1. Cell Biology: Cell Compounds and Biological Molecules Lesson 4 – Proteins and Nucleic Acids ( Inquiry into Life pg. 37-41 )

2. Today’s Objectives  Analyze the structure and function of biological molecules in living systems, including carbohydrates, lipids, proteins, nucleic acids  List the major functions of proteins  Draw a generalized amino acid and identify the amine, acid (carboxyl), and R-groups  Identify the peptide bonds in dipeptides and polypeptides  Differentiate among the different levels of protein organization with respect to structure and bond type, including: primary, secondary, tertiary, quaternary  Name the four bases in DNA and describe the structure of DNA using the following terms: nucleotide (sugar, phosphate, base), complementary base pairing, double helix, hydrogen bonding  Relate the general structure of the ATP molecule and its role as “energy currency”

3. 2.7 - Proteins  Proteins have many functions:  Proteins such as keratin and collagen have structural roles.  Proteins are also enzymes that speed up the chemical reactions of metabolism.  Proteins such as hemoglobin are responsible for the transport of substances within the body.  Proteins transport substances across cell membranes.  Proteins form the antibodies of the immune system that defend the body from viruses and disease.  Proteins such as insulin are hormones that regulate cellular function.  Contractile proteins such as actin and myosin allow parts of cells to move and muscles to contract.

4. What are proteins?  Contain carbon, hydrogen, oxygen, and nitrogen  Also often contain sulfur, and sometimes phosphorus and iron  The basic structure of a protein is a chain of amino acids (polypeptides)  There are about 20 different amino acids

5. What are amino acids?  Proteins are polymers with amino acid monomers  An amino acid has a central carbon atom bonded to a hydrogen atom and three groups:  One of the three groups is an amino group (-NH 2 ),  One of the groups is an acidic group (-COOH)  Hence called an amino acid!  The third group is called an R Group  Amino acids differ from one another by their R group

6. What are R groups?  An R group is a variety of atoms attached to amino acids  R group = radical group or remainder group  An R group distinguishes one amino acid from another

7. Examples of amino acids

8. Formation of Proteins  An amino acid can be referred to as a peptide  Dehydration synthesis of amino acids result in the bonding of amino acids together and the release of water molecules  When two amino acids bond together, they produce a dipeptide  Example: amino acids glycine and alanine bond to form the dipeptide gly-ala

9. Formation of proteins  The bond that connects amino acids is called a peptide bond  A dipeptide has one peptide bond holding together two amino acids  A Tripeptide would have two peptide bonds holding together three amino acids  A polypeptide would have numerous peptide bonds holding together numerous amino acids  A polypeptide is a single chain of amino acids  The order or combination of these amino acids determines which protein is produced

10. Dehydration synthesis of amino acids

13. Formation of proteins  This process when repeated form long sequences of amino acids, or proteins  These sequences take on specific features and characteristics of the individual amino acids that are bonded together

14. Protein Structure  There are three to four levels of protein structure  Primary structure – sequence of amino acids (polypeptide)  Secondary structure – orientation of polypeptide  Tertiary structure – final 3-D shape of polypeptide  Quaternary structure* - arrangement of multiple polypeptides  *not all proteins have multiple polypeptides

15. Primary Structure  Simply the sequence of amino acids  Because there are twenty amino acids, it is easy to see that there are literally millions of different possible amino acid sequences  Consequently, there are millions of proteins

16. Secondary Structure  As the amino acid chains (polypeptides) get longer, they begin to twist or fold  This is a result of stress on the peptide bonds  Two types of secondary structure:  Alpha helix – like a spiral  Beta pleated sheet – like folded paper  The alpha helix is most common

17. Secondary Structure – alpha helix  As the polypeptide bends into a spiral, hydrogen bonds form between the hydrogen of one amino acid and an oxygen further down the chain  This hydrogen bond helps the alpha helix hold its shape  An alpha helix contains 3.6 amino acids per spiral

18. Secondary Structure – Beta pleated sheet  Hydrogen bonds can form between parallel lengths of the polypeptide chain creating beta pleated sheets

19. Secondary Structure

20. Tertiary Structure  The third level of protein structure or tertiary structure is described as the bending and folding of the alpha helix  As the helix gets longer there are some amino acids that cannot fit the configuration and therefore cause kinks  New bonds will form to hold it into a three dimensional (3-D) shape  These bonds can be ionic, covalent, and/or hydrogen bonds

21. Tertiary Structure Alpha helix

22. Quaternary Structure  Only occurs in proteins with more than one polypeptide  The quaternary structure is where different 3-D (tertiary) configurations are associated with and function with each other  Imagine multiple kinked helixes tied up with each other in knots  An example of a protein with quaternary structure is hemoglobin which transports substances through our body in our blood

23. Quaternary Structure

24. Levels of Protein Structure

25. More about Protein Functions  Enzyme proteins speed up chemical reactions in our body  Reactions that normally would take several hours will take only a fraction of a second  Proteins such as hemoglobin transport nutrients and other substances through our body  Antibody proteins fight infections and attack viruses  The protein keratin is the main structural component of fingernails and hair  Collagen makes up the connective tissues in our muscles  Actin/myosin make up muscle fibers that allow for movement

26. 2.8 Nucleic Acids  Nucleic Acids are polymers made up of monomers called nucleotides  There are two types of nucleic acids:  DNA – deoxyribonucleic acid  RNA – ribonucleic acid  Some functions of Nucleic Acids:  They form genetic material and are involved in the functioning of chromosomes and protein synthesis  DNA stores genetic information  DNA codes for the order of amino acids in a protein  RNA is an intermediary in the sequencing of amino acids into a protein

27. What are Nucleotides?  Nucleotides are made from a pentose sugar, a phosphate group, and a nitrogen containing base

28. Nucleotides  There are five basic nucleotides:  Adenine and Guanine  Double ring structure purines  Cytosine, Uracil, and Thymine  single ring structure pyrimidines  These bases are found in DNA and RNA  DNA contains A,G,T and C  RNA contains A,G,U and C

29. DNA structure compared to RNA structure

30. Nucleotides  The bases found in DNA form complementary base pairs (the same two bases always bond with each other)  The structure of DNA is a double helix (we will talk more about DNA later this year

31. Complementary Base Pairs in DNA

32. ATP (Adenosine Triphosphate)  One particularly important nucleic acid is the modified nucleotide known as ATP  ATP is an RNA nucleotide with an adenine (A) base (adenine + ribose = adenosine) attached to 3 phosphate groups  ATP is a very high energy molecule  When ATP undergoes hydrolysis, large amounts of energy are released

33. ATP: The energy currency of cells  ATP is a high energy molecule because the last two phosphate bonds are unstable and easily broken  A lot of energy is required to maintain these bonds  If the bonds are broken, this energy is released  When an ATP molecule loses a phosphate, it becomes the molecule ADP (adenosine diphosphate) and a phosphate molecule  With the addition of energy, this process can be reversed, creating the ATP cycle  Muscle cells use the energy for muscle contraction  Cells use the energy to synthesize carbohydrates and proteins  More on this later in the year

34. ATP Cycle

35. Pop Quiz!  An amino acid is a central carbon atom attached to a hydrogen atom and what?  What are the monomers called that make up proteins?  Describe primary protein structure  Describe secondary protein structure  What are the two main types of secondary structure  Describe tertiary protein structure  Describe quaternary protein structure  What are 3 main functions of proteins?  What are the monomers called that make up nucleic acids?  How do cells get energy from the hydrolysis of ATP?  What are the 4 bases found in DNA?