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MCS > TBL 1 - Protein (amino acids) > Flashcards

TBL 1 - Protein (amino acids) Flashcards

1
Q

What is the structure of proteins (3 things)?

A

1) Proteins are linear, unbranched polymers constructed from 20 different amino acids that are encoded in the DNA of the genome.

2) All living organisms use the same 20 amino acids and the same genetic code.

3)Proteins are large molecules (e.g. antibiotics): 10,000 - 50,000 M.Wt for single chain/ 100,000 - 250,000 for multichain (oligometic)

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2
Q

What are the functions of proteins (7 things)?

A

1) ENZYMATIC CATALYSIS. - All known enzymes are proteins.
2) TRANSPORT & STORAGE. - of small molecules and ions
3) SYSTEMATIC MOVEMENT. - Muscle
4) MECHANICAL STRENGTH.
5) IMMUNE SYSTEM. - antibodies
6) COMMUNICATION:
- Some hormones are proteins
- Cellular receptors that recognise hormones and neurotransmitters are proteins.
7) GROWTH & DIFFERENTIATION (Control of gene expression)
- Response proteins supress certain gene sequences.
Protein initiation & termination factors serve in the transcription and translation phases of gene function

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3
Q

What happens when proteins lose their shape?

A

1) Proteins exhibit specificity of biologic function which is a consequence of their unique 3D structural shape or conformation. - when it loses it shape won’t be able to function. e.g. enzymes denature.
2) In man, disease states are often regulated to the altered function of the protein.

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4
Q

What are the 2 models (theories) relating to enzyme?

A

1) The lock and key theory
2) Induced fit model

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5
Q

What happens during the lock and key model?

A

The shape of the substrate and the confirmation of the active site are complementary to one another.

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6
Q

What happens during the induced fit model?

A

The enzyme undergoes a conformational change upon binding to the substrate. The shape of the active site becomes complementary to the shape of the substrate only after the substrate binds to the enzyme.

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7
Q

What are the essential amino acids? ESSENTIAL AMINO ACID: nemonic - PVTIMHALL

A

P - PHENYLALAMINE
V - VALINE
T - TRYTOPHAN
I - ISOLENUCINE
M - METHIONINE
T - THRENONINE
H - HISTIDINE -BASIC
A - ARGININE - BASIC
L - LYSINE
L - LEUCINE

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8
Q

What is the composition of an amino acid?

A

Each contains an amino group, a carboxyl group, a hydrogen atom and a distinctive side chain (‘R’ group) all bonded to a carbon atom (the a- carbon)

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9
Q

What is the name of the imino acid which contains a secondary amino group?

A

Proline

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10
Q

What are the names for the aliphatic non-polar neutral amino acid? (GAVLI)

A

G - GLYCINE (GLY)
A - ALANINE (ALA)
V - VALINE (VAL)
L - LEUCINE (LEU)
I - ISOLEUCINE (ILE)

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11
Q

What are the names for the aromatic non-polar neutral amino acid? (FYW)

A

F - PHENYLALANINE (PHE)
Y - THYROSINE (TYR)
W - TRYPTOPHAN (TRY)

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12
Q

What are the names for the aliphatic hydroxyl polar neutral amino acid? (ST)

A

S - SERINE (SER)
T - THREONINE (THR)

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13
Q

What are the names for the acidic polar negatively charged amino acid? (DE)

A

D - ASPARATE (ASP)
E - GLUCAMATE (GLU)

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14
Q

What are the names for the amidic polar neutral amino acids? (NQ)

A

N - ASPARAGINE (ASN)
Q - GLUTAMINE (GLN)

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15
Q

What are the names for the basic polar positively charged amino acids? (KRH)

A

K - LYSINE (LYS)
R - ARGININE (ARG)
H - HISTIDINE (HIS)

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16
Q

What are the names for the sulpheric amino acids? (CM)

A

C - CYSTEINE (CYS)
M - METHIONINE (MET)

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17
Q

What is the name for the imino acid? (P)

A

P - PROLINE (PRO)

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18
Q

What is the process of the Fredrick Sanger - protein sequencing?

A

Amino acids labelled with 1,2,4 - fluorodinitrobenzene (FDNB) that reacts with free amino groups of a protein to from a DNP derivative that is hydrolysed with acid.

Peptide bonds in the chain split, leaving with N-terminal residue in the form of its DNP-derivative.

DNP-amino acids are identified by comparison of their chromatographic rates with those of synthetic DNP-derivatives.

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19
Q

Following optical activity which amino acid is an exception to optical activity?

A

GLYCINE

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20
Q

What does the optical active amino acids contain?

A

All amino acids contain at least one asymmetric carbon and are optically active.

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21
Q

What directions of rotation of plane polarised light can the amino acids be?

A

Irrespective of the direction of rotation of plane polarised light, which can be detro- or laevo.

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22
Q

What direction is the optically active amino acid in protein?

A

The only optically active amino acids that are incorporated into proteins are of the L- CONFIGURATION.

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23
Q

Where are D-Amino acid found?

A

D- Amino acids are found in bacteria & some invertebrates, but are not incorporated into protein by the ribosomal protein synthesized system.

