SCIE1106 Study Guide - Final Guide: Variable Number Tandem Repeat, Cytoskeleton, Thermal Cycler
TOPIC THREE: Proteins and Recombinant DNA Technology
Protein Structure:
Proteins are the most abundant and diverse
groups of molecule in either a prokaryotic
or eukaryotic cell. They are involved in
nearly all cellular processes. The building
blocks of proteins are called amino acids, which have one carbon atom that is
bonded to an amino group, carboxyl group and a side chain. The side chains of
amino acids give them their unique characteristics that are reflected in proteins.
There are 20 amino acids in total and can either be polar or unpolar, charged or
uncharged.
Amino acids can join together to form peptides, bound together by a peptide
bond. The formation of the peptide bond is a condensation reaction, formed with
the removal of water. The peptide bond forms the backbone of a polypeptide
chain, and side chains are not involved in the peptide bond formation. Generally,
a polypeptide is made up of > 10 amino acids. The simple sequence of amino
acids in a polypeptide is referred to as the primary structure of a protein.
Polypetides are flexible molecules, however there is no rotation around the
peptide bond. Noncovalent interactions, like electrostatic attractions, hydrogen
bonds and Van der Waals attractions, restrict the conformations a polypeptide
can take. These hydrophobic interactions are also important in determining
secondary protein structures.
The secondary protein structure is different for different proteins, depending on
the amino acid sequence. It is comprised of a folding motif and random coils.
There are two different types of folding motifs – alpha helices and beta sheets.
Disulphide bonds, through covalent bonds or cysteine side groups, can stabilize
the secondary structure of some proteins.
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In alpha helices the carbonyl oxygen of a peptide bond is
hydrogen bonded to the amide hydrogen of the amino
acid 4 residues away. Many transmembrane proteins
contain alpha helical regions.
Beta sheets are strands that are laterally packed either
antiparallel or parallel to one another. The beta strands
making up the sheets may be within the same protein or
in different polypeptide chains. Many proteins have a rigid
core of beta sheets.
Some proteins can have tertiary or quaternary structures. The tertiary structure
of a protein is the full three-dimensional conformation, where all alpha helices,
beta sheets and random coils loop together. The quaternary structure of a
protein is the three-dimensional relationship of polypeptides in a multisubunit
protein (e.g. haemoglobin).
The protein domain is the region of a polypeptide that can fold independently
into a complex, stable structure, whether it be secondary, tertiary or quaternary.
Domains in evolutionary related proteins often have similar function, and similar
domains are found in proteins with similar functions in evolutionary distinct
organisms. As the complexity of an organism increases, so does the number of
domains.
Protein Function:
Proteins can never function alone – they have to bind to other molecules. These
other molecules are called ligands and can be an ion, small molecule or
macromolecule. The binding of a protein to a ligand is very specific and driven by
electrostatic and hydrogen bonds (non-covalent bonds).
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Enzymes are proteins that bind specific ligands, binding together in the active
site. The organization of atoms in the active site is optimized for catalysts,
speeding up chemical reactions without being altered. Enzyme names typically
end in -ase and the name indicates the substrate and nature of the catalyzed
reaction.
Enzyme Class
Biological Function
Protease
Hydrolyses peptide bonds between amino acids
Polymerase
Catalyze polymerization reactions (e.g. DNA and RNA
synthesis)
Kinase
Catalyze addition of phosphate groups to molecules
Phosphatase
Catalyze hydrolytic removal of a phosphate group from a
molecule
The products of one enzyme-catalyzed reaction may be the substrate for
another, and are often referred to as metabolic pathways. The regulation of these
pathways is at the level of the enzyme, and regulation can occur at the level of
gene expression, by compartmentalizing enzymes, by regulating enzyme
degradation, by binding other molecules or by phosphorylation.
Many proteins can give structure to a cell, an example of which is keratin. Keratin
is a fibrous protein whose monomers assemble into intermediate filaments.
Intermediate filaments are part of the cytoskeleton for many different types of
cells, including epithelial cells.
Many proteins are able to generate movement, which is coupled with the
hydrolysis of ATP and conformational changes in the protein. For example,
kinesin and dynein move cytoplasmic components (cargo) along microtubules in
opposite directions. ATP hydrolysis occurs at the head regions of these proteins
while the cargo is bound at the tail regions of the motor proteins.
Many proteins also belong to large families. These relationships are determined
by comparing similarities and differences in amino acid sequences. Proteins with
more similar sequences cluster on the same branches of evolutionary trees.
Functionality is also typically reflected in clustering.
Introduction to Cloning:
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Document Summary
Proteins are the most abundant and diverse groups of molecule in either a prokaryotic or eukaryotic cell. They are involved in nearly all cellular processes. The building blocks of proteins are called amino acids, which have one carbon atom that is bonded to an amino group, carboxyl group and a side chain. The side chains of amino acids give them their unique characteristics that are reflected in proteins. There are 20 amino acids in total and can either be polar or unpolar, charged or uncharged. Amino acids can join together to form peptides, bound together by a peptide bond. The formation of the peptide bond is a condensation reaction, formed with the removal of water. The peptide bond forms the backbone of a polypeptide chain, and side chains are not involved in the peptide bond formation. Generally, a polypeptide is made up of > 10 amino acids.
