1. Proteins AP Biology clockwise:
Rubisco — most important protein on the planet?
Hemoglobin — a red blooded protein :-)
Collagen — strings you together
Growth Hormone — working hard in you right now!
AP Biology

2. Proteins
Most structurally & functionally diverse group of biomolecules
Function:
involved in almost everything
enzymes
structure (keratin, collagen)
carriers & transport (membrane channels)
receptors & binding (defense)
contraction (actin & myosin)
signaling (hormones)
storage (bean seed proteins)
Storage: beans (seed proteins)
Movement: muscle fibers
Cell surface proteins: labels that ID cell as self vs. foreign
Antibodies: recognize the labels
ENZYMES!!!!
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3. Proteins Structure: monomer = amino acids polymer = polypeptide
20 different amino acids
polymer = polypeptide
protein can be 1 or more polypeptide chains folded & bonded together
large & complex molecules
complex 3-D shape
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4. Amino acids O | H || —C— C—OH —N— R Structure: central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
confers unique chemical properties of the amino acid
—N— H |
—C—
C—OH || O R
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5. Why are these nonpolar & hydrophobic?
Nonpolar amino acids
nonpolar & hydrophobic
Why are these nonpolar & hydrophobic?
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6. Why are these polar & hydrophillic?
Polar amino acids
polar or charged & hydrophilic
Why are these polar & hydrophillic?
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7. AP Biology

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9. Sulfur containing amino acids
Disulfide bridges
cysteines form cross links
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10. Building proteins Peptide bonds: dehydration synthesis
linking NH2 of 1 amino acid to COOH of another
C–N bond
free COOH group on one end is ready to form another peptide bond so they “grow” in one direction from N-terminal to C-terminal
peptide bond
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11. Building proteins Polypeptide chains N-terminal = NH2 end
C-terminal = COOH end
repeated sequence (N-C-C) is the polypeptide backbone
grow in one direction
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12. Protein structure & function
function depends on structure
3-D structure
twisted, folded, coiled into unique shape
Hemoglobin
Hemoglobin is the protein that makes blood red. It is composed of four protein chains, two alpha chains and two beta chains, each with a ring-like heme group containing an iron atom. Oxygen binds reversibly to these iron atoms and is transported through blood.
Pepsin
Pepsin is the first in a series of enzymes in our digestive system that digest proteins. In the stomach, protein chains bind in the deep active site groove of pepsin, seen in the upper illustration (from PDB entry 5pep), and are broken into smaller pieces. Then, a variety of proteases and peptidases in the intestine finish the job. The small fragments--amino acids and dipeptides--are then absorbed by cells for use as metabolic fuel or construction of new proteins.
Collagen– Your Most Plentiful Protein
About one quarter of all of the protein in your body is collagen. Collagen is a major structural protein, forming molecular cables that strengthen the tendons and vast, resilient sheets that support the skin and internal organs. Bones and teeth are made by adding mineral crystals to collagen. Collagen provides structure to our bodies, protecting and supporting the softer tissues and connecting them with the skeleton. But, in spite of its critical function in the body, collagen is a relatively simple protein.
pepsin
hemoglobin
AP Biology
collagen

13. Protein structure & function
function depends on structure
all starts with the order of amino acids
what determines that order of amino acids?
Lysozyme
Lysozyme protects us from the ever-present danger of bacterial infection. It is a small enzyme that attacks the protective cell walls of bacteria. Bacteria build a tough skin of carbohydrate chains, interlocked by short peptide strands, that braces their delicate membrane against the cell's high osmotic pressure. Lysozyme breaks these carbohydrate chains, destroying the structural integrity of the cell wall. The bacteria burst under their own internal pressure.
Glycolytic enzymes
Glucose powers cells throughout your body. Glucose is a convenient fuel molecule because it is stable and soluble, so it is easy to transport through the blood from places where it is stored to places where it is needed. Glucose is packed with chemical energy, ready for the taking. In a test tube, you can burn glucose, forming carbon dioxide and water and a lot of light and heat. Our cells also burn glucose, but they do it in many small, well-controlled steps, so that they can capture the energy in more useable forms, such as ATP (adenosine triphosphate). These ten enzymes control those small steps in the process of extracting energy from glucose.
Glycolysis (sugar-breaking) is the first process in the cellular combustion of glucose. Glycolysis is endlessly fascinating. In these ten enzymes, you can find examples of many of the important molecular processes that animate our cells. They have been perfected by evolution to perform their diverse chemical tasks quickly and efficiently--adding, removing, and shifting atoms without making mistakes. The pathway is carefully regulated, so that glucose is only broken down when energy is needed
Point out the active sites on each glycolytic enzym
lysozyme: enzyme in tears & mucus that kills bacteria
the 10 glycolytic enzymes used to breakdown glucose to make ATP
AP Biology

