Polymers and Life

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  • Created by: LBCW0502
  • Created on: 26-10-16 16:21
What is the functional group in carboxylic acids?
Carboxyl group (-COOH)
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What is the general formula when the remainder of the carboxylic acid molecule is an alkyl group?
R-COOH
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Name the first three alkanes
Methane, ethane and propane
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Name the first three carboxylic acids
Methanoic acid, ethanoic acid and propanoic acid
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Which ending is used when two carboxyl groups are present?
-dioic
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What is benzoic acid also known as?
Benzenecarboxylic acid (a carboxyl group attached to a benzene ring)
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What is a compound called when an -OH group is attached to an arene ring?
Phenol (group)
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Which type of compounds can react with strong bases to form salts?
Carboxylic acids and phenols (alcohols do not react in this way)
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What is produced when a carboxylic acid reacts with a carbonate?
A carboxylate salt, carbon dioxide and water is produced
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What happens when phenols or alcohols react with carbonates?
No reaction (do not have enough concentration of hydrogen ions to react)
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Which type of compounds can form salts with metals?
Carboxylic acids, phenols and alcohols (the reaction is redox rather than acid-base)
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How are esters formed?
An alcohol reacts with a carboxylic acid. The reagents are heated under reflux with a small amount of concentrated sulfuric acid/hydrochloric acid as a catalyst
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What is a condensation reaction?
Two molecules react together to form a larger molecule with the elimination of a small molecule (such as water)
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What is esterification?
An ester link is formed by the condensation reaction of the hydroxyl group in the alcohol and the carboxyl group in the acid
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How can the yield of ester be improved?
Excess alcohol is added or water can be distilled off as it is formed (reaction is reversible and comes to an equilibrium). Sulfuric acid catalyst absorbs some water formed, which would move the equilibrium position to the right
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What is ester hydrolysis?
The reverse reaction of the esterification process
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Describe the features and uses of esters
Strong, sweet smells, used in food flavourings and perfumes, used as solvents e.g. glue (organic compounds dissolve readily in esters)
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What are condensation polymers?
Polymers formed from condensation reactions (addition reactions)
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Describe condensation polymerisation
Monomers must have at least two suitable functional groups per molecule from a condensation polymer to be produced. Monomers react together to give a longer chain and a small stable molecule (e.g. water or HCl)
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What is the difference between addition polymerisation and a condensation reaction?
Addition polymerisation produces one product (polymer). Condensation reaction produces a polymer and another small molecule
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How do you make esters from phenols?
The -OH group in phenol is less reactive to esterification than the -OH of ethanol, so it needs a more vigorous reagent to esterify it e.g. an acid anhydride
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What are primary amines?
Amines with one alkyl group
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What are diamines?
Found on condensation polymers (two amino groups attached)
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Volatile amines resemble which compound?
Ammonia (strong smells)
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Which structure in amines is the reason for the properties in amines?
Lone pair of electrons on the nitrogen atom (responsible for amines being soluble in water and acting as bases)
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Why are small alkyl groups soluble in water?
There is a strong attraction between amine molecules and water so amines can form hydrogen bonds. Formation of a solution is more energetically feasible for smaller-chain amines compared to larger-chain amines
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Why are large alkyl groups less soluble in water?
They are unable to break the hydrogen bonds between the water molecules. The enthalpy change to break these hydrogen bonds is greater than the enthalpy change in the formation of new intermolecular forces between the alkyl group and water
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What type of bonding can the lone pair on the nitrogen atom take part in?
Dative covalent bonding (amine acts as a H+ acceptor and is a base)
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Which ions can amines react with and goes to completion (solution loses its strong amine smell)
H3O+ ions (Hydronium ions)
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How are primary amides produced?
Reacting acyl chlorides with ammonia to produce primary amide and hydrochloric acid (example of a condensation reaction)
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What is the difference between a primary amide and a secondary amide?
A primary amide has one variable group whereas a secondary amide has two variable groups
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Which compounds are used to make a polyamide?
