3.13 Flashcards
what are the two functional groups of amino acids?
NH2 and COOH (amine and carboxylic acid)
How many are naturally occurring amino acids there in the human body?
20
What type of amino acids are found in the body?
alpha amino acids
What does this mean about the structure
It means NH2 is always on the carbon next to COOH
Draw general formula for alpha-amino acids.
Are alpha-amino acids chiral?
Yes
Why are alpha-amino acids chiral?
One carbon has 4 different substituents (except glycine where R=H)
Which enantiomer do alpha-amino acids exist as in nature?
(-) enantiomer
How can amino acids be synthesized industrially?
RCHO + NH4CN –> RCH(NH4)CN via Nucleophillic addition
RCH(NH2)CN + HCl + 2H2O –> RCH(NH2)COOH + NH4Cl
(Hydrolysis, HCL is dilute)
How can amino acids be synthesized industrially?
RCHO + NH4CH —> RCH(NH2)CN via nucleophilic addition
RCH(NH2)CN + HCl + 2H2O —> RCH(NH2)COOH + NH4Cl (hydrolysis, HCl is dilute)
Need to reflux the reaction mixture
Is the product from amino acid being synthesized naturally optically active?
No
Why is the product from amino acid being synthesized naturally optically active?
A racemic mixture is formed as the CN_ ion can attack from above or below the planar C=O bond with equal likelihood. An equal amount of each enantiomer is formed, so no net effect on plane polarised light.
In what form do amino acids exist as solids?
Zwitterions (ionics lattice)
What consequences does amino acid solids have?
High M.P. and B.P.’s
What colour are most zwitterions at room temperature?
White solids
Do zwitterions dissolve in water?
Yes
Do zwitterions dissolve in non-polar solvents?
No
Why do/don’t zwitterions dissolve in non-polar solvents?
Zwitterions have polar bonds
Define a zwitterions
Ions which have a permanent positive and negative charge, but are overall neutral.
How do zwitterions occur in amino acids?
COOH is de-protonated —> COO_
NH2 is protonated —> NH3+
What happens to amino acids in acidic conditions?
Gains a proton at the NH2 group.
What happens to amino acids in alkaline conditions?
Loses a proton at the COOH group.
What is the peptide linkage?
CONH
What is a dipeptide? Draw a general one for amino acids
Two amino acids bonded together (a dimer).
What name is given to amino acid chains up to 50 amino acids long?
Polypeptides
What is the name given to chains of more than 50 amino acids?
Proteins
What are polypeptides and proteins found in?
Enzymes
Wool
Hair
Muscles
What is the process by which polypeptides and proteins are broken down into their constituent amino acids?
Hydrolysis
What conditions are needed for hydrolysis to occur?
6 mol dm_3 HCl
Reflux for 24 hours
What is the primary structure of a protein?
The sequence of amino acids along the protein chain
How is the primary structure of a protein bonded?
The sequence of amino acids along the protein chain
How is the primary structure represented?
Sequence of 3 letter abbreviations of the amino acids
How can the primary structure of a protein by broken?
Hydrolysis
6M HCl
24-hour reflux
What is the secondary structure of a protein chain?
The shape of a protein chain
What is the two option of the secondary structure?
Alpha-helix shape
Beta-pleated sheets
How is the secondary structure held together?
Via hydrogen bonds
E.g. C=O and N-H groups
What is the tertiary shape of a protein?
Alpha-helix/Beta-pleated is folded into a complex 3D-shape
How is the tertiary structure held together?
Hydrogen bonding
Ionic interactions between R groups
Sulfur-sulfur bonding (disulfide bridges)
van der Waal forces of attraction
Why is the tertiary structure important?
The shape of protein molecules is vital to their function
E.g. enzymes
How many amino acids can be attracted to each other?
Hydrogen bonding
Ionic interactions between groups on side chains
Disulfide bridges, so 2S atoms oxidized to form an S-S bond
What is wool? How is it held together?
