Insulin: Weight = 5733, 51 amino acids Glutamine Synthetase: Weight = 600,000, 468 amino acids

Amino Acids & Dehydration Synthesis Amino acid structure: Functional groups Peptide bonds

Sample amino acid structures: carboxyl group-bluealpha carbon-gray amino group-greenR groups-beige

The twenty essential amino acids. Note R groups in blue

Amino Acids w/ various R groups

Nonpolar amino acids

Neutral Amino Acids

Ionic amino acids

Amino acids are joined together in proteins by peptide bonds. A peptide bond forms between the carboxyl group of one amino acid (amino acid 1 in the figure preceding) and the amino group of the adjacent amino acid (amino acid 2).

Dehydration synthesis

Dehydration synthesis animation

Dehydration Synthesis

Dehydration Synthesis : Amino acid 1 Amino acid 2 Dipeptide (Peptide bond) Amino group

Protein Structure Amino acid structure Dehydration synthesis

Insulin: Weight = 5733, 51 amino acids Glutamine Synthetase: Weight = 600,000, 468 amino acids

Four ‘levels’ of protein structure

Four levels of protein structure

Primary structure: Visualized as a straight chain of aa’s, but with a specific sequence, As determined by its gene

Secondary structure: alpha helix or beta pleated sheet

Tertiary structure: coiled chains of aa’s are folded & wound around themselves

Close up of 2 o & 3 o Protein Structure

Quarternary structure: separate polypeptide chains are combined

Levels of Protein Structure

Four Levels of Protein Structure (note change in scale from 2 o to 3 o )

Collagen molecule

Actin molecule

Myosin molecule

Hemoglobin molecule

Antibody molecule

(purple) Reverse transcriptase of HIV1 w/ a fragment of DNA (colors)

Protein Synthesis: Transcription & Translation

Transcription: Making a copy of the blueprint

Morse Code Key

Using the Genetic Code: DNA :: mRNA :: Protein Get from ‘language’ of DNA (A,G,C,orT) to ‘language’ of protein (aa’s) DNA’s ‘language’ is a triplet code in which 3 nucleotide bases (a codon) specify 1 amino acid in protein.

DNA (1 gene) :: mRNA :: polypeptide

Steps in Transcription

Transcription: Note the free nucleotides

DNA unzips

Complementary base pairing

mRNA- final product of Transcription mRNA moves off to ribosome

Transcription: Getting the plan straight (copying the gene)

Transcription animation

Translation Building the protein from the plan

Using the Genetic Code: DNA :: mRNA :: Protein Get from ‘language’ of DNA (A,G,C,orT) to ‘language’ of protein (aa’s) DNA’s ‘language’ is a triplet code in which 3 nucleotide bases (a codon) specify 1 amino acid in protein.

Structure of a Ribosome

Structure of a tRNA

Translation : purple = mRNA blue = ribosome yellow = tRNA (note anticodon) white = amino acids red = peptide bond

Translation initiation

Translation initiation (cont)

Translation- elongation

Translation- termination

A Polysome: With more than one ribosome translating an mRNA at one time, it is possible to produce many polypeptides simultaneously from a single mRNA.

Protein Synthesis

In a prokaryotic cell, transcription and translation are coupled; that is, translation begins while the mRNA is still being synthesized. In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs in the cytoplasm.

Protein synthesis in eukaryotes

Antibiotic Mechanism

Antibiotic Mechanism

Collagen molecule

Actin molecule

Myosin molecule

Antibody molecule

Hemoglobin molecule

Enzymes

Definitions: Catalyst = An additive that speeds up a chemical reaction without itself being consumed or changed by the reaction Enzyme = A protein that acts as a catalyst, usually in a biological context. –All enzymes are proteins, not all proteins are enzymes

Enzyme mechanism of action: An enzyme improves the odds of ‘useful’ collisions between substrate molecules.

Steps in enzyme function

Enzyme-substrate animation

S = substrate E = enzyme P = product ES = enzyme- substrate complex

Lock & Key Model: Enzymes are very specific and it was suggested by Emil Fischer in 1890 that this was because the enzyme had a particular shape into which the substrate(s) fit exactly. This is often referred to as "the lock and key" hypothesis. An enzyme combines with its substrate(s) to form a short- lived enzyme-substrate complex.

Induced fit hypothesis: In 1958 Daniel Koshland suggested a modification to the "lock and key" hypothesis. Enzymes are rather flexible structures. The active site of an enzyme could be modified as the substrate interacts with the enzyme. The amino acids side chains which make up the active site are molded into a precise shape which enables the enzyme to perform its catalytic function. In some cases the substrate molecule changes shape slightly as it enters the active site. A suitable analogy would be that of a hand changing the shape of a glove as the glove is put on.

Enzyme Animation

Enzyme Websites: Enzyme notes in ppt format, few diagrams: animation of enzyme action written outline- enzymes by Worthington asd

Enzyme & Cell Regulation Gene activation Feedback loops for enzyme activity

Various possible routes of feedback in the production-regulation of a given protein

Changing the conformation (shape) of an enzyme’s active site changes its ability to act as a catalyst

Zymogens: Enzyme Precursors

Competitive Enzyme Inhibition

Allosteric Modulation of an Enzyme

Genes can be either inducible or repressible. Many genes are normally blocked by the action of a repressor protein. This prevents the RNA polymerase enzyme from binding to the gene and transcribing the structural gene. Such genes are induced by the arrival of an inducer molecule which binds to the repressor protein and rendering it inactive. This allows transcription from the structural gene and the production of a protein. Other genes are normally active and able to be constantly transcribed, because the repressor protein is produced in an inactive form. On the arrival and binding of the corepressor molecule the complex can act as a functional repressor and block the structural gene by binding at the operator site.

Steps in Transcription

DNA Technology

Bases: A- adenine G- guanine T- thymine C- cytosine

Other translation animations: Add an amino acid to tRNA- Initiation of Translation- Elongation of Polypeptide- Termination of Polypeptide-