unit 6 section 4 amino acids, proteins and DNA Flashcards
what two functional groups does an amino acid have
it has a carboxyl group (COOH) and an amine group (NH2)
are amino acids amphoteric and what does that mean
yes amino acids are amphoteric, this means that they have the properties of an acid and a base
how can an amino acid act as an acid
they can act as an acid because the carboxyl group is acidic - it can donate an proton
COOH = COO^- + H +
how can an amino acid act as a base
they can act as a base because the amino group ( amine group ) is basic - it can except a proton
NH2 + H^+ = NH3^+
how do you name an amino acid systematically
- find the longest chain that has the carboxylic acid group and write its name
- number the carbons in the chain starting with the carbon in the carboxylic acid group as number 1
- write down the position of any NH2 groups and use the word amino to show that
-write down the name of any other functional groups and say what carbon they are on
what is a zwitterions
amino acids can exist as zwitterions. a zwitterions is an ion that is dipolar - it has both positive and negative charge in different parts of the molecule
where can zwitterions exist and what is an isoelectric point
zwitterions only exist near an amino acids isoelectric point. the isoelectric point is the PH where the overall charge of the amino acid is zero.
when does an amino acid become a zwitterion
an amino acid becomes a zwitterion when its amino group is protonated into NH3^+ and its COOH group is deprotonated into COO^-
what happens to the amino acid when the conditions is more acidic ( low ph ) than the isoelectric point
in conditions more acidic than the isoelectric point, the NH2 group is likely to be protonated but the COOH group is unchanged - so the amino acid will carry positive charge but not a negative charge.
what happens to an amino acid when the conditions is more basic ( high ph ) than the isoelectric point
in conditions more basic than the isoelectric point, the COOH group is likely to loose a proton but the NH2 group will be unchanged - so the amino acid will carry a negative charge but not a positive charge.
in what conditions is a zwitterions formed
only at or near when the isoelectric point are both the carboxylic group and the amino group are likely to be ionised - forming a zwitterion
how do you separate mixtures of amino acids and why does that happen
through thin layer chromatography (TLC)
- this is because the amino acids have different R groups, they will have different solubilities in the same solvent
how do you make an amino acid visible (coloured)
-this can be done by spraying ninhydrin on the plate which will make the amino acid turn purple.
- another way is by using a special plate which has fluorescent dye added to it. the dye glows in UV light. when there are spots of chemicals on the plate, they cover the fluorescent dye - so the spots appear dark.
how do you identify amino acids
this is done by using the chromatogram to calculate the Rf value
what is the formula for the Rf value
Rf = x/y = distance travelled by spot/ distance travelled by solvent
what is a protein and what is it made of
proteins are condensation polymers of amino acids- they are made of up lots of amino acids joined together by peptide links .
explain how two amino acids join together to form a dipeptide
this is done by removing a molecule of water between the two amino acids. and OH from on of the COOH groups will be remove and from the other amino acid a H will be removed from the NH2 group
what happens if two different amino acids combine together
then two different dipeptides will form because the amino acid can join either way round.
how do you break up a protein into its amino acids
you use hydrolysis
what is the method of hydrolysing proteins
this can be done by adding 6 mol dm^-3 of hydrochloric acid, and then heat the mixture under reflux for 24 hours
how do you describe the structure of proteins
proteins are big. so they are describe in four levels, primary, secondary, tertiary and quaternary.
what is the primary structure of an protein
the primary structure is the sequence of amino acids in a long chain that makes up the protein.
what is the secondary structure of a protein
the peptide links can form hydrogen bonds with each other, meaning the chain isnt a straight line. the shape of the chain is called the secondary structure.
what are the common structures for a secondary structure of a protein
the most common secondary structure is spiral called α-helix. another common secondary structure a β-pleated sheet. this is a thin layer of protein folded like a concertina
what is the tertiary structure of a protein
extra bonds can form between different parts of the polypeptide chain, which gives the protein a 3 dimensional shape.
