Back to AI Flashcard MakerChemistry /Chemistry: 3.13 Amino Acids Part 2
What are proteins?
Naturally occurring polymers of amino acids.
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Key Terms
Term
Definition
What are proteins?
Naturally occurring polymers of amino acids.
What are amino acids usually joined by?
A peptide link.
What 3 levels of structure do all proteins have?
Primary, secondary, and tertiary.
What do proteins with more than one polypeptide chain also have?
Quaternary structure.
Primary structure
The sequence of amino acids in a protein chain.
How can the primary structure be represented?
Using the sequence of 3 letter codes for the amino acid residues in the chain.
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| Term | Definition |
|---|---|
What are proteins? | Naturally occurring polymers of amino acids. |
What are amino acids usually joined by? | A peptide link. |
What 3 levels of structure do all proteins have? | Primary, secondary, and tertiary. |
What do proteins with more than one polypeptide chain also have? | Quaternary structure. |
Primary structure | The sequence of amino acids in a protein chain. |
How can the primary structure be represented? | Using the sequence of 3 letter codes for the amino acid residues in the chain. |
What is the primary structure's stability? | Relatively stable. |
Secondary structure | A regular 3D structure formed by part of a protein chain such as an alpha helix or beta pleated sheet. |
How is the secondary structure of proteins held together? | By hydrogen bonding between the delta + H of one peptide link and the lone pair O of an adjacent peptide link. |
Why is secondary structure disrupted more easily than primary? | Hydrogen bonds are much weaker than covalent bonds. |
Tertiary structure | 3D arrangement of a single polypeptide chain. |
What is the tertiary structure held together by? | Van der Waals forces, hydrogen bonds, ionic bonds, and disulfide bonds. |
Where do Van der Waals forces form in tertiary structure? | Between non-polar amino acid side chains. |
Where do hydrogen bonds form in tertiary structure? | Between C=O and N-H groups in the backbone of the protein and between side chains containing groups such as OH. |
Where do ionic bonds form in tertiary structure? | Between amino acid side chains containing charged groups, e.g., NH3+ and COO-. |
Where do disulfide bonds form in tertiary structure? | Link different parts of the protein chain together and help stabilize the tertiary structure. |
S-S bonds | A covalent bond formed from the thiol groups of a pair of cysteine residues. |
Enzymes | A protein-based catalyst that speeds up the rate of a particular reaction in a living organism. |
Substrate | The compound that an enzyme acts upon. |
What is the region responsible for an enzyme's catalytic activity called? | An active site. |
Which molecules can fit the enzyme's active site and bind to the enzyme? | Only substrate molecules with a correct stereochemistry. |
Stereospecificity | Active site can be so selective of the substrate shape that many enzymes only catalyze the reaction of one enantiomer of an optically active compound. |
What does substrate bind to active site using a combination of and what is this called? | Van der Waals forces, dipole-dipole, hydrogen bonds, and ionic bonds. |
Lock and key hypothesis | The idea that the active site of an enzyme and the substrate have specific complementary geometric shapes that fit exactly into one another. |
What does the induced fit model state that the substrate binding to the active site induces a change in? | The shape of the active site to allow the substrate to fit perfectly. |
Induced fit model: bonds between enzyme and substrate promote | Movement of electrons within the substrate. |
Induced fit model: what does movement of electrons in substrate make easier? | Breaking and forming bonds. |
Induced fit model: what does ease of breaking and forming bonds lower? | Activation energy for enzyme-catalyzed reaction. |
What can lactic acid be oxidized using? | An enzyme catalase LDH. |
Equation for oxidation of lactic acid | H3COHHCOOH > CH3=O HCOOH. |
Why does lactic acid have two enantiomers? | Due to the presence of a chiral C atom. |
Why can LDH only bind to one of the enantiomers of lactic acid? | It’s stereospecific. |
What does an inhibitor have a similar shape to? | The substrate. |
What is the inhibitor able to do due to it being a similar shape to the substrate? | Bind to the active site and prevent the substrate from binding. |
What does amount of inhibition depend on? | Relative concentrations of inhibitor and substrate. |
How do many drugs act? | By inhibiting the activity of an enzyme that catalyzes a harmful reaction. |
What is the modern-day drug design known as? | Structure-directed drug design. |
Structure-directed drug design: how can tertiary structure of enzymes be determined? | Using X-ray crystallography, NMR, and other techniques. |
Structure-directed drug design: how else is it possible to predict the tertiary structure from an enzyme's primary structure? | Using computer modeling. |
Structure-directed drug design: what can information about the structure of the active site be used for? | To design inhibitor molecules, again using computer modeling. |
What is DNA? | Deoxyribonucleic acid. |