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Chemistry > Unit 3: Section 8 - Amino Acids, Proteins and DNA > Flashcards

Unit 3: Section 8 - Amino Acids, Proteins and DNA Flashcards

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1
Q

What are the 2 functional groups of amino acids?

A

NH2 and COOH (amine and carboxylic acid)

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2
Q

How many naturally occuring amino acids are there in the 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

α - amino acids (alpha) it means that NH2 is always on the carbon next to COOH

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4
Q

Are α-amino acids chiral? Why?

A

Yes, one carbon has 4 different substituents - except glycerine where R = H

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5
Q

Which enantiomer do α-amino acids exist as in nature?

A

(-) enantiomer

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6
Q

How can amino acids be synthesised naturally?

A

RCHO + NH4CN -> RCH(NH2)CN via nucleophilic addition
RCH(NH2)CN + HCl + 2H2O -> RCH(NH2)COOH + NH4Cl - hydrolysis, HCl is dilute - need to reflux the reaction mixture

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7
Q

Is the product from amino acids being synthesised naturally optically active? Why?

A

No, a racemic mixture is formed as the CN- ion can attack from above or below the planar C=O bond with equal probablitity
An equal amount of each enantiomer is formed, so no net effect on the plane polarised light

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8
Q

In what form do amino acids exist as solids? What consequences does this have?

A

Zwitterions (ionic lattice) - high melting and boiling points

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9
Q

What colour solids are most zwitterions at room temperature?

A

White solids

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10
Q

Do zwitterions dissolve in water? Non-polar solvents? Why?

A

Yes, but not in non-polar solvents - due to ionic nature/polar bonds

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11
Q

What is the definition of a zwitterion?

A

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

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12
Q

How do zwitterions occur in amino acids?

A

COOH is deprotonated -> COO-
NH2 is protonated -> NH3+

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13
Q

What happens to amino acids in acidic conditions?

A

Gains a proton on NH2 group

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14
Q

What happens to amino acids in alkaline conditions?

A

Loses a proton from COOH group

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15
Q

What is the peptide bond?

A

-CONH-

O H
= -
-C-N-

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16
Q

What is a dipeptide?

A

Two amino acids bonded together (a dimer)

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17
Q

What name is given to chains of amino acids up to 50 amino acids?

A

Polypeptides

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18
Q

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

A

Proteins

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19
Q

What are polypeptides and proteins found in?

A

Enzymes
Wool
Hair
Muscles

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20
Q

What is the process called by which polypeptides or proteins can be broken down into their constituent amino acids?

A

Hydrolysis

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21
Q

What conditions are needed for hydrolysis to occur?

A

6 moldm^-3 HCl, reflux for 24 hours

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22
Q

What is the primary structure of a protein? How is it bonded?

A

The sequence of amino acids along the protein chain - bonded by covalent bonds

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23
Q

How is the primary structure represented?

A

Sequence of 3 letter abbreviations of the amino acids

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24
Q

How can the primary structure of a protein be broken up?

