coils The and folds of secondary structure result from hydrogen bonds between repeating constituents of the polypeptide backbone Typical secondary structures are a coil called an helix and a folded structure called a pleated sheet
Animation: Secondary Protein Structure
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-21c
Secondary Structure
pleated sheet
Examples of amino acid subunits
helix
Fig. 5-21d
Abdominal glands of the spider secrete silk fibers made of a structural protein containing pleated sheets. The radiating strands, made of dry silk fibers, maintain the shape of the web. The spiral strands (capture strands) are elastic, stretching in response to wind, rain, and the touch of insects.
Tertiary structure is determined by interactions between R groups, rather than interactions between backbone constituents These interactions between R groups include hydrogen bonds, ionic bonds, hydrophobic interactions, and van der Waals interactions Strong covalent bonds called disulfide bridges may reinforce the proteins structure
Animation: Tertiary Protein Structure
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-21e
Tertiary Structure
Quaternary Structure
Fig. 5-21f
Hydrophobic interactions and van der Waals interactions Polypeptide backbone Hydrogen bond
Disulfide bridge
Ionic bond
Fig. 5-21g
Polypeptide chain
Chains
Iron Heme Chains Hemoglobin Collagen
Quaternary structure results when two or more polypeptide chains form one macromolecule Collagen is a fibrous protein consisting of three polypeptides coiled like a rope Hemoglobin is a globular protein consisting of four polypeptides: two alpha and two beta chains
Animation: Quaternary Protein Structure
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Sickle-Cell Disease: A Change in Primary Structure A slight change in primary structure can affect a proteins structure and ability to function Sickle-cell disease, an inherited blood disorder, results from a single amino acid substitution in the protein hemoglobin
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-22
Normal hemoglobin Primary structure Secondary and tertiary structures
Val His Leu Thr Pro Glu Glu
1
2
3
4
5
6
7
Primary structure Secondary and tertiary structures
Sickle-cell hemoglobin
Val His Leu Thr Pro Val Glu
1
2
3
4
5
6
7
subunit
Exposed hydrophobic region
subunit
Quaternary structure
Normal hemoglobin (top view)
Quaternary structure
Sickle-cell hemoglobin
Function
Molecules do not associate with one another; each carries oxygen.
Function
Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.
10 m Red blood cell shape Normal red blood cells are full of individual hemoglobin moledules, each carrying oxygen. Red blood cell shape Fibers of abnormal hemoglobin deform red blood cell into sickle shape.
10 m
Fig. 5-22a
Normal hemoglobin Primary structure Secondary and tertiary structures
Val His Leu Thr Pro Glu Glu
1
2
3
4
5
6
7
subunit
Quaternary structure
Normal hemoglobin (top view)
Function
Molecules do not associate with one another; each carries oxygen.
Fig. 5-22b
Primary structure Secondary and tertiary structures
Sickle-cell hemoglobin
Val His Leu Thr Pro Val Glu
1 Exposed hydrophobic region
2
3
4
5
6
7
subunit
Quaternary structure
Sickle-cell hemoglobin
Function
Molecules interact with one another and crystallize into a fiber; capacity to carry oxygen is greatly reduced.
Fig. 5-22c
10 m
10 m
Normal red blood cells are full of individual hemoglobin molecules, each carrying oxygen.
Fibers of abnormal hemoglobin deform red blood cell into sickle shape.
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 proteins native structure is called denaturation A denatured protein is biologically inactive
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-23
Denaturation
Normal protein
Renaturation
Denatured protein
Protein Folding in the Cell It is hard to predict a proteins structure from its primary structure Most proteins probably go through several states on their way to a stable structure Chaperonins are protein molecules that assist the proper folding of other proteins
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-24
Polypeptide folded Cap
Correctly protein
Hollow cylinder
Chaperonin (fully assembled)
Steps of Chaperonin 2 Action: 1 An unfolded polypeptide enters the cylinder from one end.
The cap attaches, causing the 3 The cap comes cylinder to change shape in off, and the properly such a way that it creates a folded protein is hydrophilic environment for released. the folding of the polypeptide.
