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Chemistry (A2) > Amino Acids > Flashcards

Amino Acids Flashcards

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1
Q

What are the two functional groups of amino acids?

A

NH2 and COOH

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2
Q

How many naturally occurring amino acids are there in a human body

A

20

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3
Q

What type of amino acids are found in the body?

What does this mean about their structure?

A

Alpha-Amino aicids

NH2 functional group is on the adjacent carbon to COOH

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4
Q

Draw a general formula for alpha amino acids

A
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5
Q

Are alpha amino acids Chiral?

A

Yes , one carbon has four different subsistent

Exception = Glycine where R = H

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6
Q

Write the equation for the first step of industrial amino acid synthesis

A

Aldehyde + Nitrile to produce an amino nitrile

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7
Q

Write an equation for the second step of industrial amino acid synthesis
And any conditions

A

Amino nitrile (in step 1) + Hydrochloric acid + Water —> Amino acids + Ammonium Chloride
Hydrolysis, use dilute HCl and under reflux

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8
Q

In what form do amino acids exist as solids?

A

Alpha amino acids as zwitterions in an ionic lattice - High melting and boiling point

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9
Q

What colours are zwitterions at room temperature

A

White solids

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10
Q

Do Zwitterions disolve in water

A

Yes, zwitterions have permanent +Ve and -Ve charges which causes electrostatic attraction between the +Ve charge and the lone pair within water molecules

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11
Q

Define a zwitterion

A

Ions which both have a permanent positive and negative charge, but are neutral overall

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12
Q

How do zwitterions occur in amino acids

A

COOH is deprontonated
NH2 is protonated
When the acid has reached its isoelectric point in ph

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13
Q

What happens to amino acids when the ph is lower then its isoelectric point

A

NH2 group is protonated

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14
Q

What happens to amino acids when it’s ph is higher then the isoelectric point

A

COOH is depotonated

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15
Q

Draw a peptide linkage

A
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16
Q

What is a dipeptide
Draw a general one for amino acids

A

Two amino acids bonded together
Under a peptide link

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17
Q

What name is given to amino acid chains up to 50 monomers

A

polypeptides

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18
Q

What name is given to chains of amino acids with more then 50

A

proteins

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19
Q

What is the process in which polypeptides are broken down into their constituent amino acids

A

Hydolysis

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20
Q

What conditions are needed for the hydrolysis oof amino acid chains

A

6moldm^-3 HCl
Reflux for 24h
110 Degrees

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21
Q

Draw the formation of a peptide link using trio generalised amino acids

A

hydrolysis

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22
Q

What is the primary structure of a protein?

A

The sequence of amino acid monomers along the peptide chain bonded by covalent bonds.

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23
Q

How is the primary structure of an amino acids represented

A

Sequence of 3 letter add revisions of amino acids

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24
Q

What is the secondary structure of a protein

A

The shape of the protein chain
Alpha Helix or Beta pleated sheet

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25
Q

What are the two options for the secondary structure of a protein

A

Alpha-helix shape or beta-pleated sheet

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26
Q

How is the secondary structure held together

A

Hydrogen bonding Between C=O and N-H on the polypeptide backbone

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27
Q

What is the tertiary shape of a protein

A

Alpha helix or beta pleated sheet is folded into a. complex 3D shape

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28
Q

How is the tertiary structure held together

A

a combination between
Hydrogen bonding
Ionic interactions between R groups
Sulphur-Sulphur bonding (disulphide bridges)
Van Der Waals

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29
Q

Why is tertiary structure important

A

The shape of the protein molecules is vital in their function

Eg active sites in enzymes

30
Q

How can amino acids. be attracted to each other

A

Hydrogen bonding
Ionic interactions between groups or side chains
Sulphur-Sulphur/ Disulphide bridges

2 S atoms are oxidised to form an S-S bond

31
Q

What is wool
How is it held together

A

Protein fibre with a secondary alpha helix structure held together by hydrogen bonds

32
Q

What does the structure and bonding in wool mean for its properties

A

wool= Protein fibre with a secondary alpha helix structure held together by hydrogen bonds

Can be stretched and elastic —> Hydrogen bonds extend and when the force is removed they return to their original shape

Wash too hot and the H bonds permanently break so the garment looses its shape

33
Q

What is a Thin layer Chromatography plate made of

A

Plastic sheet coated with silica ( SiO2) This is the stationary phase

The solvent is the mobile phase

34
Q

Amino acids have basic and acidic properties what is this quality called?

A

Amphoteric

35
Q

How would you cary out thin Layer Chromotography

A

Spot the samples onto a pencil line a few cm above the talc plate

Place this in as breaker or tank, with solvent level below the pencil line

Ensure there is a lid on the beaker to keep the inside saturated with solvent vapour

Wait until sol;vent is almost a that the top of the TLC plate

Remove from beaker and analyse

36
Q

How do you name an amino acid using IUPAC

A

1) Find longest carbon chain - carboxylic acid
2) Number carbons - 1 is the carboxyl group carbon
3) Note the carbon number where the amide groups lie
4) Use prefix amino over amide
5) Name other groups that aren’t COOH or NH2 first

37
Q

Why does TLC separate amino acids

A

Solvent carries amino acids up the TLC plate.
The rate of moment depends on the balance between the amino acids affinity for the stationary and the affinity for mobile phase

38
Q

What is the isoelectric point

A

Zwitterions only exist in an amino acid at its isoelectric point

Isoelectric point = The PH at which the average overall charge of a zwitterion is zero as there is a permanent positive charge at the amine group and a permanent negative charge at the carboxylate group

