Polymers and Life Flashcards
What is the formula for a carboxylic acid?
R-COOH
What is the name of the carboxylic acid for ethane?
ethanoic acid
What is the ending of the name when two carboxylic acid groups are present?
-dioic acid
How are phenols with additional groups named?
The position of the OH is the first position and the position of the group is numbered accordingly.
e.g. 2-methylphenol has a methyl group on the carbon next to the alcohol group
What is the suffix of the name of a ketone?
-one
What is the suffix of the name of a aldehyde?
-al
Where is an aldehyde found on the carbon chain?
Always at the end
How do carboxylic acids react with carbonates?
They react to form carbon dioxide and water
CO3^2- (aq) + 2H+ (aq) ==> CO2(g) + H2O(l)
What types of bases can phenols react with?
Phenols can only react with Strong Bases
Which can react with metals to form salts?
a) Carboxilic acids
b) Phenols
c) Alcohols
They all can
How can esters be formed? and what type of reaction is this?
With an alcohol and a carboxylic acid
This is a condensation reaction and is also called esterification
What is a condensation reaction?
It is the joining of two molecules together to form a larger molecule and a small molecule like water
How can the position of an equilibrium reaction between an alcohol and a carboxylic acid to make an ester be changed?
Excess alcohol can be added or the water can be distilled off
How are esters named?
They consist of to parts, the part before the oxygen in the carbon chain and the bit after.
The first part is the part with the O and the second part is the part with the double bond O
CH3CH2O-C(O)CH3
This is ethyl ethanoate
What is another way that polymers can form other than additionally?
With a condensation reaction
Describe a condensation polymerisation
This is when two monomers each with two functional groups react to form a polymer and something else.
e.g. Ethan-1,2-diol + ethan-1,2-dicarboxylic acid
Can esters be made from phenols? If so, how?
Yes but they need a stronger reagent
What is the result from the condensation polymerisation of HO-CH2CH2CH2-OH and HOOC-CH2CH2CH2CH2-COOH
-O-CH2CH2CH2-OOC-CH2CH2CH2CH2-CO- + 2H2O
What is the product of the condensation polymerisation of Propan-1,3-diol and Decan-1,10-dioic acid
-O-(CH2)3-OOC-(CH2)8-CO- + 2H2O
What is an amine?
It is a molecule with the functional group -NH2
How are amines protonated? why? and what does this make an amine?
They become R-NH3 because the lone pair on the nitrogen attracts a H+ ion
It makes an amine a form of base
How are amines soluble in water?
Because the lone pair on the nitrogen can form a hydrogen bond with the water
What is formed in the reaction:
CH3NH2 + H2O ==>
CH3NH2 + H2O ==> CH3NH3+ + OH-
What type of bond is formed between the H+ ion and the NH2 when NH2 is protonated?
Dative covalent
What is the general PH of amine solutions? and why?
They are alkali because an -OH ion is produced
What is a primary amide?
They have the formula: R-C(O)NH2
They are a derivative of carboxylic acids where the -OH is replaced with -NH2
How is a primary amide made? and why are carboxylic acids not used?
Carboxylic acids cant be used because they dont react with ammonia.
Acyl chlorides are used instead
H3C-C(O)Cl + NH3 ==> CH3C(O)NH2 + HCl
What is a secondary amide?
It is similar to a primary amide except one of a hydrogens connected to the nitrogen is replaced with an R group
e.g. R-C(O)N(H)R
How are secondary amides made?
They are made by reacting an acyl chloride with a primary amide
What is a poly amide? and what type of reaction is makes them?
It is like a polymer where a diamine and a dicarboxylic/diacyl chloride acid are joined together to make a polyamide
It is a type of condensation reaction
How are nylons named?
They are named based off the number of carbons in the amine part and the number of carbons in the acyl chloride / carboxylic acid part. The amine part is numbered first.
e.g. Nylon 4,6 is NH(CH2)4NHCO(CH2)4CO
What is a Nylon?
It a polyamide
What is the suffix of an acyl chloride?
-oyl
What is an acyl chlorde?
It is a relative form of a carboxylic acid. Instead of an OH there is a Cl
R-COCl
How do acyl chlorides react with primary amines?
They from secondary amides
How do acyl chlorides react with alcohols? What happens in the reaction:
C2H5COCl + CH3OH ==>
They form esters
C2H5COCl + CH3OH ==> C2H5COOCH3 + HCl
How are esters hydrolysed in a neutral solution? what is made?
A carboxylic acid and an alcohol is made. It is a reversible reaction with an equilibrium.
C2H5COOCH3 + H2O <=> C2H5COOH + CH3OH
What happens when an ester is hydrolysed in an alkaline solution?