A

Hydrolysis, 6M HCl, 24 hour reflux

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25
What are the 2 options for the secondary protein strucuture?
Alpha-helix shape or beta-pleated sheets
26
How is the secondary structure held together?
Hydrogen bonding e.g. between C=O and N-H groups
27
What is the tertiary shape of a protein?
Alpha-helix or beta-pleated sheet is folded into a complex 3D shape
28
How is the tertiary protein strucutre held together?
* Hydrogen bonding (mainly) * Ionic interactions between R groups * Sulfur-sulfur bonding (disulfide bridges) * Van der Waals forces of attraction
29
Why is the tertiary structure of proteins important?
The shape of protein molecules is vital in their functions e.g. enzymes
30
How can amino acids bond/be attracted to each other? (3 main ways)
1. Hydrogen bonding 2. Ionic interactions between groups on side-chains 3. Sulfur-sulfur bonds/disulfide bridges; 2 S atoms oxidised to form an S-S bond
31
What is a TLC plate made of?
Plastic sheet coated with silica, SiO2 This is the stationary phase
32
Describe how you would carry out thin layer chromatography
1. Spot the samples onto a pencil line a few cm above the base of the TLC plate 2. Place this in a beaker or tank, with solvent level below the pencil line 3. Ensure there is a lid on the beaker to keep the inside saturated with solvent vapour 4. Wait until the solvent front is almost at the top od the TLC plat; then remove from the beaker and analyse
33
Why does TLC separate amino acids (or other molecules)?
1. Solvent carries amino acids up the TLC plate 2. The rate of movement depends on the balance between that amino acid's affinity for the solvent (solubility in it) and affinity for the stationary phase (attraction to the silicon with hydrogen bonding)
34
What do you often have to do to enable the amino acids to be seen on the chromatogram?
Spray with ninhydrin (amino acids are colourless, ninhydrin turns their spots purple Shine UV light on them
35
How do you calculate an Rf value?
Distance moved by that substance divided by the distance moved by the solvent front
36
How can Rf values verify which amino acid is which?
1. Compare the experimental Rf values to known/accepted values in the same solvent 2. Run pure amino acids int the same solvent and compare results to identify amino acids
37
What is 2D TLC?
* Uses a square TLC plate * Spot the amino acids in one corner, then run TLC in first solvent * Flip the plate through 90° and repeat TLc in a separate solvent
38
What are the benefits of 2D TLC (2 main ones)?
1. Separates the spots more - it is extremely unlikely that 2 amino acids will have identical Rf values in 2 solvents 2. Gives you 2 Rf values for each amino acids; you can be more confident in verifying the identity of the amino acids when comparing to known values, as 2 Rf values can be verified
39
How do you find the primary structure of a protein?
1. Reflux with 6M HCl and reflux for 24 hours 2. Carry out TLC to find the number and types of amino acids present
40
How you find the secondary and/or tertiary structure of a protein?
Various techniques e.g. X-ray diffraction
41
What is an enzyme?
Protein based catalyst that speed up rate of reaction by factors of up to 10^10
42
How many reactions is each enzyme designed to catalyse?
One reaction - they are very specialised
43
What is the structure of an enzyme?
Globular protein with a creft/crevice in it, known as an "active site" - stereospecific
44
How does its structure help the function of the enzyme? What is this hypothesis known as?
The reacting molecules fit precisely into the active site and are held at exactly the right orientation to react This is the lock and key hypothesis
45
How else do enzymes increase the rate of reaction?
* Reacting molecules form temporary bonds (via intermolecular forces) to the enzyme * This weakens the bonds in the molecules, promotes electron movement and lowers EA
46
What does the stereospecificity of enzymes mean?
Active sites are so selective of the shape of substrates that only reactions involving one enantiomer are catalysed
47
How does enzyme inhibition work?
1. A molecule with a very similar shape and structure to the substrate is devised 2. Binds to the enzyme's active site 3. Blocks the active site (does not desorb easily) 4. Substrate cannot absorb to the active site, so reaction cannot be catalysed
47
What does stereospecificity mean for most naturally occurring molecules?
Most naturally occurring molecules only occur as one enantiomer due to stereospecific enzymes
47
How are enzymes denatured?
Change in temperature or PH
47
What is an example of a drug that works through enzyme inhibition?
Penicillin
48
What are the benfits of modelling new molecules on computers?
Now we understand factors that affect shapes of extremely complex proteins, we can model drugs that haven't even been synthesised, predict their properties and design drugs that will treat a range of medical conditions
49
What does DNA stand for?
Deoxyribonucleic acid
50
What does DNA do?
It is present in all cells and is a blueprint from which all organisms are made
51
What structure does DNA take?
A polymer with 4 monomers; they can be combined differently
52
What constitutes a nucleotide?
A phosphate ion A sugar (2-deoxyribose) A base (A - adenine, C- cytosine, G - guanine, T - thymine)
53
What forms between bases of adjacent nucleotides?
Hydrogen bonding
54
Which bases pair up between nucleotides?
Adenine with thymine (A and T) Guanine with cytosine (C and G)
55
How does DNA polymerise?
OH on phosphate group and OH on number 3 carbon of 2-deoxyribose react to eliminate a molecule of H2O
56
What kind of polymer does the polymerisation of DNA lead to?
Condensation polymer chain -> backbone of phosphate and sugar molecules, with bases attached
57
What defines the properties of the DNA molecule?
The order of the bases
58
Why does DNA have a double helix shape?
* Exists as 2 strands; held together by hydrogen bonding between C and G and A and T * The complementary DNA molecule has bases that hydrogen bond in the same order to those on another molecule -> double helix shape is formed
59
Why is it important that DNA is exactly copied when cells divide?
It codes for proteins and makes all cells
60
How is DNA exactly copied when cells divide?
* Hydrogen bonds between base pairs break * Covalent bonds in polymer chains remain intact * The sequence for bases is maintained * Separate nucleotide molecules that have been created move to hydrogen bond to their relevant bases * They polymerise
61
How does the body use information that is stored in DNA?
* Template for arranging amino acids into protein chains - codes for proteins * "Recipe" for proteins that make up all living things; enzymes, flesh
62
What is the structure of cisplatin?
Central platinum atom surrounded by two ammonia (NH₃) molecules and two chloride (Cl) ions in a square planar arrangement
63
What is cisplatin's function? How does it do this?
* Anti-cancer drug * Bonds to strands of DNA to distort shape and prevent cell replication * It bonds to the N (nitrogen) atoms on 2 adjacent G bases * The N atoms replace the Cl- ligands in a ligand substitution reaction
64
Why are CL- ions able to be replaced by N on the base?
* N atoms on the G base have lone pairs of electrons that can co-ordinately bond the the Pt ion * N atoms are better ligands that Cl- so replace them
65
What are the drawbacks of using cisplatin?
* Affects healthy cells that are replicationing quickly e.g. hair follicles * Thought to damage kidneys
66
What happens when excess bromomethane is added to an amino acid?
CH3Br is in excess, so every H on the N atom and the lone pair on the N atom is replaced by a CH3 group -> quaternary ammonium ion (makes a salt with Br-)
67
What happens if an amino acid is added to an excess of methanol in the presence of concentrated sulfuric acid?
Methyl ester forms with COOH group -> COOCH3 NH2 is protonated by the acid -> NH3+

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