1.4

• What is the general structure of an amino acid?

  Amino acids have a -COOH carboxyl group, an -NH2 amine group, and an R variable side group.
• What does the R variable side group of an amino acid consist of?

  The R variable side group consists of a carbon chain and may include other functional groups such as a benzene ring or -OH (alcohol).

  
• What test is used to confirm the presence of proteins in a sample?

  The Biuret test confirms the presence of peptide bonds.
• What are the steps involved in the Biuret test for proteins?

  1. Add equal volume of sodium hydroxide to the sample at room temperature. 2. Add drops of dilute copper (II) sulfate solution and swirl to mix.
• What indicates a positive result in the Biuret test?

  A positive result is indicated by a color change from blue to purple.
• How many amino acids are there?

  There are 20 amino acids.
• How do amino acids differ from one another?

  Amino acids differ only by their side 'R' group.
• How do dipeptides and polypeptides form?

  Dipeptides and polypeptides form through a condensation reaction that creates a peptide bond and eliminates a molecule of water.
• What is a dipeptide?

  A dipeptide consists of 2 amino acids.
• What is a polypeptide?

  A polypeptide consists of 3 or more amino acids.
• How many levels of protein structure are there?

  There are 4 levels of protein structure.
• What is the primary structure of a protein?

  The primary structure is the sequence, number, and type of amino acids in the polypeptide, determined by the sequence of codons on mRNA.
• What defines the secondary structure of a protein?

  The secondary structure is defined by hydrogen bonds forming between the oxygen of the carbonyl group and the hydrogen of the amine group.

  
• What are the two types of secondary protein structure?

  The two types of secondary protein structure are α-helix and β-pleated sheet.
• Describe the α-helix structure.

  The α-helix has all N-H bonds on the same side of the protein chain, forming a spiral shape with hydrogen bonds parallel to the helical axis.
• Describe the β-pleated sheet structure.

  The β-pleated sheet has N-H and C=O groups alternating from one side to the other.
• What is the tertiary structure of a protein?

  The tertiary structure is the 3D structure formed by further folding of the polypeptide.
• What types of bonds are present in the tertiary structure of proteins?

  The bonds present in the tertiary structure include disulfide bridges, ionic bonds, and hydrogen bonds.
• Describe disulfide bridges in the tertiary structure of proteins.

  Disulfide bridges are strong covalent S-S bonds between molecules of the amino acid cysteine.
• Describe ionic bonds in the tertiary structure of proteins.

  Ionic bonds are relatively strong bonds between charged R groups, which can break due to pH changes.
• Describe hydrogen bonds in the tertiary structure of proteins.

  Hydrogen bonds are numerous and easily broken interactions that contribute to the protein's 3D structure.
• What is the quaternary structure of a protein?

  The quaternary structure consists of functional proteins that may consist of more than one polypeptide, held together by the same types of bonds as the tertiary structure.

  
• What may be involved in the quaternary structure of proteins?

  The quaternary structure may involve the addition of prosthetic groups such as metal ions or phosphate groups.
• Describe the structure and function of globular proteins.

  Globular proteins are spherical and compact, with hydrophilic R groups facing outwards and hydrophobic R groups facing inwards, making them usually water-soluble and involved in metabolic processes.

  
• Describe the structure and function of fibrous proteins.

  Fibrous proteins can form long chains or fibers, are insoluble in water, and are useful for structure and support, such as collagen in skin.
• How can chromatography be used to identify amino acids in a mixture?

  Chromatography can identify amino acids by spotting the mixture onto a pencil origin line, allowing the solvent to run, and then using a revealing agent or UV light to see spots.

  
• What is the first step in using chromatography to identify amino acids?

  The first step is to use a capillary tube to spot the mixture onto a pencil origin line and place chromatography paper in solvent.

  
• What do amino acids move based on during chromatography?

  Amino acids move different distances based on their relative attraction to the paper and their solubility in the solvent.
• How can Rf values be used in chromatography?

  Rf values can be calculated and matched to a database to identify the amino acids.
• What are enzymes?

  Enzymes are biological catalysts for intra and extracellular reactions.
• How does the specific tertiary structure of an enzyme affect its function?

  The specific tertiary structure determines the shape of the active site, which is complementary to a specific substrate.
• What is the role of enzyme-substrate (ES) complexes?

  The formation of enzyme-substrate complexes lowers the activation energy of metabolic reactions.
• What is the induced fit model of enzyme action?

  The induced fit model suggests that the shape of the active site is not directly complementary to the substrate and is flexible, allowing for conformational changes to form ES complexes.

  
• How have models of enzyme action changed over time?

  Models of enzyme action have changed from the lock and key model, which suggested a rigid shape of the active site, to the induced fit model, which accounts for flexibility and allosteric site binding.

  
• How can a student identify the activation energy of a metabolic reaction from an energy level diagram?

  The activation energy can be identified as the difference between the free energy of the substrate and the peak of the curve.

  
• Name 5 factors that affect the rate of enzyme-controlled reactions.

  The factors are enzyme concentration, substrate concentration, concentration of inhibitors, pH, and temperature.
• How does enzyme concentration affect the rate of reaction?

  When substrate is in excess, the rate increases proportionally to enzyme concentration until the maximum number of ES complexes form.
• How does substrate concentration affect the rate of reaction?

  When enzyme concentration is fixed, the rate increases proportionally to substrate concentration until the maximum number of ES complexes form.
• How does temperature affect the rate of reaction?

  The rate increases as kinetic energy increases and peaks at optimum temperature, but above optimum, bonds in the tertiary structure break, leading to denaturation.

  
• How does pH affect the rate of reaction?

  Enzymes have a narrow optimum pH range, and outside this range, H+/OH- ions can interact with bonds in the tertiary structure, causing denaturation.