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24
Q

What kind of molecules are amino acids?

A

Amino acids are AMPHOTERIC MOLECULES - they are both ACIDIC & BASIC GROUPS.

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25
Q

What does monoamino - monocarboxylic acids exists in Aq solution as?

A

ZWITTERIONS (Dipolar molecules).

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26
Q

What charge is the a - carbonxyl group and the amino group? So, what is the charge of the overall molecule?

A

The a - carboxyl group is dissociated and negative charged.
Amino protonated - positive
So overall molecule is ELECTRICALLY NEUTRAL.

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27
Q

What happens when the molecule has a low pH?

A

At low pH, carboxyl group accepts a proton and becomes uncharged, so overall charge is positive.

28
Q

What happens when the molecule has a high pH?

A

At high pH, amino group loses proton and becomes uncharged, so overall charge is negative.

29
Q

What do side chains of amino acids contain and what does dissociation depend on?

A

Some amino acids have SIDE CHAINS containing DISSOCIATING GROUPS.
Whether or not these groups are dissociated depends on the prevailing PH and Pka of the group.
These dissociating amino acids also exist in soln.

30
Q

How is a peptide bond formed?

A

PEPTIDE BOND - formed between the a- carboxyl group of one amino acid and a- amino group of another.

Formed by removal of elements of water

Process highly ENDERGONIC. Requires the concomitant hydrolysis of high energy phosphate bonds.

31
Q

What is the process of peptide bond being formed?

A

A peptide bond - covalent bond that forms when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.

32
Q

What is the structure of the peptide bond?

A

Peptide unit RIGID/PLANAR
2 adjacent a - carbons, a CARBONYL OXYGEN and a- AMINO-N and it’s associated H atom and the carbonyl carbon all lie in the SAME PLANE.

C - N bond has a PARTIAL DOUBLE BOND CHARACTER that prevents rotation about the bond axis.

33
Q

How are polypeptide chains produced?

A

POLYPEPTIDE CHAINS are produced by linking together of many amino acids by PEPTIDE BONDS.

34
Q

What are amino acids in polypeptide chains referred as and how long are they?

A

Amino acids in polypeptide chains are referred to as RESIDUES.
Protein polypeptide chains are >100 residues long.

35
Q

What is the recurring sequence in a polypeptide chain and what is it referred as?

A

The recurring sequence:
C - C - N - C - C- N - C - C -N
Referred to as “BACKBONE” of chain.

36
Q

How long a small peptide residues?

A

Smaller peptides (3-30 residues

37
Q

What is the structure of peptides?

A

PEPTIDE STRUCTURES - written from left to right, starting with residue having a free a - amino group (the N -TERMINAL AMINO ACID) and ending with the residue having a free a - carboxyl group (the C - TERMINAL)

38
Q

What is the meaning of conformation of proteins?

A

Every protein in its NATIVE STATE has a unique 3-D STRUCTURE which is referred as its CONFORMATION.

39
Q

What are the 2 protein classes and what are their function/structure?

A

1) GLOBULAR: tight folding of polypeptide chains. Usually soluble.

2) FIBROUS: polypeptide chains lie straight and parallel (or antiparallel) to one another along a single axis forming FIBRES OR SHEETS. Usually insoluble.

40
Q

How is the primary structure of protein formed?

A

PRIMARY STRUCTURE: is covalent ‘BACKBONE’ of the polypeptide formed by the SPECIFIC AMINO ACID SEQUENCE.
This sequence (encoded in DNA) specifies the conformation adopted by the protein in its native state, which is thermodynamically stable.

41
Q

How is the secondary structure of protein formed?

A

SECONDARY STRUCTURE: is the spatial relationship between neighbouring amino acid residues and the occurrence of regular periodic structures.
Secondary ordered polypeptide chains of soluble proteins tend to fold into GLOBULAR STRUCTURES

42
Q

How are polypeptide chains ordered in the secondary structure of protein?

A

ORDERING OF POLYPEPTIDE CHAINS: the 2 degree structure is formed by the ordering of the polypeptide chain as dictated by the DNA-ENCODED 1 degree sequence and may begin as the peptide chain comes of the ribosome.

43
Q

How is hydrogen bonding an important characteristic in the ordering of polypeptide chains in the secondary structure of protein?

A

HYDROGEN BONDING: important characteristic of the ordering, is the formation of H-Bonds between the carboxyl group of one peptide bond and the - N - of another nearby peptide bond.

44
Q

What structure forms if H bonds form between peptide bonds on the same chain?

A

If H -bonds form between peptide bonds in the SAME CHAIN then HELICAL structures develop.

45
Q

What structure forms if H bond form between peptide bonds on different chains?

A

If H-Bonds form between peptide bonds in DIFFERENT chains EXTENDED structures form.

46
Q

What is the structure of the a-helix?

A

Rod - like structure with the peptide bonds coiled tightly inside and the side chains of the residues protruding outward.

47
Q

In the a-helix which group is H-bonded to another group on the same chain?

