Office Hours: MWF 2:00 p.m. – 4:00 p.m. BICH411. Biochemistry I M W 4:00 p.m. – 5:20 p.m. Dr. Shubo Han Website:http://faculty.uncfsu.edu/shan/ Phone: 672-1303 Email: shan@uncfsu.edu Office Hours: MWF 2:00 p.m. – 4:00 p.m. T 11:00am-1:00 pm

Course Summary Grading: Total: 100 points Three hour exams (10  3) 30 80% - 89% B 70% - 79% C 60% - 69% D 0% - 59% F    Three hour exams (10  3) 30 Homework and quizzes 30 Final examination 40 Total 100 Please check the syllabus from the website of Blackboard.

Chapter 1

What is Biochemistry? Biochemistry is the application of chemistry to the study of biological processes at the cellular and molecular level.

What is Biochemistry?

What Do Biochemists Study?

Plant

Urchin

Cat

Three Domains of Life Prokaryotes – single celled organisms (bacteria) Escherichia coli – best studied prokaryote – harmless intestinal bacteria Many laboratory strains – some harmful pathogenic strains Has extra circular DNA called plasmids. Well-studied eukaryote is humans

The characteristic: a well-defined nucleus within each cell. Prokaryotes – single celled organisms (bacteria) Escherichia coli – best studied prokaryote – harmless intestinal bacteria Many laboratory strains – some harmful pathogenic strains Has extra circular DNA called plasmids. Well-studied eukaryote is humans Eukarya: all macroscopic organisms, including human beings as well as many microscopic, unicellular organism such as yeast. The characteristic: a well-defined nucleus within each cell.

Unicellular organisms lacking a nucleus are prokaryotes, including Prokaryotes – single celled organisms (bacteria) Escherichia coli – best studied prokaryote – harmless intestinal bacteria Many laboratory strains – some harmful pathogenic strains Has extra circular DNA called plasmids. Well-studied eukaryote is humans Unicellular organisms lacking a nucleus are prokaryotes, including (1)Bacteria and (2) Archaea.

The Mammalian Cell Cytoplasm Lipid bilayer Our focus in this class will be on humans Depicted above is a mammalian cell Cells are the units of which our body is made Cells are specialized for a certain job. Muscle cells, skin cells, nerve cells, brain cells, red blood cells, etc.. We are going to study the processes that make a cell function. How does a cell duplicate itself, talk to other cells, know when to die, etc… All these answers come down to chemistry. The chemistry of life (biochemistry) In chemistry classes small molecules react in a test tube. In our bodies much larger molecules are reacting our assisting in reactions in a cell. Certain reactions take place in certain compartments within a cell. These compartments are called organelles and are encased by a lipid bilayer. The lipid bilayer separating the inside of the cell from the outside is the plasma membrane The interior of a cell is called the cytoplasm The aqueous portion of the cytoplasm is the cytosol. The shape and rigidity of a cell is controlled by a cytoskeleton, a network of filamentous structural proteins on the inside of the plasma membrane. Cytoplasm Lipid bilayer

The nucleus contains the cell’s DNA (genome) The nucleus contains the cell’s DNA, which makes up the genome. The nucleus is surrounded by a nuclear envelope, two membrane bilayers Molecules come into and out of the nucleus through nuclear pores The inside of the nucleus is called the nucleoplasm. Chromatin is the name given to DNA complexed with proteins (histones) The nucleolus is a region where the DNA is concentrated for replication Nucleus

Eukaryotic Cell Structure Substances enter a cell through the endocytosis. Substances leave the cell by exocytosis. These processes are mediated through the budding off of a portion of a lipid bilayer to form a vesicle. These vesicles carry molecules to a specific region of a cell where they are needed. Or they are sent out of the cell if they are not needed.

Human erythrocytes (red blood cells) skeletal muscle cell plant stem cell Human erythrocytes (red blood cells) sperm cells Muscle cell.

Molecular Organization of Cells

Types of molecules in a cell Deoxyribonucleic acids (DNA) Are constructed of four different kinds of monomeric units, the deoxyribonucleotides, G, A, T, C Ribonucleic acids (RNA) Are constructed of four different kinds of monomeric units, the ribonucleotides, G, A, U, C Proteins Are composed of twenty different kinds of monomeric units, the amino acids Lipids (Fat) Water insoluble molecule containing fatty acids. Used for membrane structure and energy storage Carbohydrates (sugar) Are constructed of monomeric units called monosaccharides. Also called polysaccharides.

