Biomolecules I

Biological MoleculesToday: amino acids, proteins

DNA, RNA

April 14, 2009

Organic Chemistry

Study of carbon containing compounds. Originally encompassed only compounds isolated from biological sources because it was thought that the molecules contained a “life-force”. The definition of organic chemistry now consists of man-made and biological molecules consisting mostly of Carbon and Hydrogen plus Nitrogen, Oxygen, Fluorine, Chlorine, Bromine, Sulfur, and Phosphorus.

So what makes carbon so special?

Here is an organic molecule

Isopropyl alcohol(rubbing alcohol)

Construct a model of isopropyl alcohol

Here is an organic molecule

Isopropyl alcohol(rubbing alcohol)

Carbon skeleton

Functional group

Does your model look like this?

Benzene

Our plastic model looks a little different

As opposed to …

Amino Acids

Standard amino acids

• 20 amino acids make up all proteins.

• Our bodies produce all but eight

• Isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine – essential amino acids.

Terms to know

Two amino acids joined together is called a dipeptide. Example Ala-Ala

Three amino acids joined together is called a . Example Glu-Cys-Gly

Many many, many amino acids joined together are called .

Terms to know

Two amino acids joined together is called a dipeptide. Example Ala-Ala

Three amino acids joined together is called a tripeptide . Example Glu-Cys-Gly

Many many many amino acids joined together are called protein .

Formation of a peptide bond

An example of an enzyme

Proteins

• Large organic compound (macromolecules)

• Composed of amino acids

• Essential parts of all living organisms– Enzymes that catalyze bioreactions– Play a role in structural or mechanical

functions– Cell signaling

Sucrose is first digested in the stomach by stomach acid. Any remaining sucrose split into glucose and fructose by sucrase in the walls of the intestines.

Protein synthesis

Proteins are assembled from amino acids using the information encoded in genes. (one gene contains the information for one entire enzyme)

Each protein has its own unique amino acid sequence that is specified by the nucleotide sequence of the gene encoding this protein. Each three-nucleotide combination, called a codon, stands for an amino acid.

RNA and DNA

Thymine T

Nitrogenous Bases

Hydrogen Bonding

5’end

3’ end

Nucleotide

Nucleotide in RNA

Sugar (ribose)

phosphate

Nitrogenous base (A)

Protein synthesis

RNA polymerase makes this step happen

Answer the questions on your handout

http://vcell.ndsu.edu/animations/translation/movie.htm1. What is transcription?2. What is the role of RNA polymerase?3. What is the role of Poly A polymerase?4. What do ATP and ADP stand for? What does ATP

supply?5. What is splicing?6. What is the difference between an intron and an exon?7. What is translation?8. What are the three processes within translation?9. What is a codon?10. What’s the difference between mRNA and tRNA?

Structure of proteins

• Primary Structure: The exact sequence of amino acids

• Secondary Structure: The arrangement of amino acids that give local segments of a protein a specific shape. Includes structures alpha-helix, beta pleated sheets and random coils.

• Tertiary Structure: The three dimensional structure of the protein as a whole.

• Quaternary Structure: The three dimensional structure of protein that are assembled from separate protein chains.

Structure of proteins

ProteinsExamples of proteins

α-keratin contains long strands of alpha helix structures. Found in hair, hooves, nails, skin and wool. (fibrous protein)

Silk

These pleated sheet structures make the material resistant to stretching. The small R groups make the chains compact giving the material a smooth feel. The uniform surface makes it a good reflector of light.

Artificial Silk

Polymer continues on in each direction

Another fibrous proteinCollagen most abundant protein in

vertebrates, found in bone, cartilage, tendons, teeth and blood vessels. Contain mostly glycine and proline.

Globular protein- soluble in water

Hemoglobin

Heme

Where do biological molecules come from?

USAToday Posted 8/8/2006

This is an artist’s rendition of the cosmic chemistry cycle. Stars eject matter into space. Diffuse gas clouds condense into stars and planets or comets and meteorites.