Macromolecules of Life Proteins and Nucleic Acids Chapter 5

You already know a lot about proteins! You’ve been working with them in lab for the past 2-3 weeks! Biuret – [protein] Gel Electrophoresis Enzymes

Protein Definition Consists of one or more polypeptides folded, coiled, and twisted into a specific 3D shape Proteios – “first place” There are many different shapes of proteins depending on its FUNCTION Enzymes Cell signaling Defense Structural support Transport Receptors

Two similar terms Protein – already defined Polypeptide – polymer made of repeating subunits of amino acids (monomer) – usually refers to a long linear strand of amino acids that will then get folded into a 3D shape (protein)

Dehydration removes a water molecule, forming a new bond H2O Fig. 5-2a HO 1 2 3 H HO H Short polymer Unlinked monomer Dehydration removes a water molecule, forming a new bond H2O Figure 5.2 The synthesis and breakdown of polymers HO 1 2 3 4 H Longer polymer (a) Dehydration reaction in the synthesis of a polymer

HO 1 2 3 4 H H2O HO 1 2 3 H HO H (b) Hydrolysis adds a water Fig. 5-2b HO 1 2 3 4 H Hydrolysis adds a water molecule, breaking a bond H2O Figure 5.2 The synthesis and breakdown of polymers HO 1 2 3 H HO H (b) Hydrolysis of a polymer

Fig. 5-UN1  carbon Amino group Carboxyl group

Fig. 5-17 Figure 5.17 The 20 amino acids of proteins Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Methionine (Met or M) Phenylalanine (Phe or F) Trypotphan (Trp or W) Proline (Pro or P) Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Figure 5.17 The 20 amino acids of proteins Electrically charged Acidic Basic Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Fig. 5-17a Nonpolar Glycine (Gly or G) Alanine (Ala or A) Valine (Val or V) Leucine (Leu or L) Isoleucine (Ile or I) Figure 5.17 The 20 amino acids of proteins Methionine (Met or M) Phenylalanine (Phe or F) Tryptophan (Trp or W) Proline (Pro or P)

Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Fig. 5-17b Polar Serine (Ser or S) Threonine (Thr or T) Cysteine (Cys or C) Tyrosine (Tyr or Y) Asparagine (Asn or N) Glutamine (Gln or Q) Figure 5.17 The 20 amino acids of proteins

Electrically charged Acidic Basic Aspartic acid (Asp or D) Fig. 5-17c Electrically charged Acidic Basic Figure 5.17 The 20 amino acids of proteins Aspartic acid (Asp or D) Glutamic acid (Glu or E) Lysine (Lys or K) Arginine (Arg or R) Histidine (His or H)

Amino end (N-terminus) Carboxyl end (C-terminus) Fig. 5-18 Peptide bond (a) Side chains Peptide bond Figure 5.18 Making a polypeptide chain Backbone Amino end (N-terminus) Carboxyl end (C-terminus) (b)

Fig. 5-UN5

Fig. 5-21 Primary Structure Secondary Structure Tertiary Structure Quaternary Structure  pleated sheet +H3N Amino end Examples of amino acid subunits  helix Figure 5.21 Levels of protein structure—primary structure

Primary Structure Amino end Amino acid subunits +H3N 1 5 10 15 20 25 Fig. 5-21a Primary Structure 1 5 +H3N Amino end 10 Amino acid subunits 15 Figure 5.21 Levels of protein structure—primary structure 20 25

Fig. 5-21b Figure 5.21 Levels of protein structure—primary structure +H3N Amino end 5 10 15 Amino acid subunits 20 25 75 80 Figure 5.21 Levels of protein structure—primary structure 85 90 95 105 100 110 115 120 125 Carboxyl end

Secondary Structure  pleated sheet Examples of amino acid subunits Fig. 5-21c Secondary Structure  pleated sheet Examples of amino acid subunits Figure 5.21 Levels of protein structure—secondary structure  helix

Hydrophobic interactions and van der Waals interactions Polypeptide Fig. 5-21f Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond Disulfide bridge Figure 5.21 Levels of protein structure—tertiary and quaternary structures Ionic bond

