3.13 amino acids Flashcards
what two groups do amino acids contain
an amine group and a carboxylic acid group
what are the amino and carboxylic acid group attached to in alpha amino acids
the same carbon
why are amino acids amphoteric
they react with acids and bases
what happes to an amino acid when it reacts with an acid
the lone pair on the N of the NH2 group accepts a H+ ion
when happens to an amino acid when it reacts with a base
the lone pair on the OH- of the base takes the H off to COOH group to leave COO- and H2O
isoelectric point
the pH at which the molecule has no net electrical charge
what does the amino acid exist as at the isoelectric point
a dipolar ion or zwitter ion
when do zwitterions form
when the carboxyl group of one amino acid donates a proton to the amine group of another amino acid molecule
what is the pH of a zwitterion the same as
its isoelectric point
how does an amino acid behave at a pH that is lower than its isoelectric point
as a base and accepts H+ ions
how does an amino acid behave at a pH that is higher than its isoelectric point
as an acid and donates H+ ions
what is the structure of an amino acid
crystalline solids
what do amino acids have as a result of their crystalline structure
relatively high melting points
what do zwiterions form with eachother that require a lot of energy to break
ionic bonds
what do amino acids dissolve well in
water
what do amino acids dissolve poorly in
non polar solvents
why do amino acids dissolve readily in polar solvents
the zwitterions react with polar solvent molecules
what is a peptide
a compound made of amino acids joined by peptide links
how are peptide links formed
in a condensation reaction between amino acids
what is removed in a condensation reaction between amino acids
water
what are the remains of an amino acid after a condensation reactions called
an amino acid residue
how can two different amino acids join together
in two different ways to give two different dipeptides
eg alanine and glycine- ALAGLY/GLYALA
in what conditions can peptides be hydrolysed under
acidic or alkaline
acid hydrolysis: reagents:
dilute acid
acid hydrolysis: conditions:
heat and reflux
acid hydrolysis: products
amino acids but with NH3+ group
alkaline hydrolsis: reagents:
dilute alkali
alkaline hydrolsis: conditions:
heat and reflux
alkaline hydrolsis: products
amino acids but with COO- group
what does the structure of the products in acid and alkali hydrolysis depend on
the pH of the hydrolysis mixture
how can the mixture of amino acids be separated after hydrolysis
TLC
what do different amino acids have
different sidechains
what is chosen to separate the amino acids in tlc
a suitable stationary phase
how can separated amino acids be seen in tlc
if plate is sprayed with ninhydrin
when can 2D tlc be used to separate amino acids
if the two amino acids have very similar Rf values in a particular solvent
2D TLC: what shape is the plate thats used
square
2D TLC: where is the mixture spotted
in one corner and a chromatogram is run in the usual way so spots are separated along one edge of the plate
2D TLC: how many degrees is plate turned
through 90 degrees
2D TLC: what happens aafter tlc plate has been turned 90 degreen
the chromatogram is run again with a different ssolvent
what does 2D TLC give
2 rf volues for each spot (one for each slvent)
what are proteins
naturally occuring polymers of amino acids
what are amino acids usually joined by
a peptide link
what 3 levels of structure do all proteins have
primary, secondary and tertiary
what do proteins with more than one polypeptide chain also have
quaternary structure
primary structure
the sequence of amino acids in a protein chain
how can the primary structure be resprested
using the sequence of 3 letter codes for the amino acid residues in the chain
what is the primary structures stbaility
relatively stable
secondary structure
a regular 3d structure formed by part of a protein chain such as an a helix or b pleated sheet
how is the secondary structure of proteins held together
by h bonding between the delta + H of one peptide link and the lp O of an adjacent peptide linkq
why is secondary structure disrupted more easily thn primary
h bonds much weaker than covalent bonds
tertiary structur
3d arrangement of a single polypeptide chain
what is the tertiary strucure held together by
VDWs and H bonds AND IONIC BONDS AND DISULPHIDE BONDS
where do VDWs forces form in teritary structure
between non polar amino acid side chains such
where do h bonds form in tertiary structure
between C=O and n-h groups in back bone of protein and between side chains containg groups such as OH
where do ionic bods form in tertiary structure
between amino acid side chains containing charrrged groups eg NH3+ and COO-
where do disulphine bonds form in tertiary structure
link different part of protin chain together and help stabilise the teritary structure
s-s bonds
a covalent bond formed from the thiol groups of a pair of cysteine residues
enzymes
a protein based catalyst, whihc speeds up te rate of a particular reaction in a living organism
substrate
the compound that an enzyme acts upon
what is the region responsible for an enzymes catalytic activity called
an active site
which molecules can fit the enxymes active site and bind to the enzyme
