1. Chapter 3
Proteins

2. You Must Know
How the sequence and subcomponents of proteins determine their properties.
The cellular functions of proteins. (Brief – we will come back to this in other chapters.)
The four structural levels of proteins and how changes at any level can affect the activity of the protein.
How proteins reach their final shape (conformation), the denaturing impact that heat and pH can have on protein structure, and how these may affect the organism.
The directionality of proteins (the amino and carboxyl ends).

3. Proteins account for more than 50% of the dry mass of most cells.
Concept 3.5: Proteins include a diversity of structures, resulting in a wide range of functions
Proteins account for more than 50% of the dry mass of most cells.
Protein functions include defense, storage, transport, cellular communication, movement, and structural support.
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4. Life would not be possible without enzymes.
Enzymatic proteins act as catalysts, to speed up chemical reactions without being consumed by the reaction
Enzyme
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5. Polypeptides are unbranched polymers built from the same set of 20 amino acids
A protein is a biologically functional molecule that consists of one or more polypeptides
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6. Amino Acids: the monomers of proteins
Figure 3.UN04
Amino Acids: the monomers of proteins
Side chain (R group)
 carbon
Amino acids are organic molecules with carboxyl and amino groups.
Amino acids differ in their properties due to differing side chains, called R groups.
Amino
group
Carboxyl
group 6

7. What do the side chains of these amino acids have in common?
Figure 3.17a
What do the side chains of these amino acids have in common?
Side chain
(R group)
Glycine
(Gly or G)
Alanine
(Ala or A)
Valine
(Val or V)
Leucine
(Leu or L)
Isoleucine
(le or )
Nonpolar side chains; hydrophobic
Methionine
(Met or M)
Phenylalanine
(Phe or F)
Tryptophan
(Trp or W)
Proline
(Pro or P) 7

8. What do the side chains of these amino acids have in common?
Figure 3.17b
What do the side chains of these amino acids have in common?
Serine
(Ser or S)
Threonine
(Thr or T)
Cysteine
(Cys or C)
Figure 3.17b The 20 amino acids of proteins (part 2: polar)
Polar side chains; hydrophilic
Tyrosine
(Tyr or Y)
Asparagine
(Asn or N)
Glutamine
(Gln or Q) 8

9. What do the side chains of these amino acids have in common?
Figure 3.17c
What do the side chains of these amino acids have in common?
Aspartic acid
(Asp or D)
Glutamic acid
(Glu or E)
Figure 3.17c The 20 amino acids of proteins (part 3: charged)
Electrically charged side chains; hydrophilic
Acidic amino acids are those with side chains that are generally negative charge owing to the presence of a carboxyl group, which is usually ionized at cellular pH. 9

10. What do the side chains of these amino acids have in common?
Figure 3.17c
What do the side chains of these amino acids have in common?
Arginine
(Arg or R)
Lysine
(Lys or K)
Histidine
(His or H)
Figure 3.17c The 20 amino acids of proteins (part 3: charged)
Electrically charged side chains; hydrophilic
Basic amino acids have amino groups in their side chains that are generally positive in charge. 10

11. You don’t need to memorize all the different side chains of the amino acids, but when shown a side chain you should be able to identify its properties (e.g. polar, ionized, etc.)

12. N-terminus peptide bond C-terminus
Amino acids are linked by peptide bonds
A polypeptide is a polymer of amino acids
Polypeptides range in length from a few to more than a thousand monomers
Each polypeptide has a unique linear sequence of amino acids, with a carboxyl end (C-terminus) and an amino end (N-terminus)
Peptide bonds are formed by dehydration reactions, which link the carboxyl group of one amino group of the next.

13. Protein Structure and Function
A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape.
A protein’s structure determines its function!
Hemoglobin protein
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14. How does an organism “know” what proteins to make?
DNA dictates the sequence of amino acids.
The sequence of amino acids leads to the protein’s three-dimensional structure.

15. Four Levels of Protein Structure
Proteins are very diverse, but share three superimposed levels of structure called primary, secondary, and tertiary structure.
A fourth level, quaternary structure, arises when a protein consists of more than one polypeptide chain
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16. Primary structure of transthyretin
Figure 3.21a
Primary structure
Amino
acids 1 5 10
Amino end 30 25 20 15 35 40 45 50
Primary structure of transthyretin 55 70 65 60
The sequence of amino acids make up the primary structure of a protein. 75 80 85 90 95
115
110
105
100
120
125
Carboxyl end 16

17. Secondary structure  helix Hydrogen bond  pleated sheet  strand
Figure 3.21ba
Secondary structure
 helix
Hydrogen bond
 pleated sheet
 strand
The secondary structure is the result of hydrogen bonds between the repeating constituents of the polypeptide backbone (not the amino acid side chains).
Hydrogen
bond 17

18. Tertiary structure Hydrogen bond Hydrophobic interactions and
Figure 3.21d
Tertiary structure
Hydrogen
bond
Hydrophobic
interactions and
van der Waals
interactions
Disulfide
bridge
Ionic bond
The tertiary structure is the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids.
The disulfide bridge is a covalent bond that forms between sulfhydryl groups.
Polypeptide
backbone 18

19. Quaternary Structure Heme Iron  subunit  subunit  subunit  subunit
Figure 3.21f
Quaternary Structure
Heme
Iron
 subunit
 subunit
Some proteins consist of two or more polypeptide chains aggregated into one functional macromolecule. Quaternary structure is the overall protein structure that results from the aggregation of these polypeptide subunits.
 subunit
 subunit
Hemoglobin 19

20. “mad cow disease” You will not be tested on this material.
“A prion (i/ˈpriːɒn/[1]) in the Scrapie form (PrPSc) is an infectious agent composed of protein in a misfolded form.[2] This is the central idea of the Prion Hypothesis, which remains debated.[3] This would be in contrast to all other known infectious agents, like viruses, bacteria, fungi or parasites—which must contain nucleic acids (either DNA, RNA, or both). The word prion, coined in 1982 by Stanley B. Prusiner, is derived from the words protein and infection.[4] Prions are responsible for the transmissible spongiform encephalopathies in a variety of mammals, including bovine spongiform encephalopathy (BSE, also known as "mad cow disease") in cattle. In humans, prions cause Creutzfeldt-Jakob Disease (CJD), variant Creutzfeldt-Jakob Disease (vCJD), Gerstmann–Sträussler–Scheinker syndrome, Fatal Familial Insomnia and kuru.[5] All known prion diseases in mammals affect the structure of the brain or other neural tissue and all are currently untreatable and universally fatal.[6] In 2013, a study revealed that 1 in 2,000 people in the United Kingdom might harbour the infectious prion protein that causes vCJD.[7]
Prions are not considered living organisms but are misfolded protein molecules which may propagate by transmitting a misfolded protein state. If a prion enters a healthy organism, it induces existing, properly folded proteins to convert into the disease-associated, misfolded prion form; the prion acts as a template to guide the misfolding of more proteins into prion form. These newly formed prions can then go on to convert more proteins themselves; this triggers a chain reaction that produces large amounts of the prion form.[8] All known prions induce the formation of an amyloid fold, in which the protein polymerises into an aggregate consisting of tightly packed beta sheets.”
From

21. 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. 21

22. Normal protein Figure 3.23-1
Figure Denaturation and renaturation of a protein (step 1)
Normal protein 22

23. Normal protein Denatured protein Figure 3.23-2
Figure Denaturation and renaturation of a protein (step 2)
Normal protein
Denatured protein 23

24. Normal protein Denatured protein Figure 3.23-3
Figure Denaturation and renaturation of a protein (step 3)
Normal protein
Denatured protein 24