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

Proteins: Structure and Function

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 near its isoelectric point and exists mainly as a zwitterion.

Peptide Bond Formation

Peptide bonds are formed by condensation reactions between the amino group of one amino acid and the carboxyl group of another, releasing water.

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

• Hydrolysis: The reverse reaction, breaking peptide bonds with water.

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

• 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) or Ala-Gly-Ser (three-letter).

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.

Attractive Forces: Include hydrogen bonding, ionic interactions, hydrophobic effects, and covalent disulfide bonds.

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, organic solvents, heavy metals, detergents.

• Effects: Disruption of secondary, tertiary, and quaternary structures.

• Hydrolysis: Cleaves peptide bonds, breaking the protein into amino acids.

Functions of Proteins

Proteins perform diverse roles in biological systems:

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

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

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

• Defense: Antibodies in the immune system.

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

Structure-Function Relationship: The specific shape of a protein determines its function (e.g., the active site of an enzyme).

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 or organic molecule).

• Coenzyme: Organic cofactor (often derived from vitamins).

• Prosthetic Group: Tightly bound cofactor.

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

• Induced-Fit Model: Active site molds to fit the substrate upon binding.

• Activation Energy: Enzymes lower the energy barrier for reactions.

Enzyme Activity Regulation

Enzyme activity is influenced by several factors:

• Substrate Concentration: Increased substrate increases rate until saturation.

• pH: Each enzyme has an optimal pH.

• Temperature: Rate increases with temperature up to a point, then decreases due to denaturation.

• Inhibition:

  • Competitive: Inhibitor competes with substrate for active site.

  • Noncompetitive: Inhibitor binds elsewhere, changing enzyme shape.

  • Irreversible: Inhibitor permanently inactivates enzyme.

Nucleic Acids: Structure and Function

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 structure).

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

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

• Nucleoside: Base + sugar.

• Nucleotide: Nucleoside + phosphate.

Condensation Reactions: Formation of nucleosides and nucleotides involves removal of water.

Formation and Structure of Nucleic Acids

Nucleic acids (DNA and RNA) are polymers of nucleotides linked by phosphodiester bonds.

• Phosphodiester Bond: Links 3' carbon of one sugar to 5' phosphate of the next.

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

• Structural Features: DNA is double-stranded and forms a double helix; RNA is usually single-stranded.

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 pairs with cytosine (G-C).

• Hydrogen Bonds: A-T has two hydrogen bonds; G-C has three.

Example: The complementary strand of 5'-AGCT-3' is 3'-TCGA-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 during translation.

• rRNA (ribosomal RNA): Structural and catalytic component of ribosomes.

• Transcription: DNA is copied into mRNA.

• Translation: mRNA is decoded to synthesize proteins.

Transcription Example: DNA 5'-ATG-3' is transcribed to mRNA 5'-AUG-3'.

Genetic Code and Translation

The genetic code is a set of three-nucleotide codons in mRNA that specify amino acids.

• Codon Table: Used to translate mRNA sequences into protein sequences.

• Template DNA: Can be used to predict mRNA and protein sequences.

Example: mRNA codon AUG codes for methionine (start codon).

Mutations and Their Effects

Mutations are changes in the nucleotide sequence of DNA, which can alter protein structure and function.

• Types: Substitution, insertion, deletion.

• Effects: May result in silent, missense, or nonsense mutations in proteins.

Viruses and Nucleic Acids

Viruses are infectious agents composed of nucleic acid (DNA or RNA) and a protein coat.

• Differences from Cells: Viruses lack cellular structure and metabolism.

• Structure: Nucleic acid core, protein capsid, sometimes an envelope.

• Infection: Viruses inject their genetic material into host cells to replicate.

• Vaccines: Stimulate immune response to viral components.

DNA Technology

Modern biotechnology manipulates nucleic acids for various applications.

• Recombinant DNA: Combining DNA from different sources.

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

Metabolism: Food as Fuel

Features of Metabolic Reactions

Metabolism encompasses all chemical reactions in living organisms, 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.

Metabolically Relevant Nucleotides

Certain nucleotides play key roles in energy transfer and redox reactions.

• ATP (Adenosine Triphosphate): Main energy currency.

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

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

High-Energy vs. Low-Energy Forms: ATP, NADH, and FADH2 are high-energy; ADP, NAD+, and FAD are low-energy.

Digestion of Food Molecules

Hydrolysis of macronutrients yields smaller molecules for metabolism.

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

• Lipids: Broken down to fatty acids and glycerol.

• Proteins: Broken down to amino acids.

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 Metabolism: Enters glycolysis at different points, depending on tissue.

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.

Electron Transport Chain and ATP Production

Reduced nucleotides (NADH, FADH2) donate electrons to the electron transport chain (ETC), driving ATP synthesis.

• Complexes I-IV: Transfer electrons and pump protons across the mitochondrial membrane.

• Coenzyme Q and Cytochrome c: Mobile electron carriers in the ETC.

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

ATP Yield from Oxidative Catabolism

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

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

• Glucose Oxidation: Complete oxidation yields approximately 30-32 ATP per glucose molecule.

Fatty Acid and Amino Acid Metabolism

Fatty acids and amino acids can also be catabolized for ATP production.

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

• ATP Calculation: The number of ATP from a fatty acid depends on its length (e.g., palmitic acid yields ~106 ATP).

• Ketone Bodies: Produced from acetyl-CoA during prolonged fasting or low carbohydrate intake.

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

Process	Main Substrate	Main Product	ATP Yield
Glycolysis	Glucose	Pyruvate	2 ATP (net)
Citric Acid Cycle	Acetyl-CoA	CO2, NADH, FADH2	1 GTP/ATP per turn
Electron Transport Chain	NADH, FADH2	ATP	~28 ATP per glucose
β-Oxidation	Fatty Acids	Acetyl-CoA	Varies (e.g., palmitate: ~106 ATP)

Additional info: Some details, such as the exact number of ATP per process, may vary depending on cell type and conditions.