only substrate molecules wit a correct stereochemistry
stereopecificity
active site can be so selective of the substrate shape that many enzymes only catalyse the reaction of one enantiomer of an optically active compund
what does substrate bind to active site using a combination of and what is this called
VDW, dipole dipole, h bonds and ionic
lock and key hypothesis
What does the induced fit model state that the substrate binding to the active side induces a change in
The shame of the active site to allow the substrate to fit perfectly
Induced fit model: bonds between enzyme and substrate promote
Movement of electrons within the substrate
Induced fit model: what does movement of electrons in substrate make easier
Breaking and forming bonds
Induced fit model: what does ease of breaking and forming bonds lower
Activation energy for enzyme catalysed reaction
What can lactic acid be oxidised using
An enzyme catalase LDH
Equation for oxidation of lactic acid
H3COHHCOOH > CH3=O HCOOH
Why does lactic acid have two enantiomers
Due to the presence of a chiral C atom
Why can LDH only bind to one of the enantiomers of lactic acid
It’s stereospecific
What does an inhibitor have a similar shape to
The substrate
What is the inhibitor able to do due to it being a similar shape to the substrate
Bind to the active site and prevent the substrate from binding
What does amount of inhibition depend on
Relative concs if inhibitor and substrate
How do many drugs act
By inhibiting the activity of an enzyme that catalyses a harmful reaction
What is the modern day drug design known as
Structure directed drug design
Structure-directed drug design: how can tertiary structure of enzymes be determined
Using x Ray crystallography, NMR and other techniques
Structure-directed drug design: how else is it possible to predict the tertiary structure from an enzymes primary structure
Using computer modelling
Structure-directed drug design: what can information about the structure of the active sign be used for
To design inhibitor molecules, again using computer modelling
What is DNA
Deoxyribonucleic acid
DNA is a polymer of four different
Nucleotides
What 3 components is each nucleotide made up of
- phosphate ion
- pentose sugar (2-deoxyribose)
- base
What are the 4 bases in DNA
Adenine, guanine, cytosine and thymine
What does formation of nucleotides involve
Condensation reactions
Nucleotides: what does the phosphate ion bond to and what is eliminated
Phosphate ion bonds to deoxyribose and water is eliminated
Nucleotides: what does the organise base bond to and what is eliminated
Deoxyribose and water is eliminated
What are polynucleotides
Condensation polymers of nucleotides
How are phosphodiester bonds formed
The phosphate group of one nucleotide joins to the sugar of another nucleotide
What back bone does a polynucleotide have
Sugar phosphate
Where do the organic bases attach in polynucleotides
To the sugars
Single strand of DNA
Polynucleotide
What does DNA exist as
Two polynucleotide standards in the form of a double helix
DNA structure: what are the two strands held together by
H bonds between pairs of bases
How many h bonds form between A and T
2
How many h bonds form between cytosine and guanine
3
Why does the H bonding between base pairs lead to a double helix with complementary strands
- only thymine has correct atoms in right place to H bind with adenine
- only guanine has correct atoms in right position to H bond to cyctosine
Why are other base pair combinations not possible
They wouldn’t place atoms at the correct distance or in correct alignment to H bond properly
Genetic code: what does a sequence of bases in certain sections of DNA hold the code for
The amino acid sequence of certain proteins
Genetic code: when do the two strands of the double helix separate
When the DNA is transcribed to make an mRNA template for protein synthesis/replicated during cell division
Genetic code: whu does strand separation occur without breaking the polynucleotide chain
Because the H bonds between the strands are weaker than the covalent bonds between nucleotides
What is cisplatin a complex of
Platinum (II)
How to remember structure of cisplatin
Cis means 2 Cl groups and 2 NH3 groups are together
What effect does cisplatin have when it binds to DNA
Blocks DNA replication and transcription and triggers programmed cell death
Mechanism for hydrolysis of cisplatin
[PtCl2(NH3)2] <> [PtCl(H2O)(NH3)2]+ + Cl-
Second step in mechanism of action of cisplatin
Ligand substitution reaction occurs between a nitrogen atom in a guanine base and the platinum ion
Third step in mechanism of action of cisplatin
Second nitrogen atom from a nearby guanine bonds to the platinum by replacing the chloride ligand
Fourth step in mechanism of action of cisplatin
Cisplatin complex causes DNA double helix to kink
Means DNA can’t unwind and can’t be copied coorectly. Damage to DNA triggers apoptosis
Why does cisplatin have side effects
It binds to DNA in normal cells as well as cancer wells
What do patients having chemotherapy also experience
- hair loss
- immune suppression
- anaemia
How can the side effects of chemotherapy be reduced
By using the lowest possible dose of cisplatin and by targeting delivery of the drug directly to the cancer cells in
