lecture 1: amino acids Flashcards
what are the monomers of proteins?
amino acids
what are the polymers of proteins?
polypeptide
by which bond are amino acids linked?
peptide bond
what are the components to each amino acid?
-central carbon
-hydrogen group
-amino group (NH2)
-carboxyl group (COOH)
-R group
what differentiates the 20 different amino acids?
the R group
in what form is the amino group more stable? what are the 2 forms it can exist as?
it can exist as NH2 or NH3+, but its more stable as NH3+ in our bodies so thats how it exists.
what is common between each amino acid?
backbone
what is another word for R group?
side chain
what are the properties of a non-basic/acidic hydrophilic amino acid? (polar side chains)
the side chains contain hydroxyl (OH), carbonyl (C=O) and sulfhydryl (SH) groups
what happens if you see an oxygen in the side chain of an amino acid?
it must be at least polar
what are the properties of a basic hydrophilic amino acid? (electrically charged side chains) what is the charge?
the side chain is charged positivly. the charge is due to a positive amino group (NH2/NH3) in the R group. CHARGED AT PH 7
what are the properties of an acididc hydrophilic amino acid? (electrically charged side chains) what is the charge? CHARGED AT PH 7
the side chain is charged negatively. this charge is due to a negatively charged carboxyl group (COO/COOH)
how does carboxyl exist in our bodies in the backbone of amino acids?
as COO-
what are the properties of a hydrophobic amino acid? (polar side chains)
the side chains are made up of carbons, hydrogens and methyl groups (CH3)
What happens to an amino acid in very acidic conditions?
Backbone becomes positively charged. The carbonyl group gains an H+, due to the fact that there are more H+ in the environment
What happens to an amino acid in very basic conditions?
The amino group loses its proton, therefore it is no longer positively charged and the negative charge of the carboxyl takes over.
What does an amino acid look like at PH 7?
what is the isoelectric point?
PH at which a protein has a neutral charge (charge of 0)
by which reaction are peptide bonds formed? how does this happen?
dehydration reaction. the H of the amino group of one amino acid is lost along with the OH of the carboxyl group of the next amino acid. this continues until we have a chain
what is the directionality of the peptide bond?
c terminus first (carboxyl end)
n terminus at the end (amino end)
why are proteins able to carry out so many diverse functions in cells?
-because they can form many different shapes which makes them really diverse comapred to other structures
what are the 4 levels of protein structure?
-primary structure
-secondary structure
-tertiary structure
-quaternary structure
what type of bonds are peptide bonds? why?
covalent bonds. anything formed by a dehydration reaction is a covalent bond.
what is a primary structure?
-Linear sequence of amino acids coded for by a gene sequence
-Has directionality (N-C terminus)
-linear chain of amino acids
what is a secondary structure?
spatial arangement of amino acids to form alpha helices of beta sheets.
how is a secondary structure formed?
by H bonding between amino (N-H) group of one amino acid and carbonyl (C=O) (since we lost OH during dehydration) group of another amino acid
are R groups involved in the the formation of secondary structures?
NO! only the backbone!
what are the characteristics of alpha helix?
-H-bonding between amino acids 4 places apart
-R groups oriented away from the axis
-looks like a curl
what are the characteristics of beta sheet?
-two regions of polypeptide chain lie parallel to each other like a folded sheet
what is a tertiary structure?
-structure formed when alpha helix and beta sheets interact to form a variety of shapes
-formed through the interactions between amino acid side chains
what type of bonds happen in tertiary structure?
side chains interact again through covalent and non-covalent interactions to form tertiary structures
what type of non-covalent bonds are involved in a tertiary structure?
-H bonding (between R groups)
-hydrophobic interactions between hydrophobic amino acids (2 hydrophobic)
-van der Waals (2 hydrophilic or 2 hydrophobic)
-ionic bond (charged amino acids interact through salt bridges)
what type of covalent bonds are involved in a tertiary structure?
disulphide bridge (amino acids interact with a sulfhydyl group)
what are van Der Waals?
a way in which 2 polar or 2 hydrophobic amino acids can interact with each other in a tertiary structure.
what is a quaternary structure?
-more than one polypeptide chain interacting together to form a protein
how are polypeptides held together in the quaternary structures?
by the same interactions as a tertiary structure
what is denaturation?
disrupting protein structure. proteins become unfolded as all bonds are broken. we are left with polypeptides.
is renaturation possible?
sometime possible, but highly unlikely
what are the conditions that can denature a protein? why?
-temperature (alters vibrational and rotational energy and disrupts non-covalent interactions such as H-bonds
-PH (changes the ionic state of the charged side chains, which disturbs bonds and makes for the protein to unfold)
-salt (changes the ionic environment. there are now more charges in the environment which disrupts the charges of the protein causing it to unfold)
-detergent (disrupts hydrophobic regions)
-reducing agent (breaks covalent disulphide bonds. smells and. something that you add to the protein that causes a reduction)
what is the movement od hydrophobic/hydrophilic side chains when we add detergent?
-hydrophobic side chains move from the interior of protein to the exterior of protein
-hydrophilic Side chains move to the interior of protein
what levels of protein structure are affected by denaturation?
4th, 3rd, 2nd, NOT FIRST! (cant break peptide bonds)