It does not react with water instead it reacts with OH- and forms an alcohol and a deprotonated carboxylic acid COO-
C2H5COOCH3 + OH- <=> C2H5COO- + CH3OH
What is needed for the hydrolysis of amides?
An acid or alkali catalyst
What happens in the acid hydrolysis of a primary amide?
A carboxylic acid and a ammonia molecule is produced but then the ammonia gets protonated to become NH4+
CH3CONH2 + H2O ==> CH3COOH + NH3 ==> CH3COOH + NH4+
What happens in the alkali hydrolysis of a primary amide?
A Carboxylic acid and ammonia molecule are produced but then the carboxylic acid gets deprotonated to become COO-
CH3CONH2 + H2O ==> CH3COOH + NH3 ==> CH3COO-
+ NH3+
What is an amino acid?
It contains at least one amino group and one carboxylic acid group.
NH2CH(R)COOH
What happens when an amino acid reacts with an acid and an alkali?
They from salts in both cases. They take the properties of both the amine and the carboxylic acid
What is a zwitterion?
This is when the amino acid reacts with itself and causes the amine side to become protonated and the carboxylic side to be deprotonated. The H+ ion moves from the carboxylic acid to the ammonia side.
NH2CH(R)COOH ==> NH3+CH(R)COO-
When are amino acids zwitter ions?
Most of the time when they are in a aqueous solution
What is the PH of an amino acid in aquis solution?
They are naturally neutral
What happens if acid is added to an amino acid?
Both the amine and the carboxylic groups of the acid are protonated. e.g. NH3+CH(R)COOH
What happens if alkali is added to the amino acid?
The amine gets deprotonated so both the amine and carboxylic acid groups are deprotonated. e.g. NH2CH(R)COO-
What is an optical isomer?
It is a form of stereoisomerism where there are different ways that you can arrange 4 different groups around a carbon.
What happens in the alkali hydrolysis of a primary amide?
A Carboxylic acid and ammonia molecule are produced but then the carboxylic acid gets deprotonated to become COO-
CH3CONH2 + H2O ==> CH3COOH + NH3 ==> CH3COO-
+ NH3+
What is an amino acid?
It contains at least one amino group and one carboxylic acid group.
NH2CH(R)COOH
What happens when an amino acid reacts with an acid and an alkali?
They from salts in both cases. They take the properties of both the amine and the carboxylic acid
What is a zwitterion?
This is when the amino acid reacts with itself and causes the amine side to become protonated and the carboxylic side to be deprotonated. The H+ ion moves from the carboxylic acid to the ammonia side.
NH2CH(R)COOH ==> NH3+CH(R)COO-
When are amino acids zwitter ions?
Most of the time when they are in a aqueous solution
What is the PH of an amino acid in aquis solution?
They are naturally neutral
What happens if acid is added to an amino acid?
Both the amine and the carboxylic groups of the acid are protonated. e.g. NH3+CH(R)COOH
What happens if alkali is added to the amino acid?
The amine gets deprotonated so both the amine and carboxylic acid groups are deprotonated. e.g. NH2CH(R)COO-
What is an optical isomer?
It is a form of stereoisomerism where there are different ways that you can arrange 4 different functional groups around a carbon.
what is required to form a optical isomer?
You need to have chiral carbon.
What is a chiral carbon?
It is a carbon with 4 different functional groups around it.
How many optical isomers are there for a chiral carbon with 4 functional groups attached?
2 optical isomers
What can be said about the look of the two optical isomers?
They are mirror images
What does superimposable?
This means that the look of a molecule can not be imposed on the other optical isomer of that molecule
What is an enantiomer?
These are a pair of molecules that are optical isomers
What can be said about enantiomers of amino acids in our bodies?
They are all the same enantiomers. They are all L-enantiomers so all have the same arrangement around the chiral carbon
How do the properties differ for enantiomers?
They behave identically with test tube reactions and physical properties.
They behave differently when in the presence of other enantiomers.
How are amino acids joined together? What is the reaction? What type of a reaction is it?
They are joined with a peptide link.
They are formed when a carboxylic acid group is bonded with a amine group and then a R-CONH-R is formed.
Condensation reaction. Water is produced
What is a peptide link?
It is the link formed between two amino acids. R-CONH-R
How are linked amino acids named?
The amino acid with the free (unjoined) -NH2 group is named first. Then the other amino acid is named.
e.g. glyala: the gly group has a free NH2 and the ala has a free COOH
What is a dipeptide?
This is when two amino acid groups are joined together
What is a tripeptide? or poly peptide?
A tripeptide is when three amino acid groups are joined together
A polypeptide is when there are up to 40 amino acid groups
What is a protien?
This is a natural polymer of amino acids (monomers)
What is the difference between a polypeptide and a protein?
Nothing
How many amino acids are there (in the body)?
20
What makes proteins different?
