Cell Biology: Cell Compounds and Biological Molecules

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 (-NH2), • 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 Tripeptidewould 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

11. Dehydration synthesis of amino acids

12. 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 hydrogen 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?