Diamines and dicarboxylic acids because they have reactive groups in two places in their molecules (a polymer chain can be made in which monomer units are linked by amide groups)
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Why are polymers classified as polyamides?
The group linking the monomer groups together is a secondary amide group (polyamides are also known as nylons)
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Which compound (except carboxylic acids and acid anhydrides) can react with alcohols to form esters?
Acyl chlorides
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Describe the two ways esters can be hydrolysed
Water and an ester react (sulfuric acid used as a catalyst and excess water) to produce a carboxylic acid and an alcohol. Another way is to react an ester with an alkali (e.g NaOH) to produce a carboxylate salt
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Describe acid hydrolysis
An amide is heated with moderately concentrated sulfuric or hydrochloric acid
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Which bond is broken down in during the hydrolysis of amides?
C-N bond (hydrolysis reaction/reaction with water can be catalysed with an acid or alkali)
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What is produced during the acid hydrolysis of a primary amide?
A carboxylic acid and ammonium ions
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What is produced during the acid hydrolysis of a secondary amide?
A carboxylic acid and an amine salt
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Describe alkaline hydrolysis
The amide is heated with a moderately concentrated alkali (e.g. NaOH)
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What is produced during the alkaline hydrolysis of a secondary amide?
A carboxylate ion and an amine
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Describe the general structure of an amino acid
A molecule containing an amino group, a carboxylic acid group, an R-group (variable group) and a hydrogen atom
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What is an alpha carbon?
The first carbon atom attached to the -COOH group
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What are bifunctional compounds?
Compounds with two functional groups (sometimes the properties of these compounds are the same as the properties of the two separate functional groups)
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Amino acids show the properties of which functional groups?
Amines and carboxylic acids
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What are zwitterions?
A molecule containing both the negatively charged groups and positive charged groups (the proton-donating -COOH and proton-accepting -NH2 groups can react with one another)
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Describe the solubility of amino acids in water
Very soluble in water and are effectively ionic (neutral in solution unless there is an extra -COOH or -NH2 group)
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What is the effect of adding small quantities of acid or alkali to an amino acid solution?
Causes little change to pH because the zwitterions buffer the effect of the addition of small quantities of acid or alkali
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What is the ionic form of an amino acid dissolved in an acidic solution?
H3N+ - CHR - COOH
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What is the ionic form of an amino acid dissolved in a neutral solution?
H3N+ - CHR - COO(-)
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What is the ionic form of an amino acid dissolved in alkaline solution?
H2N-CHR - COO(-)
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What are buffer solutions?
Solutions that can withstand the addition of small amounts of acid or alkali
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Which type of isomerism do amino acids present?
Optical isomerism (a type of stereoisomerism)
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How many forms does alanine have?
2 forms (mirror images are non-superimposable)
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How many forms does glycine have?
1 form (mirror images are superimposable)
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How can alanine become superimposable?
By breaking the C-NH2 and C-COOH bonds and swap the groups round
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What are optical isomers also known as?
Enantiomers
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What are chiral molecules?
Molecules that are non-superimposable on their mirror images. A carbon atom is bonded to four different groups which is called a chiral centre
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What are L-enantiomers?
The proteins in our bodies are built up from only one enantiomer of each amino acid (called L-enantiomers). They have the same arrangement of the four groups around the central carbon atom
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Describe the properties of enantiomers
Behave identically in ordinary test-tube chemical reactions. Most physical properties e.g. melting point, density and solubility are also the same
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How does the presence of chiral molecules affect enantiomers?
Some properties of the molecule such as smell and taste change
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Which two functional groups react to form a secondary amide group (-CONH-)?
An -NH2 group and the -COOH group in a carboxylic acid
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Why is the dipeptide formed from glycine and alanine abbreviated to GlyAla?
The amino acid with the free -NH2 group is written first
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Up to how many amino acid residues can be in a polypeptide?
40 (residue - used for an alpha amino acid which has lost the elements of water in forming a peptide or protein)
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Describe a method to break down proteins in a laboratory
