1 bich411. biochemistry i m w 4:00 p.m. – 5:20 p.m. dr. shubo han website: phone: 672-1303 email:...

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BICH411. Biochemistry IBICH411. Biochemistry IM W 4:00 p.m. – 5:20 p.m.

Dr. Shubo Han

Website:http://faculty.uncfsu.edu/shan/

Phone: 672-1303Email: shan@uncfsu.edu

Office Hours: MWF 2:00 p.m. – 4:00 p.m.T 11:00am-1:00 pm

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Course Summary

Grading: Total: 100 points

90% - 100% A80% - 89% B70% - 79% C60% - 69% D0% - 59% F

Three hour exams (10 3) 30Homework and quizzes 30

Final examination 40Total 100

Please check the syllabus from the website of Blackboard.

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Chapter 1

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What is Biochemistry?

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

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What is Biochemistry?

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What Do Biochemists Study?

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Plant

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Urchin

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Cat

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Three Domains of Life

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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.

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Unicellular organisms lacking a nucleus are prokaryotes, including

(1)Bacteria and (2) Archaea.

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The Mammalian Cell

Cytoplasm Lipid bilayer

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The nucleus contains the cell’s DNA (genome)

Nucleus

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Eukaryotic Cell Structure

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skeletal muscle cell plant stem cell

sperm cells

Human erythrocytes (red blood cells)

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Molecular Organization of Cells

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Types of molecules in a cellDeoxyribonucleic 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

ProteinsAre 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.

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Molecular Components of an E. coli Cell

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Cellular Processes

DNA

RNA

Proteins

Lipids Carbohydrates

replication

transcription

translation

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Conclusion:

•(1) Organisms are remarkably uniform at the molecular level.

•This uniformity reveals that all organisms on earth have arisen from a common ancestor.

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•(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.

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1. DNA

(1) Four simple compounds constructed DNA

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(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.

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

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• (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.

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A and T forms two hydrogen bonds.

(5) Two properties

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G and C forms three hydrogen bonds.

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• 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).

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Same shape and same size, thus fitting neatly within the double helix.

For above reason DNA is used as a hereditary material.

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RNA( ribonucleic Acid)

Similar to DNA

Linear polymer

Sugar ribose, rather than deoxyribose

Uracil instead of thymine

2. RNA: RNA is an intermediate in the flow of genetic information

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RNA is templates for protein synthesis

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3. Proteins:

Protein is the primary functional molecules in the cells.

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3. Proteins:

Facts:

Proteins: structural components of cell, or enzymesProteins are linear polymers, just like DNA and RNAProteins are more complicated.

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3. Proteins:

Protein is the primary functional molecules in the cells.

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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.

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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).

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Questions:

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

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Questions:

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

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2. The DNA backbone is made from repeating___________

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

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

5. The number of hydrogen bonds formed between C and G is

a. 1 b.2 c. 0 d.3

3. The number of hydrogen bonds formed between A and C is a. 1 b.2 c. 0 d.3

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

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

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

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

(1) The base pairs have essentially the same shape and same size, thus fit equally well into the center of the double-helical structure.

(2) The sequence of bases along one strand completely determines the sequence along the other strand.

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

----------------------------------------.

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8. RNA is constructed by 4 building blocks, which is(are)

adenine, guanine, cytosine, and uracil.

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

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

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

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Some of the amino acids of proteins

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The components of nucleic acids

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Some Components

of Lipids

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Structure of glucose, the “parent” sugar

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Elements essential to life

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Versatility of Carbon Bonding

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Versatility of Carbon Bonding

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Geometry of Carbon Bonding

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Functional Groups

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Functional Groups

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Functional Groups

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Functional Groups

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Functional Groups

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Multiple Functional Groups in a Single Biomolecule

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Common molecular representations

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Interactions between biomolecules are stereospecific

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Stereoisomers are readily distinguished by humans

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Energy Interconversions

in Living Organisms

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Adenosine triphosphate (ATP)

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Energy Coupling in Chemical Processes

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Enzymes lower the activation barrier

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ATP is an energy

currency

ATP is “spent” and “earned”

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Metabolic Pathways consist of discrete enzyme-catalyzed steps that are

carefully regulated

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Chapter 2• Water

• pH

• pKa

• Buffers