Amino Acids and Proteins

1
Chapter 18

• Amino Acids and Proteins

2
An Introduction to Biochemistry

• Goal understand the structure of biomolecules
  and the relationship between their structures and
  their functions.
• Classes proteins, carbohydrates, lipids and
  nucleic acids.
• Biomolecules are often complex but their
  interactions and functional groups are no
  different than the simple organic molecules

3
Protein Structure and Function An Overview

• Proteins result from combining amino acids via
  peptide bonds.
• 20 amino acids are responsible for all proteins
  in living organisms (Table 18.3 memorize)

4
Protein Structure and Function An Overview

• The amino acids are a-amino acids.

5
Protein Structure and Function An Overview

• As mentioned Proteins are formed by combining
  amino acids through peptide bonds (amide bonds)

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Protein Structure and Function An Overview

• Dipeptide bond - 2 different amino acids combine
• Tripeptide bond - 3 different amino acids combine
• Polypeptide bond many amino acids are attached
  through peptide bonds

7
Protein Structure and Function An Overview

• Proteins have 4 levels of structure
• Primary structure
• Secondary structure
• Tertiary structure
• Quaternary structure

8
Protein Structure an Function An Overview
9
Amino Acids

• Intermolecular forces decide the shape and
  function of proteins
• Non-polar side chains hydrophobic
• Polar, acidic, and basic side chains
  hydrophilic

10
Acid-Base Properties of Amino Acids

• Amino acids contain an acidic COOH group and a
  basic NH2 group
• They can and do perform intermolecular acid-base
  reactions where the H of the COOH group is
  transferred to the NH2 group
• Result is a zwitterion

11
Acid-Base Properties of Amino Acids

• Zwitterions can act as an acid or as a base

12
Acid-Base Properties of Amino Acids

• Amino Acids are never present in their neutral
  form.
• The charge of an amino acid molecule depends on
  the amino acid and the pH of the medium solution.
• Isoelectric Point (pI) - the pH at which the
  overall charge of all the amino acids in a sample
  is zero.

13
Handedness

• Handedness affects everything you do. Same is
  true with biomolecules

14
Handedness

• Chiral Having right- or left-handedness with two
  different non- superimposable mirror image forms.

15
Handedness

• Achiral The opposite of chiral having
  superimposable mirror images and thus no right-
  or left- handedness.

16
Molecular Handedness and Amino Acids

• Some molecules exhibit chirality while others do
  not.

17
Molecular Handedness and Amino Acids

• Note Molecules that exhibit a chiral center have
  4 different groups on the central atom
• Enantiomers (optical isomers) 2 mirror image
  forms of a chiral molecule
• Stereoisomers molecules with the same formula
  but a different arrangement of the atoms
• Section 13.3 discussed cis-trans isomers
• Amino acids enantiomers D, L

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Molecular Handedness and Amino Acids

• Pairs of enantiomers have similar physical
  properties but they differ in their biological
  activity

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Primary Protein Structure

• Primary protein structure is described by the
  sequence in which the amino acids are linked by
  peptide bonds
• The amine will always be on the left side (N
  Terminal) and the carboxylic acid on the right (C
  Terminal)
• Build onto the right of the first acid
• The individual amino acids joined in the chain
  are referred to as residues

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Primary Protein Structure

• Angiotensin II The order must be

21
Shape-Determining Interactions in Proteins

• The structure-function relationship of a protein
  depends on the internal interactions holding the
  protein chains in place.
• Hydrogen bonds along the backbone
• Hydrogen bonds of the R groups
• Ionic attractions between R groups (salt bridge)
• Hydrophobic interactions
• Sulfur-Sulfur bonds

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Shape-Determining Interactions in Proteins
23
Secondary Protein Structure

• Secondary Protein Structure describes the spatial
  arrangement of the polypeptide backbones in the
  protein
• Depends on internal interaction between backbone
  atoms
• Fibrous Proteins
• a - Helix
• ß - Sheet
• Globular Proteins (even globular proteins contain
  sections that are fibrous)

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Secondary Protein Structure

• Alpha-helix
• Single protein chain
• The coil is held in place by H bonds every 4
  amino acid residue along the chain.
• The chain is a right-handed coil and the H bonds
  lie parallel to the vertical axis.
• Viewed from the top, the side chains point to the
  exterior of the helix.

25
Secondary Protein Structure

• Beta- Sheets
• Made up of several protein chains
• Chains lie side by side
• R-groups point above and below the sheet

26
Secondary Protein Structure

• Globular Proteins
• Globe-like shape
• Often contains irregularly shaped portions as
  well as fibrous portions
• Proteins are folded in what appears to be an
  irregular manner
• Structure varies with function
• Hydrophilic R-groups on the external surface of
  the protein account for their water solubility

27
Secondary Protein Structure
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Tertiary Protein Structure

• Tertiary Structure describes how the protein is
  folded and the shape that results
• Depends on interactions of the side chains that
  are far apart along the same backbone
• Each protein folds in a distinctive manner so as
  to maximize stability
• Governed by the interactions described previously

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Tertiary Protein Structure
30
Tertiary Protein Structure

• Native protein A protein with the shape
  (secondary, tertiary, and quaternary structure)
  in which it exists naturally and functions in
  living organisms.
• Simple protein A protein composed of only amino
  acid residues.
• Conjugated protein A protein that incorporates
  one or more nonamino acid units in its
  structure.

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Tertiary Protein Structure
32
Tertiary Protein Structure
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Quaternary Protein Structure

• Quaternary Protein Structure describes how more
  than one polypeptide subunits associate to form a
  three dimensional protein unit

34
Quaternary Protein Structure
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Chemical Properties of Proteins

• Hydrolysis of a protein occurs in the same way
  as the hydrolysis of an amide because that is
  what a peptide bond is the formation of an amide

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Chemical Properties of Proteins

• Denaturation the loss of secondary, tertiary,
  or quaternary protein structure due to disruption
  of noncovalent interactions and/or disulfide
  bonds that leaves peptide bonds and primary
  structure intact.

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Chemical Properties of Proteins

• Denaturation
• Heat
• Mechanical Agitation
• Detergents
• Organic Compounds
• pH change
• Inorganic Salts

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Homework

• 18.1, 18.3, 18.4, 18.5, 18.7, 18.8, 18.11, 18.12,
  18.13, 18.14, 18.15, 18.16, 18.17, 18.20, 18.21,
  18.23, 18.24, 18.25, 18.26, 18.29, 18.30, 18.31,
  18.32, 18.33, 18.34, 18.35, 18.36, 18.38, 18.39,
  18.42, 18.43, 18.44, 18.45, 18.46, 18.47, 18.48,
  18.49, 18.51, 18.53, 18.54, 18.56, 18.57, 18.58,
  18.59, 18.60, 18.61, 18.66, 18.68, 18.69, 18.70,
  18.88, 18.89, 18.90, 18.92, 18.96