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SL12001 - Biochemistry > Lecture 1 - Amino acids > Flashcards

Lecture 1 - Amino acids Flashcards

1
Q

What is the Primary structure of a Protein

A

The sequence of Amino Acids

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2
Q

What is the secondary structure of a protein

A

Alpha Helix and Beta pleated sheet

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3
Q

What is tertiary protein structure

A

Overall 3D shape and arrangement of a polypeptide

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4
Q

What is Quaternary protein structure

A

Association of several protein chains or subunits into a closely packed arrangement

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5
Q

What is an Alpha amino acid

A

A carbon is connected to both Amine and Carboxylic acid groups

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6
Q

How many amino acids are there

A

20

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7
Q

What are the groups for Amino Acid structure

A

Aliphatic
Aromatic
Basic
Acidic
Polar
Other

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8
Q

Which amino acids are found in the aliphatic group

A

Alanine, Ala, A
Valine, Val, V
Leucine, Leu, L
Isoleucine, Ile, I
Methionine, Met, M

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9
Q

Which amino acids are in the aromatic group?

A

Phenylalanine, Phe, F
Tyrosine, Tyr, Y
Tryptophan, Trp, W

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10
Q

Which amino acids are in the basic group?

A

Histidine, His, H
Lysine, Lys, K
Arginine, Arg, R

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11
Q

Which Amino acids are in the acidic group

A

Aspartic Acid. Asp, D
Glutamic Acid, Glucose, E

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12
Q

Which Amino acids are in the polar group

A

Cystine, Cys, C
Serine, Ser, S
Threonine, T
Asparagine, Asn, N
Glutamine, Gln, Q

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13
Q

Which amino acids are in the others group?

A

Glycine, Gly, G
Proline, Pro, P

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14
Q

What is the amino acid structure and grouping based off

A

Chemical Properties, Shapes, function

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15
Q

What are some traits of aliphatic amino acids

A

Hydrophobic, Non-polar

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16
Q

What are some traits of Aromatic Amino Acids

A

Non-polar
Pi- Stacking

17
Q

What is Pi Stacking

A

The stacking of aromatic rings on top of one another causing interactions and orbital overlap between the rings involved

18
Q

What charge does Aspartic acid and Glutamic acid have on them?

A

Negative (-)

19
Q

What charge do Lysine and Arginine have on them?

A

Positive (+)

20
Q

What are some traits of Polar Amino acids

A

Very Hydrophilic

21
Q

What are the traits of the unique group of amino acids

A

No real R groups
Flexible - can allow a protein to change function

22
Q

What are the main properties that are studied in Amino acids

A

Light absorption
Ionisation states
Chirality

23
Q

What is the Beer-Lambert Law used to measure

A

Concentration of Solutions based on how they absorb light

24
Q

What is the Beer-Lambert Equation

A

A = Ɛ c l

A - Absorbance
Ɛ - Extinction Coefficient
c - Concentration
l - Path Length

25
Q

How do you calculate Protein Concentration (Using Beer-Lambert Law)

A

Slide 18 Slovell lecture

26
Q

What is pKa described as in relation to a molecule or functional group

A

Inherent property

27
Q

What is a zwitterion

A

A molecule with functional groups, of which at least one has a positive and one has a negative charge, and an overall net charge of 0

28
Q

What is the Isoelectric point (pl)

A

The pH at which a particular molecule carries no net charge (zwitterion formed)

(each amino acid is different)

29
Q

What are chiral stereoisomers

A

Same bonds between the same atoms but different spatial arrangement

30
Q

What are D and L amino acids

A

Non-superimposable mirror images (chiral stereoisomers)

31
Q

Why is chirality important

A

(D and L amino acids have) different shapes and enzymes partly recognise substrate my shape

If the substrate is wrong, it won’t be processed by enzyme

(nature tends to use L amino acids for some random reason)

32
Q

What is an example of the importance of the correct stereoisomer

A

Thalidomide D= Sedative L = Teratogenic

33
Q

What is an amino acid called if it a rotates plane of polarised light in the clockwise direction

A

Dextrorotatory or (+)
(not related to D and L)

34
Q

What is an amino acid called if it rotates a plane of polarised light in the counterclockwise direction

A

Levorotatory or (-)

35
Q

How is amino acid configuration obtained

A

(A light source and) a polarimeter (slide 32)

36
Q

How is specific rotation calculated

A

slide 32

37
Q

What is the reference molecule for the L and D system of amino acid configuration

A

Glyceraldehyde

38
Q

What is the CORN rule (slide 34)

A

CORN = L amino acid (anticlockwise)
CONR = D amino acid (clockwise)
(YouTube video if not understood https://www.youtube.com/watch?v=Nw6kIrcpWEU)

39
Q

What does the RS amino acid configuration involve

A

Absolute nomenclature - uses relative ranking of various functional groups
(https://www.youtube.com/watch?v=lwowv5bobt8)
R= Right arc
S+ left Arc

SL12001 - Biochemistry (8 decks)

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