3.3.13 Amino acids, Proteins and DNA (A2) Flashcards
what is the formula of the amine group?
H2N
what is the formula of the carboxyl group?
COOH
what does bifunctional mean?
molecule has two functional groups
how many different side chains are there? (amino acids)
20
what is a chiral carbon?
carbon with 4 different functional groups attached
how many of the 20 amino acids are chiral?
19
what are zwitterions?
molecules with both a positive and negative charge
what are the properties of zwitterions?
ionically bond due to charges
highly soluble in water
high melting points
white solids at room temp.
which end of an amino acid do we name it from?
carboxyl group end
state why each amino acid has a different Rf value when using TLC
each amino acid has different (relative) affinity/attraction to/solubility in
stationary and mobile phases
how can the amino acids be made visible after a TLC experiment?
UV light/lamp
which two bases in DNA form 3 hydrogen bonds between them?
cytosine and guanine
which bases in DNA form 2 hydrogen bonds between them?
adenine and thymine
what is the functional group of an amide?
RCONR’R’’
R - C - N - R’
O R’’
what is the functional group of an amine?
nitrogen atom with a lone pair
Suggest a suitable reagent for the hydrolysis of a protein (in TLC)
Conc HCl
what do amino acids react together to form?
peptides
what type of reaction happens between two amino acids?
condensation reaction
what is released in a condensation reaction?
molecule of water
what is a peptide bond?
secondary amide group
what is a peptide bond also called?
amide bond
what is a polypeptide?
a polymer of up to 50 amino acid residues
what is a protein?
a polymer of more than 45 amino acid residues
what is an amino acid residue?
what’s left after H2O is lost
how can a peptide bond / amide bond be broken?
heating with moderately concentrated acid or alkali
in living organisms how are proteins hydrolysed?
enzymes
what amount of bonds gives nitrogen a single positive charge?
4
why does nitrogen have a positive charge when it has 4 bonds attached?
forms a dative / coordinate bond
how is the alpha helix structure held together?
hydrogen bonds
what do hydrogen bonds form between in amino acid secondary structure?
d+ hydrogen in the N-H bond
the oxygen lone pair in the C=O bond in another amino acid residue
what are not included in hydrogen bonding in amino acids?
the R groups
are hydrogen bonds amino acid specific? why?
no
R groups not involved in H bonds
what level of protein structure is amino acid specific?
tertiary
what do ionic bonds form between in tertiary structure?
R groups which can be ionised
what do disulphide bridges (covalent bonds) form between in tertiary structure?
cysteine side chains
what is the process of disulfide bridges forming between cysteine side chains called?
oxidation ( loss of H2 )
are the hydrogen bonds involved in protein tertiary structure amino acid specific? why?
yes
occur between R groups containing O/N
what happens when an amino acid is put in alkaline solution?
the hydrogen ion is removed from the -NH3+ group
no longer a zwitterion
only has a negative charge on the COO
what happens when an amino acid is put in an acidic solution?
the COO- part of the zwitterion picks up a hydrogen ion.
no longer a zwitterion
only has a positive charge on the NH3
what method can we use to work out which amino acids are present once we have hydrolysed the peptide?
chromatography
separating compounds in a soluble mixture (all soluble)
what is a technique used to determine the secondary and tertiary structure of a protein?
x ray diffraction
what are the steps in using TLC?
- Get the TLC plate but only handle on the sides
- Using a pencil draw the base line around 1.5cm from the bottom of the plate
- Put a dot of your mixture in the middle of the baseline
- fill beaker with 1cm cubed of solvent
- put the TLC plate into the beaker and use watch glass as a lid
6.Run the chromatogram until solvent reaches near the top - Remove from beaker and mark solvent front
- leave to dry in a fumehood
why do we only handle TLC plates from the side?
to not contaminate with the proteins from our hand
why do we leave TLC chromatograms in a fumehood to dry?
solvents can be toxic
why do we use a lid for TLC?
prevent evaporation of the solvent
what is a TLC plate?
glass plate covered in a thin layer of silicon dioxide
how can we visualise the amino acids after TLC?
UV light
ninhydrin - purple stain
name an example of a protein.
enzymes such as
DNA helicase
DNA polymerase
amylase
how many reactions does one enzyme catalyse?
one
what are globular proteins?
proteins that have a compact spherical shape
what is the main property of globular proteins?
soluble in water
where does the reaction take place in an enzyme?
active site
how does the substrate bind to the active site?
intermolecular forces
what do the intermolecular forces form between in enzymes and substrates?
R groups in the enzyme’s active site and R groups of the amino acids in the substrate
what do the intermolecular forces do when an enzyme binds to the substrate?
promote the movement of electrons within the substrate
lover the Ea of the reaction
can enzymes tell the difference between E/Z isomers?
yes
how can enzymes be stopped in their reaction?
denaturing
blocking their active site
what do nucleotides contain?
deoxyribose sugar (5C)
phosphate group
nitrogen base
why is the sugar called deoxyribose?
no oxygen bound to carbon number 2
why are the nitrogenous bases basic?
they have nitrogen atom which can accept a proton
what reaction is used to create nucleotides?
condensation reaction
how many molecules of water are released in the condensation of nucleotides?
2 per nucleotide
how many condensation reactions happen in the creation of one nucleotide?
2
what direction do DNA strands run to each other?
anti parallel
what does the 2 ring base hydrogen bond to?
a 1 ring base
what does the 2 ring base binding to a 1 ring base ensure?
the DNA structure is straight and uniform
why is urea effective at separating the complimentary strands in DNA?
the amino groups are able to substitute for the H bonds in the double helix
where is the nitrogenous base located on a nucleotide?
on the first carbon
where is the phosphate group located on a nucleotide?
on the third carbon
why is cisplatin called so?
two different substituent groups next to each other around the transition metal
what is cisplatin?
anti cancer drug
what does cisplatin do?
binds to DNA
distorts the shape
prevents replication
prevents cell division
where does cisplatin bind to DNA?
nitrogen in two adjacent guanine bases
which is the better ligand? water or nitrogen?
nitrogen
what are the side effects of cisplatin?
cannot discriminate between healthy and cancerous cells
hair follicles also effected because they replicate quickly - much like cancer cells