Protein fiber with secondary alpha-helix structure; held together by by hydrogen bonds
What do wool’s structure and bonding mean for wool’s properties?
Can be stretched, H-bonds extend
Release it and it returns to its original shape
Wash too hot and H-bonds break permanently
How do you calculate an Rf value?
Distance moved by that substance divided y the distance moved by the solvent front
How can Rf values to used to identify which amino acid are which?
Compare the experimental Rf value to known values of the same solvent
Or run pure amino acids in the same in the same solvent nda compare resultsto identify amino acids
How do you find the primary structure of a protein?
Reflux with 6M HCl and reflux for 24 hours
Carry out TLC to find the number and type of amino acid present
How do you find the structure of the secondary and tertiary protein?
X-ray diffraction
What is an enzyme?
A protein-based catalyst that speeds up bodily reactions by factors of 10^10
How many reactions is each enzyme designed to catalyze?
One reaction they are very specified
What is the structure of the enzyme?
Globular protein with a crevice in it, known as an “active site”
How does the enzyme’s structure help it function?
The reacting molecules fit precisely into the active site and held at the exactly right orientation to react.
The lock and key hypothesis.
How else do enzymes increase the rate of reaction?
Reacting molecules through the intermolecular forces form temporary bonds to the enzyme at the active site.
This weakens the bonds in the molecules, promotes electron movement and lowers the activation energy.
What does the stereospecificity of enzymes mean?
Active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalyzed
What does stereospecificity mean for most naturally occurring molecules?
most naturally occurring molecules only occur as one enantiomer due to stereospecific enzymes
How are enzymes denatured?
Conditions of pH
How does enzyme inhibition work?
A molecule with a very similar shape and structure to the substrate is devised
The molecule binds to the enzymes active site.
The molecule blocks the active site.
Therefore the active site cannot absorb the substrate, so the reaction cannot be catalyzed.
An example of a drug that works through enzyme inhibition?
Penicillin
What structure does DNA take?
A polymer with 4 monomers; they can be combined diferently
What constitutes a nucleotide?
A phosphate ion
2-deoxyribose
A base (guanine, cytosine, adenine and thymine)
Draw a nucleotide.
What forms between bases of adjacent nucleotides?
H-bonding
Hoe does DNA polymerize?
OH on the phosphate group
OH on Carbon-3 of 2-deoxyribose
react to eliminate a molecule of H2O
What kind of polymer does the polymerization of DNA lead to?
condensation of a polymer chain
the backbone of sugar and phosphate molecules, with bases attached
What defines the properties of the DNA molecules?
the order of the bases
Why does DNA have a double helix shape?
exists as 2 strands
these 2 strands are held together by hydrogen bonding (C, G, T, and A)
The complementary DNA molecule has bases that hydrogen bonding in the same order to those on the the other molecule
How is DNA copied when cells divide?
H bonds break between pairs
covalent bonds in polymer chains interact
the sequence of bases is maintained
separate nucleotide molecules that have been created to move hydrogen bonds to their relevant bases
They then polymerise
Draw the structure of cisplatin
What is cisplatin’s function? How does it do this?
Anti-cancer drug
Bonds to strands of DNA in order to distort the shape and prevent cell replication.
It bonds to N atoms at 2 adjacent Guanine molecules
The N atoms replace the Cl_ ligands in a ligand substitution reaction
Why are Cl_ ions able to be replaced by N in the base?
N atoms on the Guanine base have lone pairs of electrons that can coordinately bond to the Pt on
N atoms have better ligands than Cl_ , so replace them
What are the drawbacks of using cisplatin?
Affects healthy cells that replicate quickly
Damage kidneys
What happens when excess bromoethane is added to an amino acid?
CH3Br is in excess
so every H on the N atom and the lone pair n the N atom is replaced by CH3 group
quarternary ammonium ion
(makes a salt with Br_)
What happens if an amino acid is added to an excess of methanol in the presence of concentrated of sulphuric acid?
Methyl ester forms with COOH group
—–>
COOCH3
NH2 is protonated by the acid
—–>
NH3+
