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Amino acids, proteins, DNA Flashcards

1
Q

What is an amino acid made of?

A

Amino group and carboxyl group

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2
Q

What does amphoteric mean?

A

Has both acidic and basic properties

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3
Q

Why do amino acids have basic properties?

A

The N of the amino acid can accept protons

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4
Q

Why do amino acids have acid properties?

A

Proton donor - loses H on carboxyl group

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5
Q

What is a zwitterion?

A

A dipolar ion that has both positive and negative charge in different parts of the molecule

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6
Q

When do zwitterions exist?

A

Near an amino acids isoelectric point

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7
Q

What is the isoelectric point?

A

The pH where the average overall charge on the amino acid is zero

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8
Q

What is the amino acid zwitterion in acidic conditions?

A

Protonated - N+H3 and COOH

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9
Q

What is the amino acid zwitterion in alkaline conditions?

A

Deprotonated - NH2 and COO-

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10
Q

How can you identify an unknown amino acid?

A

Thin layer chromatography

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11
Q

Why do different amino acids have different Rf values?

A

Have different R groups so have different solubilities in the same solvent

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12
Q

How do you calculate Rf value?

A

Distance travelled by spot / distance travelled by solvent

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13
Q

How can you identify an amino acid once you know its Rf value?

A

Compare it to a table of known Rf values

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14
Q

What is the problem with identifying and separating amino acids using TLC?

A

Amino acids are colourless

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15
Q

How do you make spots of amino acid visible in TLC?

A

Spray ninhydrin solution on the plate to turn spots purple

Use a plate that has fluorescent dye so when UV light it shone on it the spots will appear dark

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16
Q

What are proteins?

A

Sequences of amino acids joined by peptide bonds

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17
Q

How do you form a protein?

A

Condensation reactions between amino acids

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18
Q

What is another word for a protein?

A

Polyamide
Polypeptide chain

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19
Q

How do you get amino acids from a protein?

A

Hydrolysis

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20
Q

What are the conditions for the hydrolysis of protein to get amino acids?

A

6M HCl
Heat under reflux for 24 hours

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21
Q

What is the primary structure of protein?

A

The sequence of amino acids in the long chain that makes up the protein

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22
Q

What is the secondary structure of protein?

A

The shape of the polypeptide chain

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23
Q

Why isn’t a protein (polypeptide chain) a straight line?

A

Hydrogen bonds between peptide links

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24
Q

What are the most common protein secondary structures?

A

Alpha helix (spiral)
Beta pleated sheet (folded map)

