amino acid

Cloning Genes

to process the instructions to assemble the amino acids for insulin

The future of genetic research

buildup of the amino acid ornithine. Surprisingly, some 35 different

Prokaryotic Gene Regulation

A molecule (usually a small molecule: a sugar, or amino acid)

7.012 Genetics Supplementary Handout Page 1

example: for a soil bacterium, the wild-type organism can make all the amino acids it needs for

recessive. In the above examples: a soil bacterium that requires the amino acid proline

Large Molecules

3.1 Amino Acids

Diagram The 20 Amino Acids

Chart The pKa's of amino acids

Genetics: Introduction and Analyzing Crosses

amino acids it needs for survival; for human beings, the wild-type allele

examples: a soil bacterium that requires the amino acid proline because

3.5 Sequencing

Determine the Amino Acid Composition

In order to know which amino acids and how many of each amino acid there are

These procedures destroy several amino acids, so you must be cautious with

Disulfide cross-links complicate the determination of amino acid sequences

structure. In this case, there are no N-terminal and C-terminal amino acids.

determine the C-terminal amino acids.

Break the polypeptide into fragments by cleaving at specific amino acids.

specificity (i.e. cleave at different amino acids).

to as overlapping peptides). The amino acid sequence of each overlap peptide

polypeptide of interest. Your overlaps should be at least two amino acids in

Solving Enzyme Structure Problems

various amino acid changes in the protein sequence (Federation Proceedings, 22:75 (1963) and Science

146:1593 (1964)). Altered amino acids are shown in bold. "Wild-type" is the normal strain isolated

i) the gly -> glu and gly -> arg changes introduce a charge (+) or (-) into a region of the protein that requires an uncharged amino acid like glycine.

ii) the gly -> glu and gly -> arg changes introduce much larger amino acid side-chains into a space in the protein that requires a small amino acid like glycine.

Here, you must decide between two models for why these amino acid changes result in an

inactive enzyme: the new amino acid side chain is charged instead of neutral; or the new amino acid's

The first data set is ambiguous, because the side chains of the added amino acids are both big

and charged. However, the second data set shows that substituting valine, whose side chain is larger than glycine but uncharged, results in an inactive enzyme. This indicates that it is the size of the amino acid

amino acid with a larger side chain overfills the pocket, changing the conformation of the molecule so

b) Alterations of amino acids at another location in the protein were found to interact with alterations at

Changing the amino acid at position B partially reverses this effect. A possible explanation for this is

that the amino acids at positions A and B interact somehow, so that changes in one can compensate for

Membrane Transport Mechanisms

transport ribose, arabinose, and several amino acids.

Culturing cells in vitro

amino acids that the fibroblast cannot synthesize on its own. In

100 amino acids. They are adsorbed to the surface of cells, attaching to

(e.g. amino acids) may still be present in the medium. Clearly the

Chemical Energetics

Consider a reaction proceeding in the opposite direction, where the end products are at a higher energy level than the starting materials. As an example, suppose you want to convert a mixture of amino acids into a protein. Such a reaction requires

exergonic and converts the amino acid (aa) into a new form, which still

amino acid for making protein. Note that ATP was used in both the above

case, ATP donated another part of its molecule to an amino acid.

7.01Recombinant DNA Practice Problem

the lacZ coding region. This will add new amino acids and likely a new

(doesn't shift reading frame), and causes harmless amino acids to be

encodes a run of amino acids which still allow b-galactosidase to be

Membrane Proteins

hydrophilic amino acids) at the N-terminus is poking out in the

acid chain, often only 20-30 amino acids long, is threaded through the

amino acids having hydrophobic side chains, exists comfortably in the

domains. As one scans along the amino acid sequence of these proteins, it

3.3 Acid-Base Equilibria

For example: You are studying a bottle full of valine amino acids and

To check your answer and to find out more about amino acids charges, look at

This is a very useful chart of the pKa's of the amino acids:

Characteristics of Prokaryotes and Eukaryotes

large polymer of amino acids and sugar . Many types of eukaryotic cells

3 Proteins

different amino acids that can be arranged in any order to make a polypeptide

of up to thousands of amino acids long, their potential for variety is

3.1 Amino Acids Diagram

All amino acids have the same general formula:

The twenty amino acids found in biological systems are:

All proteins are linear chains composed of these 20 amino acids.

Check out the Amino Acid Repository, maintained by the Image Library of Biological Macromolecules, for an excellent summary of amino acid properties and great graphic images of the twenty amino acids.

Biological Macromolecules

proteins, amino acids, and the pKa of amino acids

The Peptide Bond

The amino acids are linked linearly through peptide bonds. These bonds are formed via a dehydration

acid with the amino group of the second amino acid.

Solving Problems

another 90nt along the mRNA. (the average amino acid is 0.1kDa)

amino acids added to protein W. Thirty amino acids will add roughly 3kDa

Feedback Inhibition

major molecules in cells: nucleotides, amino acids, sugars, and lipids.

3.4 Primary through Quartenary structure

amino acids . Note that this order is always written from amino end to

extend out and away from the helix. The CO group of one amino acid (n) is

hydrogen bonded to the NH group of the amino acid four residues away (n +4).

shows only the alpha-carbon of each amino acid. The

A-helices are most commonly made up of hydrophobic amino acids, because

amino acids. a-helices are found in almost all proteins to various extents.

where amino acid n hydrogen bonded to amino acid (n +3) in a hairpin