Tertiary Structure Quaternary Structure Fig. 5-21e Tertiary Structure Quaternary Structure Figure 5.21 Levels of protein structure—tertiary and quaternary structures

Polypeptide  Chains chain Iron Heme  Chains Hemoglobin Collagen Fig. 5-21g Polypeptide chain  Chains Iron Figure 5.21 Levels of protein structure—tertiary and quaternary structures Heme  Chains Hemoglobin Collagen

Normal hemoglobin Primary structure 1 2 3 4 5 6 7 Secondary Fig. 5-22a Normal hemoglobin Primary structure Val His Leu Thr Pro Glu Glu 1 2 3 4 5 6 7 Secondary and tertiary structures  subunit   Quaternary structure Normal hemoglobin (top view)   Figure 5.22 A single amino acid substitution in a protein causes sickle-cell disease Function Molecules do not associate with one another; each carries oxygen.

Sickle-cell hemoglobin Primary structure 1 2 3 4 5 6 7 Fig. 5-22b Sickle-cell hemoglobin Primary structure Val His Leu Thr Pro Val Glu 1 2 3 4 5 6 7 Exposed hydrophobic region Secondary and tertiary structures  subunit   Quaternary structure Sickle-cell hemoglobin   Figure 5.22 A single amino acid substitution in a protein causes sickle-cell disease Function Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.

10 µm 10 µm Normal red blood cells are full of individual hemoglobin Fig. 5-22c 10 µm 10 µm Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen. Fibers of abnormal hemoglobin deform red blood cell into sickle shape. Figure 5.22 A single amino acid substitution in a protein causes sickle-cell disease

What Determines Protein Structure? In addition to primary structure, physical and chemical conditions can affect structure Alterations in pH, salt concentration, temperature, or other environmental factors can cause a protein to unravel This loss of a protein’s native structure is called denaturation A denatured protein is biologically inactive Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

Denaturation Normal protein Denatured protein Renaturation Fig. 5-23 Figure 5.23 Denaturation and renaturation of a protein Normal protein Denatured protein Renaturation

The Roles of Nucleic Acids There are two types of nucleic acids: Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA) DNA directs synthesis of messenger RNA (mRNA) and, through mRNA, controls protein synthesis Protein synthesis occurs in ribosomes Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Fig. 5-26-3 DNA 1 Synthesis of mRNA in the nucleus mRNA NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore Ribosome Figure 5.26 DNA → RNA → protein 3 Synthesis of protein Amino acids Polypeptide

Nitrogenous base Phosphate group Sugar (pentose) Fig. 5-27ab 5' end 5'C 3'C Nucleoside Nitrogenous base 5'C Phosphate group Figure 5.27 Components of nucleic acids 3'C Sugar (pentose) 5'C 3'C (b) Nucleotide 3' end (a) Polynucleotide, or nucleic acid

(c) Nucleoside components: nitrogenous bases Fig. 5-27c-1 Nitrogenous bases Pyrimidines Cytosine (C) Thymine (T, in DNA) Uracil (U, in RNA) Purines Figure 5.27 Components of nucleic acids Adenine (A) Guanine (G) (c) Nucleoside components: nitrogenous bases

(c) Nucleoside components: sugars Fig. 5-27c-2 Sugars Deoxyribose (in DNA) Ribose (in RNA) Figure 5.27 Components of nucleic acids (c) Nucleoside components: sugars

The nitrogenous bases in DNA pair up and form hydrogen bonds: Nucleotide Polymers Adjacent nucleotides are joined by covalent bonds (phosphodiester linkage) The nitrogenous bases in DNA pair up and form hydrogen bonds: adenine (A) always with thymine (T) guanine (G) always with cytosine (C) Forms a double helix Copyright © 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings

5' end 3' end Sugar-phosphate backbones Base pair (joined by Fig. 5-28 5' end 3' end Sugar-phosphate backbones Base pair (joined by hydrogen bonding) Old strands Nucleotide about to be added to a new strand 3' end Figure 5.28 The DNA double helix and its replication 5' end New strands 5' end 3' end 5' end 3' end