The order of the amino acid groups
What happens during the hydrolysis of a protein?
The peptide links are hydrolysed to release different amino acids.
How can a protein be hydrolysed:
a) naturally?
b) in a lab?
a) using enzymes
b) with a concentration acid or alkali
How are proteins hydrolysed in the lab? How are the amino acids identified?
Moderately concentrated HCl is heated under reflux with the protein to hydrolyse the C-N bond.
The amino acids are identified with paper chromatography when compared with a known sample
What are the 3 different structures of proteins?
Primary
Secondary
Tertiary
What is a primary protein structure?
It is a standard single protein and the order of the amino acid residues
What is an amino acid residue?
It is just the amino acid monomers in the proteins amino acid polymer
What is a secondary protein structure?
This is the coiling of the protein into a helix shape
or
This is the formation of a sheet of protien
What is a tertiary protien structure?
This is the folding of the secondary structure
How is a secondary structure formed?
Helices or sheets are held together with hydrogen bonds between -NH groups on one peptide link and the C=O on another peptide link.
How are tertiary structures held together?
With intermolecular, ionic or covalent bonds.
Instantaneous dipole-induced dipole between non-polar side chains on amino acids
Hydrogen bonds between polar side chains or between a polar side chain and water. This makes it dissolve.
Ionic bonds form between the ionisable side chains.
How do covalent bonds form in a tertiary structure?
Covalent bonds form, for example, where -SH groups on neighbouring cysteine residues are oxidised to form -S-S- links.
What is the shape of protiens such as muscles and hair fibres?
They are long and thin.
What is the shape of proteins that control metabolism?
They are more globular
What is an enzymes?
They are highly specific catalysts. They only work with certain molecules.
What can affect an enzymes preformance? (3)
Temperature
PH
They are subject to competitive inhibition which will render it useless
What type of protein structure does an enzyme have?
A tertiary structure
Describe an active site?
This is the part of an enzyme where the catalysis takes place. The protein is structured in a certain way with functional groups in the correct position to bind with molecules and hold them in the active site.
What is a substrate?
This is the molecule that is being catalysed
What can be said about an active site and a substrate?
The active site is tailored so that the substrate can fit into the active site.
How strong are the bonds between the enzyme active site and substrate? Why?
Weak, because they have to be easily broken when the product needs to leave the active site.
What are typical bonds formed between an enzymes active site and its substrate?
Hydrogen bonds or interactions between ionic groups
How do enzymes catalyse a reaction?
They provide a route of lower activation enthalpy so less energy is required to react the molecules
What are the two possible ways that a reactions rate may be limited during a reaction between an enzyme and substrate?
- There is not enough enzymes so all the active sights are filled doing reactions
- The rate is restricted by the time that it takes for an enzyme to react a molecule
Describe the curve for a graph of substrate concentration against reaction rate.
The graph starts with a constant gradient when the substrate concentration is low and then as the concentration gets higher the graph flattens.
What is the rate determining step and the rate of a reaction as the substrate concentration is increased from zero to excess?
At the beginning the rate of reaction is directly proportional to the substrate concentration so it is a first order reaction and the rate determining step is E + S ==> ES.
At higher concentrations the rate is zero because all active sites are filled so the rate determining step is ES ==> E + P
What is a competitive inhibitor?
It is a molecule that fits into the active sight but cannot be catalysed.
They compete for the active sight and once there render the enzyme useless
What is the benefit of an enzyme over a catalyst?
They are much more specific. Catalysts will often catalyse a range of reactions
Why are enzymes so specific? What can this prevent?
They are specific because they have a precise structure that only allows certain molecules to react.
This can prevent the production of one stereo isomer that could be harmful because only the right one will fit into the active site.
How does pH affect an enzyme?
They often have an ionisable group (e.g. -COOH) that can be changed so is unable to function correctly (e.g. -COO-)
What are common groups that are often ionised?
-COOH and NH2
What graph can be draw to show the performance of an enzyme at different accidities?
pH (xaxis) against Enzyme activitiy (yaxis)
What can happen if the enzymes pH is drastically changed? What is this called?
Its shape can be destroyed because bonds within the molecule break and it is therefore it is unable to function. This is called denaturing
Why does increasing the temperature affect the enzymes preformance?
Up to the optimum temperature the activity increases because molecules have more energy to react. Past the optimum temperature, some of the dipole-dipole and hydrogen bonds will break at higher temperatures so this will cause the enzyme to denature.
What is molecular recognition?
This is the way that molecules interact in terms of intermolecular and other non-covalent bonds
What is a pharmacophore?
It is the molecule in a medicine that gives the drug its intended effect
Talk about pharmacophores (3)
- They can be modified to make the medicine more effective and reduce side effects
- They interact with receptor sites by forming weak interactions (bonds)
- They fit into receptor sites with the correct size, shape and orientation with which they can form bonds
What is the structure of DNA?