Boiling proteins with moderately concentrated hydrochloric acid to hydrolyse the amide C-N bonds (in living organisms, the hydrolysis of proteins is catalysed by enzymes rather than acid or alkali)
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Which technique can be used to identify individual amino acids present in a peptide?
Paper chromatography - The peptide is hydrolysed under reflux and the product is compared to known samples of pure amino acids using chromatography
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What is the primary structure of a protein?
A specific sequence of amino acids (the order of the amino acid residues)
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What is the secondary structure of a protein?
The coiling of parts of the chain into a helix or the formation of a region of sheet (beta pleated sheet)
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Which bonds are present in the secondary structure?
Hydrogen bonds between the -NH groups on one peptide link and -C=O groups on another peptide link
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What type of bonds are present in a tertiary structure? (3)
Intermolecular bonds, ionic bonds and covalent bonds
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Which bonds form between non-polar side chains on amino acids?
Instantaneous dipole - induced dipole bonds (centre of protein molecules contain amino acids so that non-polar groups do not interfere with the hydrogen bonding surrounding water molecules)
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Explain why some amino acids can dissolve in water
Hydrogen bonds form between polar side chains. If amino acids with polar side chains are situated on the outside of proteins, then hydrogen bonds can also form to water molecules surrounding the protein
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Where do ionic bonds form in a tertiary structure?
Between ionisable side chains
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Give an example of where covalent bonds would form in a tertiary structure?
E.g. -SH groups on cysteine residues (oxidised to form -S-S- links)
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Give examples of structural proteins
Muscles and hair (fibrous - long and thin). They consist of mainly helices
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Give examples of proteins that control metabolism
Enzymes and hormones (e.g. insulin) are globular and have both sheets and helices
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Describe general characteristics of enzymes
Catalysts, highly specific, sensitive to pH, sensitive to temperature, subject to competitive inhibition
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What is the active site of an enzyme?
Enzymes (with a tertiary structure) have a cleft formed by the way the protein chain folds. Within the cleft are chemical groups (e.g. R-groups) that bind molecules and react with them (catalysis takes place)
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Describe enzyme catalysis
Shape of active site is complementary to substrate. Some R-groups on amino acid residues bind to substrate. Weak bonds binding substrate (can be reversed). Bonds are H/ionic. Bonds in substrate weaken/change shape. Products released
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What is a catalyst?
E.g. enzymes, which provide an alternative route with a lower activation energy (reactions take place more quickly)
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Do enzymes have a large relative molecular mass?
Yes (so they are present in small amounts and their molar concentrations are very low)
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What happens when there is an equal amount of substrate and enzymes?
All enzyme active sites will have substrate molecules bound to them (enzyme-substrate complex, ES)
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What happens when there is a higher concentration of substrate and a lower concentration of enzymes?
No more enzyme-substrate complexes can be formed and the rate at which substrate molecules pass through the reaction pathway and change into products remains constant (reaction rate doesn't depend on substrate concentration (0 order wrt substrate)
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What happens when the substrate concentration is lower than the enzyme concentration?
Not all enzyme active sites will have a substrate molecule bound to them. Overall reaction rate will depend on how frequently enzymes counter substrates (depends on substrate concentration) - first order wrt substrate
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What are competitive inhibitors?
Molecules that fit on the active site but cannot be catalysed. They compete with the substrate molecules for active sites but once there, do not react further
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Explain specificity
Enzymes show more specificity in which substrate they will catalyse. They have a precise tertiary structure which matches to the structure of the substrate (example of molecular recognition - active site is usually 3D so one stereoisomer will fit)
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Why are enzymes sensitive to pH?
The ionisation of -COOH and -NH2 groups is changes by small differences in pH (changes shape of active site). Enzymes have an optimum pH
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What happens when an enzyme is denatured?
Enzyme will become inactive due to its shape being destroyed. Enzyme loses side chains and active site is destroyed
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What happens to enzymes when the temperature is increased (up to 40 degrees Celsius)?
Activity of the enzyme increases as more molecules have enough energy to collide with combined energy being greater than Ea
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What happens to enzymes when the temperature is too high (above 40 degrees Celsius)?
