Mcat Amino Acids

These R groups, or side chains, can be as simple as a single hydrogen atom or as complex as an imidazole ring. There are 20 different R groups—each of which you should commit to memory. We’ll discuss these side chains further in the next section.

Content Category 1A: Structure and function of proteins and their constituent amino acids

Macromolecules formed from amino acids adopt well-defined, three-dimensional structures with chemical properties that are responsible for their participation in virtually every process occurring within and between cells. The three-dimensional structure of proteins is a direct consequence of the nature of the covalently-bonded sequence of amino acids, their chemical and physical properties, and the way in which the whole assembly interacts with water.

Enzymes are proteins that interact in highly regio- and stereo-specific ways with dissolved solutes. They either facilitate the chemical transformation of these solutes or allow for their transport innocuously. Dissolved solutes compete for protein-binding sites, and protein conformational dynamics give rise to mechanisms capable of controlling enzymatic activity.

The infinite variability of potential amino acid sequences allows for adaptable responses to pathogenic organisms and materials. The rigidity of some amino acid sequences makes them suitable for structural roles in complex living systems.

Content in this category covers a range of protein behaviors which originate from the unique chemistry of amino acids themselves. Amino acid classifications and protein structural elements are covered. Special emphasis is placed on enzyme catalysis including mechanistic considerations, kinetics, models of enzyme-substrate interaction, and regulation.

• Absolute configuration at the α position
• Amino acids as dipolar ions
• Classifications
  • Acidic or basic
  • Hydrophobic or hydrophilic
  • Sulfur linkage: cysteine and cysteine
  • Peptide linkage: polypeptides and proteins
  • Hydrolysis
  • Ch. 2 Proteins: Composition and Structure, pp. 29-42
  • Ch. 3 Amino Acids, pp. 37-45
  • Ch.4 Amino Acids, pp. 80-96
  • Ch. 2 Chemical Composition of the Body, pp. 45-46
  • Ch. 7 The Nervous System and Neuronal Excitability, pp. 232-234
  • Ch. 21 The Digestive System, p. 775
  • Ch. 22 Metabolic Adaptations, Energy Balance, and Temperature Regulation, pp. 793-795
  • Ch. 2 The Chemical Basis of Life, pp. 48-60
  • Ch. 1.3D, pp. 41-42
  • Ch. 3.3-3.4 pp. 146-158
  • Ch. 15.6, pp. 309-316
  • Ch. 11.1-11.7, pp. 95-124

  Protein Structure (BIO, BC, OC)

  • 1° structure of proteins
  • 2° structure of proteins
  • 3° structure of proteins; role of proline, cystine, hydrophobic bonding
  • 4° structure of proteins (BIO, BC)
  • Denaturing and folding
  • Hydrophobic interactions
  • Solvation layer (entropy) (BC)
  • Isoelectric point
  • Electrophoresis
  • Ch. 2 Proteins: Composition and Structure, pp. 42-66
  • Ch. 3 Exploring Proteins and Proteomes, pp. 69-108
  • Ch. 4 Protein Three-Dimensional Structure, pp. 49-68
  • Ch. 5 Techniques in Protein Biochemistry, pp. 76-92
  • Ch. 3.4 Proteins
  • Ch. 5 Proteins: Primary Structure, pp. 97-130
  • Ch. 6 Proteins: Three- Dimensional Structure, pp. 131-179
  • Ch. 2 Chemical Composition of the Body, pp. 32, 45-48
  • Ch. 2 The Chemical Basis of Life, pp. 48-70
  • Ch. 18 Techniques in Cell and Molecular Biology pp. 712, 715-716
  • Ch. 2.5C pp. 113 – 115
  • Binding
  • Immune system
  • Motors
  • Ch. 7 Hemoglobin, pp. 207-225
  • Ch. 35 Immune System, pp. 1119-1149 (online chapter)
  • Chapter 36 Molecular Motors, pp. 1151-1168 (online chapter)
  • Ch. 9 Hemoglobin, An Allosteric Protein, pp. 161-173
  • 42.1 Innate Immune Response
  • Ch. 7 Protein Function: Myoglobin and Hemoglobin, Muscle Contraction and Antibodies, pp. 180-220
  • Ch. 2 Chemical Composition of the Body, pp. 48-52
  • Ch. 11 Muscle, pp. 382-385
  • Ch. 17 The Immune System, pp. 625-627
  • Ch. 2 The Chemical Basis of Life, pp. 73-76
  • Ch. 7 Interactions Between Cells and Their Environment, pp. 238-241
  • Ch. 9 The Cytoskeleton and Cell Motility, pp. 315-320
  • Function of enzymes in catalyzing biological reactions
  • Enzyme classification by reaction type
  • Reduction of activation energy
  • Substrates and enzyme specificity
  • Active Site Model
  • Induced-fit Model
  • Mechanism of catalysis
    • Cofactors
    • Coenzymes
    • Water-soluble vitamins
    • Ch. 8 Enzymes: Basic Concept and Kinetics, pp. 233-264
    • Ch. 9 Catalytic Strategies, pp. 273-306
    • Ch. 6 Basic Concepts of Enzyme Action, pp. 105-115
    • 6.5 Enzymes
    • Ch.11 Enzymatic Catalysis, pp. 322-360
    • Ch. 4 Energy and Metabolism, pp. 102-106
    • Ch. 21 The Digestive System, pp. 762-763
    • Ch. 3 Bioenergetics, Enzymes, and Metabolism, pp. 89-97, 106
    • Ch. 6.1-6.4, pp. 303-324
    • Kinetics
      • General (catalysis)
      • Michaelis-Menten
      • Cooperativity
      • Competitive
      • Noncompetitive
      • Mixed (BC)
      • Uncompetitive (BC)
      • Allosteric enzymes
      • Covalently modified enzymes
      • Zymogen
      • Ch. 8 Enzymes: Basic Concept and Kinetics, pp. 233-264
      • Ch. 10 Regulatory Strategies, pp. 309-335
      • Ch. 7 Kinetics and Regulation, pp. 119-134
      • Ch. 8 Mechanisms and Inhibitor, pp. 143-156
      • 6.5 Enzymes
      • Ch. 12 Enzyme Kinetics, Inhibition, and Control, pp. 361-401
      • Ch. 2 Chemical Composition of the Body, pp. 51-52
      • Ch. 4 Energy and Metabolism, pp. 102-106
      • Ch. 3 Bioenergetics, Enzymes, and Metabolism, pp. 97-100, 109-110

