1. Proteins

2. Multipurpose molecules
Proteins
Multipurpose molecules
clockwise:
Rubisco — most important protein on the planet?
Hemoglobin — a red blooded protein :-)
Collagen — strings you together
Growth Hormones — working hard in you right now!

3. Proteins Most structurally & functionally diverse group
Function: involved in almost everything
enzymes (pepsin, DNA polymerase)
structure (keratin, collagen)
carriers & transport (hemoglobin, aquaporin)
cell communication
signals (insulin & other hormones)
receptors
defense (antibodies)
movement (actin & myosin)
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!!!!

4. Proteins Structure monomer = amino acids polymer = polypeptide
H2O
Structure
monomer = amino acids
20 different amino acids
polymer = polypeptide
protein can be one or more polypeptide chains folded & bonded together
large & complex molecules
complex 3-D shape
Rubisco = 16 polypeptide chains
Hemoglobin = 4 polypeptide chains (2 alpha, 2 beta)
hemoglobin
Rubisco
growth hormones

5. Amino acids H O | H || —C— C—OH —N— R Structure central carbon
amino group
carboxyl group (acid)
R group (side chain)
variable group
different for each amino acid
confers unique chemical properties to each amino acid
like 20 different letters of an alphabet
can make many words (proteins)
—N— H R
Oh, I get it!
amino = NH2
acid = COOH

6. dehydration synthesis
Building proteins
Peptide bonds
covalent bond between NH2 (amine) of one amino acid & COOH (carboxyl) of another
C–N bond
H2O
dehydration synthesis
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

7. 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
collagen

8. Primary (1°) structure Order of amino acids in chain
amino acid sequence determined by gene (DNA)
slight change in amino acid sequence can affect protein’s structure & its 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.
lysozyme: enzyme in tears & mucus that kills bacteria

9. Sickle cell anemia Just 1 out of 146 amino acids!
glutamic acid is acidic & polar
valine is non-polar = tries to “hide” from water of cell by sticking to another hemoglobin molecules.
I’m hydrophilic!
But I’m hydrophobic!

10. Secondary (2°) structure
“Local folding”
folding along short sections of polypeptide
interactions between adjacent amino acids
H bonds
weak bonds between R groups
forms sections of 3-D structure
-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

11. Secondary (2°) structure

12. Tertiary (3°) structure
“Whole molecule folding”
interactions between distant amino acids
hydrophobic interactions
cytoplasm is water-based
nonpolar amino acids cluster away from water
H bonds & ionic bonds
disulfide bridges
covalent bonds between sulfurs in sulfhydryls (S–H)
anchors 3-D shape
How the whole thing holds together

13. Quaternary (4°) structure
More than one polypeptide chain bonded together
only then does polypeptide become functional protein
Structure equals function wonderfully illustrated by proteins
Collagen is just like rope -- enables your skin to be strong and flexible.
hemoglobin
collagen = skin & tendons

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

15. Protein denaturation Unfolding a protein
conditions that disrupt H bonds, ionic bonds, disulfide bridges
temperature pH
salinity
alter 2° & 3° structure
alter 3-D shape
destroys functionality
some proteins can return to their functional shape after denaturation, many cannot

16. Nucleic Acids
Information storage

17. Nucleic Acids Function: genetic material stores information
genes
recipe for building proteins
DNA  RNA  proteins
transfers information
DNA
proteins

18. A T C G
Isn’t this a great illustration!?

19. Nucleic Acids Examples: Structure: RNA (ribonucleic acid)
single helix
DNA (deoxyribonucleic acid)
double helix
Structure:
monomers = nucleotides
DNA
RNA

20. Nitrogen base I’m the A,T,C,G or U part!
Nucleotides
3 parts
nitrogen base (C-N ring)
pentose sugar (5C)
ribose in RNA
deoxyribose in DNA
phosphate (PO4) group
Nitrogen base I’m the A,T,C,G or U part!
DNA & RNA are negatively charged:
Don’t cross membranes.
Contain DNA within nucleus
Need help transporting mRNA across nuclear envelope.
Also use this property in gel electrophoresis.

