BIOL 2201 Final: BIOL2201 FINAL EXAM
9 Dec 2018
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M/C, Diagrams, Short Answer, Definitions (all 3 from the last lecture)
CHAPTER 4
Polypeptides
● Polypeptide chain is a polymer of amino acids
○ Bond formed between monomers is called peptide bond which is a
covalent bond
● Order of chain is always the same
○ N terminus to C terminus
○ First amino acid is number 1 next to N terminus and last one is next to C
terminus
● Properties of amino acids will determine the proteins
○ Dependent on bonds
● N terminus has an amino group attached to it
● C terminus has a carboxyl group attached to it
Proteins
● 20 amino acid that are each encoded by 3 nucleotides
○ 3 nucleotides that code for amino acid is called codon
○ Gives rise to genetic code
○ Formation of protein from DNA sequence
○ 3 nucleotides gives 1 amino acids
○ Variance in proteins and genes
● Reading frame can be changed as a result of reading codons
○ Depending on where you start reading sequence, you can get different
reading frame
○ Within each sequence, there is the possibility of having 3 different start
codons
● Condensation rxn causes covalent bond between amino acids
○ Peptide bond
○ Polymers known as polypeptides
○ Side chains provide different properties for proteins
○ Backbone of proteins remains the same
Protein Structure
● Having non-covalent bonds allows for proteins to change their conformation
○ Different processes and different functions
○ Same with RNA and DNA
● Side chains have different characteristics which will give protein final
characteristic or properties
○ A lot of hydrophobic side chains will result in hydrophobic protein
○ Protein with more polar side chains will result in hydrophilic protein
○ Conformation of side chains will change characteristics
○ Folding of protein, etc. give protein final properties
Protein Folding
● Depending on environment, the protein can be inside or outside the cell
membrane, organelles, etc.
○ Ex: polar amino acids will be in aqueous solution (i.e. cytosol)
● Polypeptide chains give rise to specific proteins
● If you unfold a protein and leave it at room temp, it will take the conformation it
was originally in
● If proteins are within aqueous solution, all hydrophilic side chains will be on the
surface of the protein
○ Hydrophobic amino acids will form the core of the protein
○ Membrane proteins are all made on ER membrane
○ Soluble proteins are made inside ER or in cytosome
● When proteins are misfolded, they will give rise to structures called prions
Primary Structure
● A sequence of amino acid chains
● Peptide bonds are formed between the amino group of one amino acid and
carboxyl group on another amino acid
Secondary Structure
● Alpha helix
○ Stabilized by hydrogen bonds between nearby residues
● Beta sheets
○ Stabilized by hydrogen bonds between adjacent segments that may not
be nearby
Other Structures
● Tertiary Structures
○ Involved the way random coils, alpha helices, and beta sheets fold in
respect to each other
● Quaternary Structures
○ Complex of several polypeptide structures
Protein domains
● Proteins that form independently into a stable structure
● If you take that form of protein and imbed it into another protein, it will remain in
the same structure
○ Ex: binding sites
Protein Families
● Specific proteins that have similar function, evolutionarily related and involved in
similar processes
○ Amino acids similar to other proteins within that protein family
● Can be made of different subunits (ex dimer)
○ Based on attraction to other proteins, they can have different processes
Disulfide Bonds
● Covalent bond
● Will stablize protein structure
● Found in extracellular space
● Made in the ER because they require oxidation
○ Cytosol is a reducing environment and will result in breakage of the bond
● In a reducing environment, they will break
○ Requires oxidation (in ER)
Protein Binding
● Attractions could be between proteins and proteins, or between proteins and
other molecules
● Rely on covalent bonds (don’t want them to attract very strongly to each other)
Ligands
● Form weak interactions with proteins at binding sites
● Highly specific attractions
○ Transporters will only attract to one type of molecules
○ They work in a way that if binding sites are blocked, they inhibit the
function of the protein
Antibodies
● Produced by immune system in response to foreign molecules
○ If foreign object enters cell, the cell will produce antibodies
● Recognize a target molecule, antigen
○ Antibodies recognize antigens and kill them off
○ Can be used in lab for protein purification
● Found in immune cells (B and T cells)