Some bonds holding tertiary structure together are weak dipole-dipole and hydrogen bonds. These can be broken easily (high temperature causes them to vibrate more vigorously/weaken/break). Enzyme denatures and activity falls.
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What is the optimum temperature for most human enzymes?
35-40 degrees Celsius (body temperature - 37 degrees Celsius)
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What is molecular recognition?
Ways in which molecules interact in terms of intermolecular and other non-covalent bonds
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What is the pharmacophore of a medicine?
The part of its molecule that gives that medicine its particular pharmacological effect
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Describe features of pharmacophores
Can be modified by changing functional groups (reduce side effects), interact with receptor sites to form various bonds and can fit into receptor sites with the correct size etc. to form correct weak bonds
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Describe the components in a nucleotide
A phosphate group, a deoxyribose sugar and an organic nitrogenous base
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What are the four organic nitrogenous bases?
Adenine, thymine, cytosine and guanine
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Describe the components of a DNA strand
Deoxyribose molecules, phosphate groups, organic nitrogenous bases and an alternative sugar-phosphate backbone
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What is the name of the bond joining the deoxyribose sugar of one nucleotide to a phosphate groups on the adjacent nucleotide?
Phosphodiester bond
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Describe the complementary base pairing
Adenine bonds to thymine (2 hydrogen bonds, cytosine binds with guanine (3 hydrogen bonds)
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What are the two things base pairing in DNA enables chemists to do?
Synthesise a complementary copy of a strand (DNA replication) and one strand can make a complementary copy of another nucleic acid (mRNA)
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Describe the process of transcription
Enzymes are used to unzip a section of DNA relating to one protein (strand used as a template). RNA nucleotides join using enzymes to form mRNA. Double helix reforms. mRNA passes out of cell nucleus
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How does mRNA differ from DNA?
Has a ribose sugar (not deoxyribose) so it is called ribonucleic acid (not deoxyribonucleic acid). Has uracil as a base (not thymine) which joins to adenine. Exists as a single strand (does not pair up)
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What is a triplet code?
Three bases code for each amino acid (codon)
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Why is the code said to be degenerate?
There is more than one code for each amino acid (there are 64 arrangements of three bases and only 20 amino acids)
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What is the start code?
AUG
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What are the three stop codes?
UAA, UGA, UAG
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Where does protein synthesis take place within a cell?
Ribosomes
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What happens during protein synthesis?
Amino acids join together in a primary structure. mRNA provides a template. Amino acids are taken to mRNA in ribosomes and join to small lengths of RNA (tRNA)
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Why is the code on the tRNA that fits to the mRNA called an anti-codon?
It is the complementary sequence of bases to the codon
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What is the difference between DNA and RNA in terms of production of molecules?
Each DNA molecule contains information for the production of many difference mRNA molecules but each mRNA molecule is a set of instructions for just one protein
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What is a gene?
A DNA segment responsible for a particular protein
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Modern mass spectrometers exist can measure the relative molecular masses of ions to how many decimal places?
Four decimal places
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Describe the method of fragmentration
MS can be used to find peaks. Very stable cations are produced. This enables you to make use of mass differences between peaks
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What is chemical shift?
The extent to which a signal differs from TMS (features of nuclear magnetic resonance - NMR)
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What two things can 13C NMR be used for?
Work out the number of carbon atoms that have different environments in a molecule. Work out the groups to which these carbon atoms are attached
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What can be deduced from 1H NMR spectrum?
The number of different H environments in the molecule, the number of H atoms in each environment, the nature of these environments and the number of H atoms attached to neighbouring carbon atoms
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What evidence can be deduced from a low resolution MS?
Mr of the M+ ion and the fragments which can be used to suggest structure
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What evidence can be deduced from a high resolution MS?
Molecular formula from the M+ ions
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What evidence can be deduced from an IR?
Certain functional groups
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Card 2

Front

What is the general formula when the remainder of the carboxylic acid molecule is an alkyl group?

Back

R-COOH

Card 3

Front

Name the first three alkanes

Back

Preview of the front of card 3

Card 4

Front

Name the first three carboxylic acids

Back

Preview of the front of card 4

Card 5

Front

Which ending is used when two carboxyl groups are present?

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