39
Q

Name 2 ways to analyse a sample of TLC chromotography

A

Amino acids are colourless

Spray on ninhydrin - Amino acids are colourless, the vapours of this substance sticks to the chemicals turing the amino acids purple

Add fluorescent dye to the stationary phase, Shine UV light, Colourless amino acids block the flow from the fluorescent dye

40
Q

How do you calculate an Rf Value

A

Distance moved by substance / Distance moved by solvent

41
Q

How do you find the primary structure of a protein

A

Reflux with 6M HCl for 24h

to break down the peptide links, separating it into its monomers

Carry out TLC to find the number and types of amino acids present

42
Q

How do you find the secondary/ tertiary structure of a protein

A

X-ray Crystallography

43
Q

What is an enzyme

A

Biological catalyst
Specialised to increase the rate of reactions of a specific reaction.
Made of amino acids

44
Q

Describe the structure of an enzyme

How does its structure helps its function

A

Globular protein with a creft in it know as the active site.
This active site is a unique shape that is designed to fit a very limited umber of substrate
Has a chiral centre

2)

active site is a unique shape that is designed to fit a very limited umber of substrate held at the perfect orientation for them to react/bind (stereospecificity) Locks and key hypothesis.

45
Q

How else do enzymes increase the rate of reaction

A

binding molecules to the active site via forming temporary bonds with intermolecular forces

This weakens the bonds int the molecules, promotes electron movement and lowers the acitvation energy

46
Q

What does the stereospecificity of an enzyme mean?

How does this effect naturally occurring molecules

A

Active sites are so selective of the shape of the substrates that can fit, it only catalyses reactions of a specific enantiomer but not the other one.

Most naturally occurring molecule have a much larger abundance of one enantiomer compared with he other due do an enzymes stereospecificity

47
Q

How does enzyme inhibition work

A

A molecule with a a very similar shape and structure to the substrate is devised

Binds to the enzyme’s active site very strongly

Blocks the active site

As substrate cannot adsorb to the active site so reaction cannot be catalysed

48
Q

What drug works via enzyme inhibition?

A

Penicillin

49
Q

What causes enzymes to Denature

A

Change in Temperature or PH

50
Q

What does DNA stand for

A

Deoxyribonucleic Acid

51
Q

What consititutes as a nucleotide

A

A phosphate ion
A Sugar (2-deoxyribose)
A Base (Adenine cytosine guanine or thymine)

52
Q

Draw the general structure for a nucleotide

A
53
Q

What forms between bases of adjacent nucleotides

A

Hydrogen bonding

54
Q

Which bases pair up between nucleotides

A

A & T
C & G

55
Q

How does DNA Polymerise?

What type of polymer chain is this

A

OH on phosphate
OH on 3rd Carbon on 2 deoxyribose react to eliminate a molecule of water.

Condensation Polymer

56
Q

What determines the properties of the DNA molecule

A

Unique order of bases

57
Q

Explain the Structure of DNA

A

2 strands of amino acids held together by hydrogen bonding between complimentary base pairs wound together in a double helix

58
Q

How is DNA Replicated exactly when Cells Divide

A

DNA Helixase unzips the chain by breaking the hydrogen bonds holding the base pairs together

Free nucleotides that are activated attach to their complimentary base pairs

The activated nucleotides bind to their complimentary bases with he aid of DNA Polymerase

Bases link together by forming the sugar phosphate backbone

59
Q

How does the body use the information stored in DNA

A

Template for arranging amino acids into specific proteins, such as enzymes or flesh

60
Q

Draw the Structure of CISplatin

A
61
Q

What is Cisplatins Function?
How does it do this? (3)

A

Anti-Cancer Drug

Bonds to strands of DNA to distort shape and prevent cell replication.

It bonds to the Nitrogen atoms on 2 adjacent Guaneines.

Nitrogen atoms replace the Chlorine ligands in a ligand substitution reaction

62
Q

What are the Cl- ligands are able to be replaced by Nitrogen on the base (Amino acids)

A

N atoms on the Guanine have lone pairs of electrons ions that can coordinately bond to the platinum

N atoms can donate electrons more readily so it replaces the chlorine ligands

63
Q

What are the Disadvanatges to cisplatin

A

Affects Healthy cells that are replicating quickly as well as the cancer cells such as hair follicles

64
Q

ph= 11.8

A

1.26 x 10^-24

65
Q
A

Enzyme has a stereo-specific active site

G-enantiomer has the correct stereochemistry and the only accepted complimentary shape

66
Q

State the meaning of the term complimentary in reference to DNA strands

A

complimentary means that the two strands must have base sequences that match

A to T and C to G

67
Q
A

Secondary

N & O are very electronegative

therefore C=O and N-H are polar bonds

These polar bonds are sufficiently polarised to form hydrogen bonding between N & H and O&H on oppposing bases

In which a lone pair of electrons on an oxygen atom is strongly attracted to a delta positive hydrogen

68
Q
A

series of nucleophilic substitution reactions

(amine + excess haloalkane = quaternary ammonium ion)

69
Q
A

Base A
Top N-H forms hydrogen bonds with lone pair O of Guanine

The lone pair of electrons on N bonds to N-H of Guanine

A Lone pair of electrons on O bonds to lower H-N of guanine

70
Q

Draw Hydrogen Bonds between each of the complimentary bases, include where the connection is to the sugar

A
71
Q
A

Hydrogen Bonds form between urea and DNA strands

Urea has 2 amino groups, that goes in-between the strands to separate them

Chemistry (A2) (15 decks)

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