A

Each carbonyl group is H - bonded to the amino group of the peptide bond that is FOUR RESIDUES AWAY from it along the SAME CHAIN.
There are 3.6 residues per turn of the helix, which is right-handed (e.g. the coils turn in a clockwise fashion around the axis)

48
Q

What is the structure of B-pleated sheets?

A

’ pleated’ the C - C bonds are TETRAHDRAL and cannot be in straight lines

49
Q

In the B-pleated sheets which group is H-bonded to another group?

A

Chains lay side by side with H-BONDS forming between the C = O (carbonyl) group of one peptide bond and the - NH (amino) group of another in the NEIGHBOURING CHAIN.

50
Q

In what directions can the B-pleated sheets run?

A

Chains may run in same direction (PARALLEL B-SHEET) or run in opposite directions, as they would in a GLOBULAR PROTEIN in which an extended chain is folded back on itself, forming an ANTI-PARALLEL B- STRUCTURE.

51
Q

Who discovered a-helix and b-sheet?

A

Linus Pauling - discovery of a helix and B sheet

52
Q

What is the the structure of the tertiary structure of protein?

A

TERTIARY STRUCTURE - refers to spatial arrangement of residues far apart in the linear sequence.

53
Q

Why is the inside of the tertiary structure of protein non-polar and the outside polar?

A

HYDROPHOBIC side chains on the INSIDE. - non-polar
HYDROPHILIC outside. - polar outside

54
Q

Why does folding occur during the tertiary structure?

A

Folding due to associations between segments of a - Helix, B-sheet and other 2 degree structures and represents the lowest energy state or state of GREATEST STABILITY.

55
Q

What does conformation of protein result from?

A

The conformation results from:
1) H-Bonding within a chain or between chains.

2) The FLEXIBILITY of the chain at POINTS OF INSTABILITY, allowing water to gain maximum entropy

56
Q

What is the structure of quaternary structure of protein?

A

QUATERNARY STRUCTURE: is spatial arrangement of individual polypeptide chains in a multi-chain protein, that is the characteristic non-covalent contacts between the chains that form the native conformation.

Most proteins > 50,000 M.wt. has more than one chain - OLIGOMERIC.
Most oligomeric proteins are composed of different kinds of functional subunits.

57
Q

What is denaturation?

A

Disruption of weak types of interaction (H-Bond ionic links, hydrophobic interactions, van der Waals forces) which maintain the 3-D shape of a protein with consequent LOSS OF BIOLOGICAL ACTIVITY.

58
Q

What type of structure is protein that causes it to be easily disrupted?

A

Proteins are LABILE structures (e.g. easily disrupted).

59
Q

What are the type of factors that causes the denaturation of protein?

A

1) Extremes of temperature
2) PH
3) High salt concentrations
4) Organic solvents

60
Q

The collagen triple helix has high tensile strength which can be found where within the body?

A

High TENSILE STRENGTH. Found in skin, bone, tendon, cartilage, blood vessels & teeth.

61
Q

Collagen triple helix consist of what 3 strands?

A

1) Consists of 3 strands, each ~ 1000 residues long.
2) Repeating motif: GLY- PRO- PRO -OH
3) Stability due to ‘locking effect’ of pro & pro - OH
And transverse H-Bonding between residues of different strands.

62
Q

How is the super helix formed?

A

SUPER HELIX: formation due to the smallest amino acid (glycine) occupying every 3rd residue and crowding inside the helix.

63
Q

Strongest to weakest bond rank….

A

1) Disulphide bridge (covalent bond)
2) Ionic bond
3) Van der Waals interaction
4) Hydrophobic interaction
5) Hydrogen bond

64
Q

What is a globular protein and what enzyme is formed?

A

Src protein, 2 of the domains form protein kinase enzyme, while the SH2 and SH3 domains perform regulatory functions.
The enzyme neuraminidase - a ring of four identical polypeptide chains.

65
Q

What is a fibrous protein?

A

Collagen: triple helix formed by 3 extended protein chains that wrap around one another.

66
Q

What happens to the haemoglobin which causes sickle cell anaemia (protein folding disease) - (3 things)?

A

A single genetic point mutation changes a glutamic acid in the B-globulin chain of haemoglobin into valine.
The protein changes conformation exposing a hydrophobic patch that leads to polymersation in individuals homozygous for genetic mutation.
This reduces the elasticity of red blood cells causing anaemia. The allele is maintained at a high level in African populations cus, it affords some protection against malaria parasite, which replicates in red blood cells.

67
Q

What are the drug treatments available for sickle cell anaemia (6 things)?

A

1) Sickle cell pain: hydroxycarbamide (hydroxyurea) increases haemoglobin levels but can lower amount of white blood cells/platelets.
2) Sickle cell crisis: paracetamol or ibuprofen, warm towel or wrapped heated pad to gently massage the affected body part.
3) Preventing infections: daily dose of antibiotics, usually penicillin.
4) Sickle cell-related anaemia: folic acid if severe, blood transfusions or hydroxycarbamide.
5) Sickle cell cure: stem cell or bone marrow transplants. Main risk- graft versus host disease, transplanted cells attack other cells.
6) Other problems treated e.g. delayed puberty, gallstones, joint pain.

MCS (12 decks)

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