21. Types of nucleotides 2 types of nucleotides different nitrogen bases
Purine = AG
Pure silver!
2 types of nucleotides
different nitrogen bases
purines
double ring N base
adenine (A)
guanine (G)
pyrimidines
single ring N base
cytosine (C)
thymine (T)
uracil (U)

22. Nucleic polymer Backbone sugar to PO4 bond phosphodiester bond
new base added to sugar of previous base
polymer grows in one direction
N bases hang off the sugar-phosphate backbone

23. Pairing of nucleotides
Nucleotides bond between DNA strands
H bonds
purine :: pyrimidine
A :: T
2 H bonds
G :: C
3 H bonds
The 2 strands are complementary.
One becomes the template of the other & each can be a template to recreate the whole molecule.

24. DNA molecule Double helix H bonds between bases join the 2 strands
A :: T
C :: G
H bonds = biology’s weak bond
• easy to unzip double helix for replication and then re-zip for storage
• easy to unzip to “read” gene and then re-zip for storage

25. Matching halves? Why is this a good system?
Copying DNA
Replication
2 strands of DNA helix are complementary
have one, can build other
have one, can rebuild the whole
when cells divide, they must duplicate DNA exactly for the new “daughter” cells
Why is this a good system?
Matching halves? Why is this a good system?

26. When does a cell copy DNA?
When in the life of a cell does DNA have to be copied?
cell reproduction
mitosis
gamete production
meiosis
when cells divide, they must duplicate DNA exactly for the new “daughter” cells
Why is this a good system?

27. DNA replication
“It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material.”
James Watson
Francis Crick
1953
The greatest understatement in biology!

28. Watson and Crick … and others…
1953 | 1962
Watson and Crick … and others…
Discovered & published in 1953
Nobel Prize in 1962:
Watson, Crick, Wilkins

29. 1953 | 1962
Maurice Wilkins… and…

30. Rosalind Franklin ( )
A chemist by training, Franklin had made original and essential contributions to the understanding of the structure of graphite and other carbon compounds even before her appointment to King's College. Unfortunately, her reputation did not precede her. James Watson's unflattering portrayal of Franklin in his account of the discovery of DNA's structure, entitled "The Double Helix," depicts Franklin as an underling of Maurice Wilkins, when in fact Wilkins and Franklin were peers in the Randall laboratory. And it was Franklin alone whom Randall had given the task of elucidating DNA's structure. The technique with which Rosalind Franklin set out to do this is called X-ray crystallography. With this technique, the locations of atoms in any crystal can be precisely mapped by looking at the image of the crystal under an X-ray beam. By the early 1950s, scientists were just learning how to use this technique to study biological molecules. Rosalind Franklin applied her chemist's expertise to the unwieldy DNA molecule. After complicated analysis, she discovered (and was the first to state) that the sugar-phosphate backbone of DNA lies on the outside of the molecule. She also elucidated the basic helical structure of the molecule.
After Randall presented Franklin's data and her unpublished conclusions at a routine seminar, her work was provided - without Randall's knowledge - to her competitors at Cambridge University, Watson and Crick. The scientists used her data and that of other scientists to build their ultimately correct and detailed description of DNA's structure in Franklin was not bitter, but pleased, and set out to publish a corroborating report of the Watson-Crick model. Her career was eventually cut short by illness. It is a tremendous shame that Franklin did not receive due credit for her essential role in this discovery, either during her lifetime or after her untimely death at age 37 due to cancer.

31. Another interesting note…
ATP Adenosine triphosphate
modified nucleotide
adenine (AMP) + Pi + Pi + +

32. Macromolecule Review

33. Carbohydrates Structure / monomer Function Examples monosaccharide
energy
raw materials
energy storage
structural compounds
Examples
glucose, starch, cellulose, glycogen
glycosidic bond

34. Lipids Structure / building block Function Examples
glycerol, fatty acid, cholesterol, H-C chains
Function
energy storage
membranes
hormones
Examples
fat, phospholipids, steroids
ester bond (in a fat)

35. Proteins Structure / monomer Function Examples amino acids
levels of structure
Function
enzymes u defense
transport u structure
signals u receptors
Examples
digestive enzymes, membrane channels, insulin hormone, actin
peptide bond

36. Nucleic acids Structure / monomer Function Examples nucleotide
information storage & transfer
Examples
DNA, RNA
phosphodiester bond