Fig. 5-24a
Cap
Hollow cylinder
Chaperonin (fully assembled)
Fig. 5-24b
Polypeptide
Correctly folded protein
Steps of Chaperonin Action: 1 An unfolded polypeptide enters the cylinder from one end.
2 The cap attaches, causing the
cylinder to change shape in such a way that it creates a hydrophilic environment for the folding of the polypeptide.
3 The cap comes
off, and the properly folded protein is released.
Scientists use X-ray crystallography to determine a proteins structure Another method is nuclear magnetic resonance (NMR) spectroscopy, which does not require protein crystallization Bioinformatics uses computer programs to predict protein structure from amino acid sequences
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
Fig. 5-25
EXPERIMENT Diffracted X-rays X-ray source X-ray beam Crystal Digital detector X-ray diffraction pattern
RESULTS RNA polymerase DNA
RNA
Fig. 5-25a
EXPERIMENT Diffracted X-rays X-ray source X-ray beam Crystal Digital detector X-ray diffraction pattern
Fig. 5-25b
RESULTS
RNA polymerase
DNA
RNA
Concept 5.5: Nucleic acids store and transmit hereditary information The amino acid sequence of a polypeptide is programmed by a unit of inheritance called a gene Genes are made of DNA, a nucleic acid
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings
The Roles of Nucleic Acids There are two types of nucleic acids:
Deoxyribonucleic acid (DNA) Ribonucleic acid (RNA)
DNA provides directions for its own replication 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
Fig. 5-26-1
DNA
1 Synthesis of mRNA in the nucleus
mRNA
NUCLEUS CYTOPLASM
Fig. 5-26-2
DNA
1 Synthesis of mRNA in the nucleus
mRNA
NUCLEUS CYTOPLASM mRNA 2 Movement of mRNA into cytoplasm via nuclear pore
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
3 Synthesis of protein
Polypeptide
Amino acids
The Structure of Nucleic Acids Nucleic acids are polymers called polynucleotides Each polynucleotide is made of monomers called nucleotides Each nucleotide consists of a nitrogenous base, a pentose sugar, and a phosphate group The portion of a nucleotide without the phosphate group is called a nucleoside
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Fig. 5-27
5 end 5C 3C Nucleoside Nitrogenous base Cytosine (C)
Nitrogenous bases Pyrimidines
Thymine (T, in DNA) Uracil (U, in RNA) Purines
Phosphate group 5C 3C 3 end (a) Polynucleotide, or nucleic acid (b) Nucleotide
Sugar (pentose) Adenine (A) Sugars Guanine (G)
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components: sugars
Fig. 5-27ab
5' end 5'C 3'C Nucleoside Nitrogenous base 5'C
5'C 3'C 3' end (a) Polynucleotide, or nucleic acid
Phosphate group
3'C
Sugar (pentose)
(b) Nucleotide
Fig. 5-27c-1
Nitrogenous bases Pyrimidines
Cytosine (C)
Thymine (T, in DNA) Uracil (U, in RNA)
Purines
Adenine (A)
Guanine (G)
(c) Nucleoside components: nitrogenous bases
Fig. 5-27c-2
Sugars
Deoxyribose (in DNA)
Ribose (in RNA)
(c) Nucleoside components: sugars
Nucleotide Monomers Nucleoside = nitrogenous base + sugar There are two families of nitrogenous bases:
Pyrimidines (cytosine, thymine, and uracil) have a single six-membered ring Purines (adenine and guanine) have a sixmembered ring fused to a five-membered ring
In DNA, the sugar is deoxyribose; in RNA, the sugar is ribose Nucleotide = nucleoside + phosphate group
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Nucleotide Polymers
Nucleotide polymers are linked together to build a polynucleotide Adjacent nucleotides are joined by covalent bonds that form between the OH group on the 3 carbon of one nucleotide and the phosphate on the 5 carbon on the next These links create a backbone of sugarphosphate units with nitrogenous bases as appendages The sequence of bases along a DNA or mRNA polymer is unique for each gene
Copyright 2008 Pearson Education, Inc., publishing as Pearson Benjamin Cummings