      Proteins for the MCAT: Everything You Need to Know

      Learn key MCAT concepts about proteins, the structure and classification of amino acids, plus practice questions and answers

      

      (Note: This guide is part of our MCAT Biochemistry series.)

      Part 1: Introduction to proteins

      Part 2: Amino acids

      a) Structure of amino acids

      b) Classifying amino acids

      Part 3: Peptide bonds

      a) Formation

      b) Hydrolysis

      Part 4: Protein structure

      a) Primary, secondary, tertiary, and quaternary structures

      b) Specialized amino acids

      c) Stability and interactions

      d) Protein folding

      Part 5: High-yield terms

      Part 6: Passage-based questions and answers

      Part 7: Standalone questions and answers

      Part 1: Introduction to proteins

      Proteins are an incredibly high-yield concept on the MCAT, but like a lot of biochemistry topics, they aren’t easily mastered without a great deal of practice. These topics are especially intimidating because there is virtually no limit to what you can learn about proteins, amino acids, and everything else.

      This guide will serve as an introduction to amino acids, protein structure, and protein interactions. While it will not be a comprehensive handbook to everything about proteins, it will be a good place to start studying these basic principles of biochemistry. Be sure to refer to our other biochemistry guides for further information on proteins, enzymes, and other biological molecules.

      Throughout the guide, you will encounter several bolded terms. Their definitions are particularly important and can also be found in Part 4 of this guide. At the end of this guide, you will also find several passage-based and standalone questions to sharpen your skills.

      Part 2: Amino acids

      a) Structure of amino acids

      Amino acids are the building blocks of all proteins. The structures of amino acids are an extremely high-yield topic to study.

      The structure of each amino acid can be divided into three separate regions:

      • The amino group, or N-terminus
      • The carboxylic acid group, or C-terminus
      • A unique identifying side chain, or R-group

      

      Recall that an amino group is a functional group composed of NH3+. It is similar to ammonium (NH4+), except that at one position, the nitrogen is attached to a carbon instead of a hydrogen (NH2C instead of NH3). Note that this results in one free electron pair on the nitrogen atom. At physiological pH (pH ~7), this free electron pair is able to accept a bond to a single hydrogen atom. This results in a positive charge on the functional group.

      The acid on every amino acid is a carboxylic acid, a functional group composed of COOH. At physiological pH (pH ~7), this carboxylic acid is deprotonated, leaving a negative charge on the functional group.

      Note that at physiological pH, amino acids are zwitterions; they contain both positive and negative charges on the same molecule. Most amino acids have a net charge of zero. Exceptions arise when accounting for charges on the R-group, or side chain, of the amino acid.

      These R groups, or side chains, can be as simple as a single hydrogen atom or as complex as an imidazole ring. There are 20 different R groups—each of which you should commit to memory. We’ll discuss these side chains further in the next section.

      The R group is connected to the central carbon, which is known as the alpha carbon. This carbon is connected to every constituent of the amino acid: the amino group (-NH3+), the carboxylic acid part (-COO-), the R group, and a hydrogen atom (H).

      Note that for 19 of the 20 amino acids, the alpha carbon itself is chiral, or attached to four different constituent groups. (The exception happens to be glycine, as the R group is simply a hydrogen atom.) Chirality refers to right- or left-handedness, denoted as D- and L- molecules, respectively. The chirality of biological molecules becomes quite important, as only L-configuration (left-handed) amino acids can be used by the body. (D-amino acids are not naturally found in eukaryotic metabolic pathways.)

      b) Classifying amino acids

      Each amino acid has a characteristic side chain, and the properties of these side chains are essential for the function of proteins.