14. Primary (1°) structure Order of amino acids in chain
amino acid sequence determined by DNA
slight change in amino acid sequence can affect protein’s structure & it’s function
even just one amino acid change can make all the difference!
Sickle cell anemia: 1 DNA letter changes 1 amino acid = serious disease
Hemoglobin mutation: bends red blood cells out of shape & they clog your veins.
AP Biology

15. Sickle cell anemia glutamic acid is acidic & polar
valine is non-polar = tries to “hide” from water of cell by sticking to another hemoglobin molecules.
AP Biology

16. Secondary (2°) structure
“Local folding”
Folding along short sections of polypeptide
interaction between adjacent amino acids
-helix
-pleated sheet
It’s a helix or B sheet within a single region. Can have both in one protein but a specific region is one or another
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17. Secondary (2°) structure
The Alpha Helix
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18. Beta-Pleated Sheets

19. Representations of Protein Secondary Structure
lysozyme

20. Tertiary (3°) structure
“Whole molecule folding”
determined by interactions between R groups
hydrophobic interactions
effect of water in cell
anchored by disulfide bridges (H & ionic bonds)
How the whole thing holds together
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21. Quaternary (4°) structure
Joins together more than 1 polypeptide chain
only then is it a functional protein
collagen =
skin & tendons
Structure equals function wonderfully illustrated by proteins
Collagen is just like rope -- enables your skin to be strong and flexible.
hemoglobin
AP Biology

22. Protein structure (review)
R groups hydrophobic interactions,
disulfide bridges 3°
multiple polypeptides
hydrophobic interactions
sequence determines structure and…
structure determines function.
Change the sequence & that changes the structure which changes the function. 1°
aa sequence
peptide bonds 2°
determined by DNA
R groups
H bonds 4°
AP Biology

23. Chaperonin proteins Guide protein folding
provide shelter for folding polypeptides
keep the new protein segregated from cytoplasmic influences
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24. Protein models Protein structure visualized by X-ray crystallography
extrapolating from amino acid sequence
computer modelling
lysozyme
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25. Denature a protein Disrupt 3° structure
pH  salt
temperature
unravel or denature protein
disrupts H bonds, ionic bonds & disulfide bridges
Some proteins can return to their functional shape after denaturation, many cannot
Example:
Eggs:
Cooking an egg permanently denatures the proteins.
AP Biology

26. Let’s build some
Insulin!
AP Biology

27. The insulin protein has two chains, with a total of 53 amino acids
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28. The two chains are connected by disulfide bridges from cysteine molecules
After you link together the primary sequence through dehydration synthesis, you can join the cysteines together!

29. Each side of the room will build an insulin molecule
The abbreviations for the 20 amino acids are found in the table 

30. The amino acids are color coded by side group: non-polar, polar, acidic, and basic

31. Water molecules need to be removed by dehydration synthesis
Join the amino acids together, then work on the cysteines (part of tertiary structure)

32. Ribosome Animations of Protein Synthesis
Real Time Slo-mo Older – Gumby-Like Shows secondary structure of ribosome in action

33. Bonus Question (1st group to answer gets candy)
Some of the 20 amino acids are missing from insulin – name them all!