what causes the protein to fold or twist in a secondary or tertiary structure
the secondary and tertiary structure of proteins are formed by intermolecular forces causing the amino acid chain to fold or twist
what two main types of bond hold the shape of a protein
the two main types are hydrogen bonds and disulfide bonds
explain where hydrogen bonds exist within an protein and how they are formed
hydrogen bonding only exists between polar groups such as -OH and NH2. these groups contain electronegative atoms that induce a partial positive charge on the hydrogen atom. the hydrogen is then attracted to lone pairs of electrons on adjacent polar groups and a hydrogen bond is formed
explain when disulfide bonding occurs within a protein and how it occurs
disulfide bonding occurs between residues of the amino acid cysteine. cysteine contains a thiol group (SH) and this thiol group can loose its H atom and join together to form a disulfide -s-s- bond with another thiol group. these disulfide bonds link together different parts of the protein chain, and to help stabalise the tertiary structure.
what is a residue
it is an amino acid that is part of a protein
what factors can affect hydrogen bonding and the formation of disulfide bonds
factors such as temperature and PH affect hydrogen bonding and the formation of disulfide bonds and so can change the shape of the protein.
what do enzymes do
the speed up chemical reactions by acting as a biological catalyst. they catalyse every metabolic reaction in the bodies of living organisms
what molecules do enzymes act upon
substrates
what is the active site of an enzyme
it is an area of the enzyme that the substrate fits into so that is can interact with the enzyme.
the active site is three dimensional- it is part of the tertiary structure of a protein enzyme
what is the lock and key model
Enzymes are specific and only work with certain substrates. the lock and key models states that, for an enzyme to work, the substrate must fit into the active site
” the active site of enzymes are sterospecific “ what does sterospecific mean
it means that they only work with one enantiomer of a substrate
what is an inhibitor
it is a molecule that has a similar shape to the substrate. they compete with the substrate to bond with the active site of the enzyme however it does not cause a reaction and it stays in the active site and blocks it
what factors affect the inhibitation
the concentration of inhibitors to substrate and the strength of the bond that the inhibitor has to the active site.
give an example of how an inhibitors can be used as a drug
some antibiotics work by blocking the active site of enzymes of bacteria that helps to make the their cell walls. this causes the cell wall to weaken over time, so the bacteria eventurally burst.
explain how an inbitor can be used as a drug
some drugs are inhibitors that block the active site of enzymes that stops them from working
how are the inbitors that are drugs found
often new inhibitors are found by trial and error. scientist will carry out experiments using lots of compounds to see if they work as an inhibitor for a particular enzyme. they then adapt the one that works to improve them. this takes a long time, however this can be sped up by using a computer to model the active site of the enzyme.
what does DNA stand for and what does it contain
deoxyribonucleic acid, it contains all the genetic information of an organism.
what is DNA made of
they are made up of lots of monomers called nucleotides
what are the main three components that make up a nucleotide
a phospate group, the pentose sugar 2-deoxyribose, and a base
what are the 4 types of bases that can be in a nucleotide
one of either adenine (A), cytosine (C) , guanine (G), thymine (T)
what is the sturcture of a nucleotide
a phosphate ion bonded to a pentose sugar bonded to a base
what is a polynucleotide
it is a chain of nucleotides
how does a polynucleotide occur
covalent bonds form between the phosphate groups of one nucleotide and the sugar of another- this makes what is called the sugar-phosphate backbone of the chain
how is the sugar backbone of phosphate formed
it is formed by condensation polymerisation- the molecule fo water is lost and the phosphodiester bond is formed
what is the structure of DNA
DNA is made up of two polynucleotides stands that spiral together to form a double helix structure.
what bonds hold bases together
strong hydrogen bonds
what are the base pairs
A-T ( adenine - thymine )
C-G ( cytosine - guanine )
why do the bases only pair to a certain other base
this is because the bases are complimentary, the hydrogen’s form hydrogen bonds with anything that is highly electronegative ( N O F )
what is cisplatin
it is a complex of platinum(II) with two chloride ion ligands and two ammonia ligands in a square planar structure
what is the difference between cisplatin and transplatin
cis - functional groups are next to each other
trans - functional groups are opposite each other
how is cisplatin and anticancer drug
the cisplatin stops the tumor cells from reproducing by stopping the DNA strands from unwinding by causing a kink.
what are the adverse affects of cisplatin
cisplatin can also bind to DNA in normal cells. this is a problem for any healthy cell that reproduces regularly as it can stop them from reproducing. this can lead to hair loss and suppress the immune system
how can the adverse affects of cisplatin be reduced
- give to patient in low dosages
- target the tumor cells directly, use a method to transport it directly to the tumor cells.