There is a deoxyribose (sugar) and phosphate backbone that alternates sugar, phosphate, sugar, phosphate etc
There are then bases that attach to the sugar.
What is a nucleotide?
It is a specific part of DNA that includes one phosphate molecule attached to a deoxyribose (sugar) molecules attached to a base.
What are the 4 bases?
A: Adenine
T: Thymine
C: Cytosine
G: Guanine
When all the parts of DNA join together, what type of reactions are these?
What functional groups are needed for this?
They are condensation reactions. They all form water.
Alcohol groups are reacted with hydrogens on molecules to form water and the joined molecules
What are base pairings?
What are the pairings?
This is the pairing up of the bases in DNA to form the double helix
A-T
G-C
What do the base pairing enable to happen? (2)
One strand of the double helix is able to produce a complete copy of itself. Both are not needed. This is useful for the copying of DNA during cell replication
One strand can make a complementary copy of another nucleic acid called mRNA during transcription. This helps make protiens
What is the process for transcription?
DNA Unzips.
An enzyme runs along the unzipped DNA and copys it to mRNA.
When the mRNA has finished copying, DNA zips back up.
mRNA then passes out of the nucleus.
How does mRNA differ from DNA? (4)
It has ribose as the sugar so it is ribonucleic acid.
It has a base U (uracil) rather than Thymine but this still has the same pairing with Adenine.
It exists as a single strand.
DNA codes for multiple proteins. mRNA codes for one.
What information does RNA carry?
It carries information about the sequence of amino acids to make a protein.
What are 3 bases called?
A codon
How many bases code for an amino acid?
3 bases
How many difference codes are possible? How many amino acids are there? What does this mean?
There are 64 possible codes. There are only 20 amino acids. Some amino acids have multiple codes and some codes are unassigned.
How does the enzyme know where to start and stop to code for a protein?
There is a start codon (AUG) and 3 stop codons (UAA, UGA, UAG)
Where does protein synthesis take place?
It takes place in ribosomes
What is the process of translation?
The ribosome moves along the mRNA and brings tRNA (an anticodon) which has an amino acid on its back, it bonds with the bases on the mRNA and this joins the amino acids together.
What is high resolution mass spectrometry? How is this useful?
This is mass spectrometry that can measure up to 4dp.
This is good because it means that molecules with similar molecular masses can be differentiated more clearly.
What is fragmentation during mass spectrometry?
This is the breaking up of the molecule during mass spectrometry giving information about the masses of all the different fragments.
What is the charge of molecules during mass spectrometry? What happens to this during fragmentation?
The molecules are given a positive charge.
During fragmentation only one of the fragments retains this charge
How is fragmentation useful?
It allows scientists to work out the structure of a molecule
What is carbon-13 NMR?
This is the analysis of molecules containing carbon 13 using nuclear magnetic resonance.
How is carbon-13 NMR zerod?
Using TMS ( Si(CH3)4 ) which produces a single peak because all the carbons are in the same environment
What is chemical shift?
This is how the signals produced from Carbon-13 NMR differ from the TMS signal?
How does carbon-13 NMR work?
Peaks on the graph produced correspond to the environment that the carbon 13 is in. The more environments, the more peaks.
What is hydrogen NMR?
This is Nuclear magnetic resonance with protons
What does the number of groups of peaks correspond to?
The number of groups of peaks corresponds to the number of environments that the hydrogens / protons are in
What does the chemical shift show in hydrogen NMR?
It shows the type of environment that the hydrogen is in
What does the area under a group of peaks correspond to?
It corresponds to the number of protons in that environment.
What does the number of splitting patterns correspond to?
It corresponds to the number of hydrogen atoms on the adjacent carbon. The number of splits corresponds to n+1 of the number of peaks on the adjacent carbon.
e.g. a triplet peak means that the carbon next to the carbon with the hydrogens that have produced the group of peaks has 2 hydrogens on it.
LEARN HOW TO DO QUESTIONS ABOUT NUCLEAR MAGNETIC RESONANCE
DO IT
What can be deduced from an Hydrogen NMR spectrum? (4)
The number of different environments that hydrogens are in.
The number of hydrogen atoms in each environment.
The nature of these environments (what other atoms are around the environment / the structure).
The number of hydrogens on the neighbouring carbons.
Summarise Hydrogen NMR
Produces multiple groups of peaks corresponding to the number of environments that hydrogens in.
The area under a group of peaks corresponds to the number of hydrogens in that environment. (The area is stated above the group of peaks.
The number of peaks in a group of peaks (the number of splits) corresponds to one plus the number of hydrogens next to the carbon with the hydrogens producing the group of peaks.