Molecular Components of an E. coli Cell

Cellular Processes replication DNA transcription RNA translation Proteins Lipids Carbohydrates

Conclusion: (1) Organisms are remarkably uniform at the molecular level. This uniformity reveals that all organisms on earth have arisen from a common ancestor.

(2) All are subject to the same laws of physics and chemistry. Biochemistry is an intellectually coherent and beautiful discipline because of the underlying unity of life.

1. DNA (1) Four simple compounds constructed DNA

(2) DNA is a linear polymer of 4 kinds of units, each consisting of the same sugar-phosphate unit, but with 4 different bases attached: A, C, G, T.

(3) Two strands combine by noncovalent base-pairing of A with T; G with C.

(4) Facts a. Most DNA molecules consisted of two strands. b. This strands arranged in a double helix structure. c. The double helix structure composed of two intertwined strands. d. In the structure, the sugar-phosphate backbone lies on the outside and the bases on the inside. e. Hydrogen bonds formed between the specific base pair is the major reason of two strands holding together. f. The hydrogen bonds are weak enough to be reversibly broken in biochemical process and strong enough to help stabilize the double helix structure.

(5) Two properties A and T forms two hydrogen bonds.

G and C forms three hydrogen bonds.

Adenine only binds with Thymine (A-T) Guanine only binds with Cytosine (G-C) Therefore, One strand determines the other strand. ( Each strand can be used as a template).

Same shape and same size, thus fitting neatly within the double helix. For above reason DNA is used as a hereditary material.

2. RNA: RNA is an intermediate in the flow of genetic information RNA( ribonucleic Acid) Similar to DNA Linear polymer Sugar ribose, rather than deoxyribose Uracil instead of thymine

RNA is templates for protein synthesis

3. Proteins: Protein is the primary functional molecules in the cells.

3. Proteins: Facts: Proteins: structural components of cell, or enzymes Proteins are linear polymers, just like DNA and RNA Proteins are more complicated.

3. Proteins: Protein is the primary functional molecules in the cells.

3. Proteins: Extremely Important property: A protein spontaneously folds into a well defined and elaborate three-dimensional structure. This 3-D structure is dictated entirely by the sequence of amino acids along its chain.

3. Proteins: The self-folding nature of proteins constitutes the transition from the one-dimensional world of sequence information to the three-dimensional world of biological function. Three bases along a DNA chain encode a single amino acid. (genetic code).

Questions: 1. DNA is made from _____ building blocks (Bases) . These blocks are___________________________.

Questions: 1. DNA is made from __4___ building blocks (Bases) . These blocks are adenine, guanine, cytosine, and thymine.

2. The DNA backbone is made from repeating___________

2. The DNA backbone is made from repeating sugar-phosphate units.

3. The number of hydrogen bonds formed between A and C is 1 b.2 c. 0 d.3 4. The number of hydrogen bonds formed between A and T is 1 b.2 c. 0 d.3 5. The number of hydrogen bonds formed between C and G is 1 b.2 c. 0 d.3

6. The fundamental groups of organisms include-------------.

6. The fundamental groups of organisms include Eukarya, Bacteria, and Archaea.

7. DNA is used as a hereditary material, because:

7. DNA is used as a hereditary material, because: The base pairs have essentially the same shape and same size, thus fit equally well into the center of the double-helical structure. The sequence of bases along one strand completely determines the sequence along the other strand.

8. RNA is constructed by ---------- building blocks, which is(are) ----------------------------------------.

8. RNA is constructed by 4 building blocks, which is(are) adenine, guanine, cytosine, and uracil.

9. RNA is an ----------- in the flow of genetic information.

10. The 3-D structure of protein is dictated entirely by the ------------------- along its chain.

10. The 3-D structure of protein is dictated entirely by the sequence of amino acids along its chain.

Some of the amino acids of proteins

The components of nucleic acids

Some Components of Lipids

Structure of glucose, the “parent” sugar

Elements essential to life

Versatility of Carbon Bonding

Versatility of Carbon Bonding

Geometry of Carbon Bonding

Functional Groups

Functional Groups

Functional Groups

Functional Groups

Functional Groups

Multiple Functional Groups in a Single Biomolecule

Common molecular representations

Interactions between biomolecules are stereospecific

Stereoisomers are readily distinguished by humans

Energy Interconversions in Living Organisms

Adenosine triphosphate (ATP)

Energy Coupling in Chemical Processes

Enzymes lower the activation barrier

ATP is an energy currency ATP is “spent” and “earned”

Metabolic Pathways consist of discrete enzyme-catalyzed steps that are carefully regulated

Chapter 2 Water pH pKa Buffers