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25
What is the tertiary structure of protein?
The three dimensional shape of protein that comes from extra bonds forming between different parts of the polypeptide chain
26
How can you identify a protein from its structure?
The chain of amino acids is coiled and folded in a characteristic way that identifies the protein
27
What causes the tertiary structure of proteins?
Extra bonds (hydrogen and disulfide bonds) between different parts of the polypeptide chain
28
Why is the 3D shape of proteins caused by hydrogen and disulphide bonds important?
Vital to its function eg shape of an enzyme can stop it working
29
What protein structures do hydrogen bonds stabilise?
Secondary and tertiary
30
What protein structures do disulfide bonds stabilise?
Tertiary
31
How does hydrogen boding arise in protein structures?
Polar bonds attracted to each other in different parts of the polypeptide chain -OH groups and -NH2 groups
32
How are disulfide bonds formed in proteins to make the tertiary structure?
Amino acid cysteine contains a thiol group (-SH) which can lose its H atom to and form a disulfide bond with another thiol group
33
What is a thiol group?
-SH
34
What factors can affect the hydrogen bonding and formation of disulfide bonds in proteins and what does this change result in?
Temp. and pH Changes the shape of the protein
35
What are enzymes?
Proteins that can act as biological catalysts
36
What do enzymes catalyse?
Every metabolic reaction in the body
37
What is the active site on an enzyme?
The part of the enzyme that the substrate fits into do that it can interact with the enzyme
38
What part of the protein structure is the active site? eg primary
Tertiary - active site is 3D
39
What does stereospecific mean when referring to an active site?
Only one enantiomer will fit onto the active site
40
What type of isomerism do you need to look for in amino acids?
Stereoisomerism - contan chiral centre
41
What do inhibitors do?
Slow down the rate of reaction
42
How do inhibitors work?
Have similar shape to the substrate so bond onto active site which blocks it
43
What does the amount of inhibition depend on?
Relative concentrations of inhibitor and substrate How strongly the inhibitor bonds tp the active site
44
How do some drugs work?
Act as inhibitors
45
How are most drug molecules found?
Trial and error
46
Whats the problem with finding new drug molecules?
Takes time, effort and money to find a molecule that will fit on the necessary active site (especially if molecule is chiral as active site will be stereospecific)
47
How can scientists find new drug molecules more easily?
Use computers to model the shape of enzymes active sites
48
How do scientist use computers and models to find drug molecules?
They predict how potential drug molecules will interact with an active site so hundreds of molecules can be examined quickly which speeds up the process and perseveres resources If might be match they then state testing and synthesising in the lab
49
What does DNA stand for?
Deoxyribonucleic acid
50
What is DNA?
A polymer of nucleotides
51
What are nucleotides made from?
Phosphate Sugar A base
52
What are the four bases that can be used to make DNA?
Adenine Guanine Cytosine Thymine
53
Which nitrogen atom in bases bonds to the sugar molecule?
Bottom or bottom right
54
How do nucleotides join together to form a polynucleotide chain?
Covalent bonds from between the phosphate group of one nucleotide to the sugar of another
55
How is DNA formed?
Condensation polymerisation
56
What is the covalent bond between nucleotides called?
Phosphodiester bond
57
What shape does DNA form?
Double helix
58
Describe the double helix structure of DNA
Two polynucleotide strands spiralled together that are held together by hydrogen bonds between bases
59
What are the base pairings?
AT GC
60
What can be said about the two polynucleotide strands of DNA?
They're complimentary
61
How are the two strands of DNA complimentary?
They match up so that when there is an adenine base on one strand there's a thymine base on the other. And when there's a guanine base on one there's a cytosine base on the other.
62
Why is the DNA double helix twisted?
So that the bases on the strands are correctly aligned and at the right distance apart for the complimentary base pairs to form
63
How many hydrogen bonds from between adenine and thymine bases?
2
64
How many hydrogen bonds from between guanine and cytosine bases?
3
65
Why are there only two base combinations?
Other pairings would put the partially charged atoms too close together (would repel) or too far apart
66
Where do the hydrogen bonds form on adenine?
Top left N and one of the hydrogens on top N
67
Where do hydrogen bonds form on guanine?
three on the left =O at top H on NH H on NH2
68
Where do hydrogen bonds form on cytosine?
three top/right H on NH2 N =O
69
Where do hydrogen bonds form on thymine?
two top/right =O at top between NH and CH3 H on NH between both =O
70
What is the antic cancer drug?
Cis-platin
71
Describe the structure of cis-platin?
Complex with Platinum(II) at centre and two chloride ligands and two ammonia ligands in a square planar shape
72
What causes cancer?
Cells in the body dividing uncontrollably and forming tumours
73
What does a cell have to do in order to replicate?
Replicate its DNA
74
How does cis-platin work?
N atoms on guanine form a coordinate bond with the central platinum ion replacing the Cl lignands (ligand substitution) The presence of the cis-platin complex causes the strands to kink so DNA cant unwind and be copied properly so cells cant replicate
75
What are some side effects of cisplatin?
Hair loss Suppressed immune system (its controlled by white blood cells)
76
What is the problem with cis-platin?
Also binds to DNA in normal cells so also prevents other cells from replicating
77
Which normal cells does cis-platin affect the most?
Frequently replicating ones eg hair and blood cells
78
How can you reduce the side effects of cis-platin?
Administer low dosages Target the tumour so deliver the drug directly to cancer cells
79
Why is cis-platin still used in chemotherapy if it has such extreme side effects?
The long term positive effects outweigh the negative short term effects

Chemistry (10 decks)

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