 6\ H_2O + 30{-}32\ ATP}$

Example: Complete oxidation of one glucose yields approximately 30-32 ATP.

Fatty Acid and Amino Acid Catabolism

Fatty acids and amino acids can be oxidized to produce ATP.

• β-Oxidation: Fatty acids are broken down into acetyl-CoA units, producing NADH and FADH2.

• ATP Calculation: Each round of β-oxidation yields 1 NADH, 1 FADH2, and 1 acetyl-CoA.

• Ketone Bodies: Produced from excess acetyl-CoA during fasting.

• Urea Cycle: Converts toxic ammonia (from amino acid breakdown) to urea for excretion.

Example: Complete oxidation of palmitic acid (C16) yields about 106 ATP.

Process	Main Substrate	Main Product	ATP Yield (approx.)
Glycolysis	Glucose	2 Pyruvate	2 ATP (net), 2 NADH
Citric Acid Cycle	Acetyl-CoA	CO2	2 GTP/ATP, 6 NADH, 2 FADH2 (per glucose)
Electron Transport	NADH, FADH2	ATP, H2O	~28 ATP (per glucose)
β-Oxidation	Fatty Acids	Acetyl-CoA	~106 ATP (palmitate)

Additional info: For more detailed mechanisms and structures, refer to textbook figures and pathway diagrams.