1. Proteins and Nucleic Acids
edited by C. Kerins

2. Proteins are essential to the structures and activities of life
A protein is a polymer constructed from amino acid monomers
The unique 3D structure of the protein determines its function
The seven major classes of proteins are
Structural: hair, cell cytoskeleton
Contractile: producers of movement in muscle and other cells

4. Storage: such as ovalbumin, the protein of egg whites that serves as a source of amino acids for developing embryos
Defense: antibodies, membrane proteins
Transport: carriers of molecules (such as hemoglobin), membrane proteins
Signaling: hormones, membrane proteins that help coordinate body activities by communicating between cells
Enzymes: regulators of the speed biochemical reactions—VERY IMPORTANT

5. 3.12: Proteins, Amino Acids, and Peptide Bonds
Proteins are made from amino acids linked together by peptide bonds
Protein diversity is based on different arrangements of a common set of 20 amino acid monomers
Each amino acid contains
An amino group
A carboxyl group
One of twenty functional ("R") groups
The three groups and a hydrogen atom are bonded to a central "alpha" carbon
Hence the name “amino acid.”

6. LE 3-12a
Alpha carbon
Amino
group
Carboxyl (acid)
group

7. R-groups make amino acids different
The structure of the R group (or side chain) determines the specific properties of each of the 20 amino acids that make up proteins
An amino acid may be hydrophobic or hydrophilic, depending on the characteristics of the R group
Amino acids can also be acidic and negatively charged or basic and positively charged at the pH of a cell.
Polar and charged amino acids help proteins dissolve in the aqueous solutions inside cells.

8. LE 3-12b Leucine (Leu) Serine (Ser) Aspartic acid (Asp) Hydrophobic
Hydrophilic

9. Amino acids are linked by dehydration synthesis
Cells link amino acids together by dehydration synthesis
The bonds between amino acid monomers are called peptide bonds
Dipeptides are two amino acids long; polypeptides are from several to more than a thousand amino acids long

10. LE 3-12c Peptide bond Carboxyl group Amino group Dehydration reaction
Amino acid
Amino acid
Dipeptide

11. How do 20 amino acids make thousands of different proteins?
Think about our alphabet…26 letters, countless words
The protein “alphabet” contains only 20 “letters,” but the words are MUCH longer…most over 100 amino acids in length…and some are 1,000 or MORE!
Each polypeptide has a unique sequence of amino acids…but it is NOT a protein—like a strand of yarn is not a sweater.
A functioning protein is made from one or more polypeptide chains precisely twisted, folded, and coiled into a unique 3D shape

12. 3.13: Protein structure = function
A protein's specific shape determines its function
A protein consists of one or more polypeptide chains spontaneously folded into a unique shape
Most enzymes and other proteins are globular in shape.
Structural proteins, like those that make up hair and tendons, are long and thin—or fibrous.

13. LE 3-13
Groove
Groove

14. Structure=Function
Nearly all proteins must recognize and bind to some other molecule in order to function.
The folding of a polypeptide creates grooves that enable other molecules to bind to it, and its specific shape enables it to recognize and attach to its molecular target.
In denaturation, chemical or physical changes (such as a change in salt concentration, pH, or temperature) can cause proteins to unravel, losing their shape and thus their specific function
This is why it is important to maintain homeostasis.

15. 3.14: Four levels of protein structure
A protein's shape depends on four levels of structure
Primary structure: the unique sequence of amino acids forming the polypeptide as coded for by the DNA—this must be EXACT
Secondary structure: the coiling or folding of the chain, stabilized by hydrogen bonding
May be alpha helix or pleated sheet (which dominates the silk protein of a spider's web)

17. Tertiary structure: the overall three-dimensional shape of the polypeptide
Usually described as globular or fibrous
Generally results from the interactions among the R-groups of the amino acids
This structure may be further reinforced by covalent bonds called disulfide bridges—another interaction between amino acids
Quaternary structure: the association of two or more polypeptide chains (subunits)
Like hemoglobin or collagen (40% of your protein!)

18. Levels of Protein Structure
LE 3-14a
Levels of Protein Structure
Amino acids

19. Hydrogen bond Alpha helix Pleated sheet
LE 3-14b
Levels of Protein Structure
Amino acids
Hydrogen
bond
Alpha helix
Pleated sheet

20. LE 3-14c Levels of Protein Structure Amino acids Hydrogen bond
Alpha helix
Pleated sheet
Polypeptide
(single subunit
of transthyretin)

21. LE 3-14d Levels of Protein Structure Amino acids Hydrogen bond
Alpha helix
Pleated sheet
Polypeptide
(single subunit
of transthyretin)
Transthyretin, with
four identical
polypeptide subunits

22. Collagen is an example of a protein with a quaternary structure
Three subunits wound into a helix
Structure provides great strength to long fibers

24. 3.15: TALKING ABOUT SCIENCE OYO
Linus Pauling contributed to our understanding of the chemistry of life
Felt that the study of individual parts must come first, then putting the parts together
Began his career by studying chemical bonding
First described the alpha helix and pleated sheet protein structures
Discovered how abnormal hemoglobin causes sickle cell disease
Won two Nobel prizes, for chemistry and for peace (for helping produce a nuclear test ban treaty)

26. 3.16: Nucleic Acids
Nucleic acids serve as the blueprints for proteins.
Nucleic acids are polymers of nucleotide monomers composed of three parts:
A five-carbon sugar (ribose or deoxyribose)
A phosphate group
A nitrogenous base:

27. Nitrogenous base (A) Phosphate group Sugar
LE 3-16a
Nitrogenous
base (A)
Phosphate
group
Sugar

28. NUCLEIC ACIDS There are two types of nucleic acids: DNA and RNA
Deoxyribonucleic acid (DNA) contains the sugar DEOXYRIBOSE
STORES genetic material inherited from parents
DNA contains adenine (A), thymine (T), cytosine ( C), and guanine (G)
Bases pair in the following ways:
A pairs with T and G pairs with C

29. Genes hold the code for making proteins
Genes are specific pieces of DNA that code for the primary structure of proteins (amino acid sequence)
The specific sequence of nucleotides in a gene leads to the sequence of amino acids in a protein.
The sequence of amino acids leads to a protein’s shape and therefore determines its function.

30. Structure of DNA Double-stranded (structure is called a double helix)
Think of DNA like a twisted ladder made by two complementary strands of nucleotides:
The sugar and phosphate groups form the sides/backbone of the DNA molecule…the sugar of one nucleotide bonds to the phosphate group of the next through dehydration synthesis.
The N-bases form the “rungs”
DNA is formed by the two strands forming hydrogen bonds between their bases. More on that later.
SEE PAGE 47

31. LE 3-16b
Nucleotide
Sugar-phosphate
backbone

32. LE 3-16c
Base
pair

33. RNA: the OTHER nucleic acid
Ribonucleic acid (RNA) contains the sugar RIBOSE
TRANSMITS genetic information from DNA into proteins
Single-stranded
RNA contains A, G, C, and uracil (U)

35. Hydrogen bonding between nitrogenous bases creates the final structure of the nucleic acid
RNA usually consists of a single polynucleotide strand
DNA is a double helix
Two polynucleotides are twisted around each other
Nitrogenous bases protruding from the backbone pair with each other, A with T and G with C

36. Specific sequences of DNA make up genes that program the amino acid sequences of proteins