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SIJ1003 > AMINO ACID AND PROTEINS 1 > Flashcards

AMINO ACID AND PROTEINS 1 Flashcards

1
Q

what is amino acid

A

the basic unit of a protein

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2
Q

what are the groups in amino acid

A

chiral carbon attached to
1. hydrogen
2. alpha amino group
3. carboxyl group
4. R-group / side chain

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3
Q

in stereoisomerism, difference between L-amino acid and D-amino acid?

A

L-amino acid: amino group is located at the left side of the fischer projection

D-amino acid : amino group is located at the right side of the fischer projection

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4
Q

what is the classification of amino acid based on

A

the chemical properties of the “R” group of the amino acid.
can be :
-hydrophobic + non polar
-polar + uncharged
-polar + negatively charged
-polar + positively charged

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5
Q

what other method can u classify amino acid

A

according to the R group of the amino acid :
1. aliphatic (leu,ile,ala,val)
2. aromatic (phe, trp, tyr)
3. AA containing sulphur (cys, met)
4. AA containing a hydroxyl group (thr, ser)
5. acidic AA (asp, glu)
6. basic AA (lys, arg, his)
7. Imino AA (pro ; has cyclic R group)
8. Amides (Gln, Asn)

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6
Q

Examples of nonpolar AA

A

-LEU
-PRO
-ALA
-VAL
-MET
-PHE
-TRP
-ILE

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7
Q

Examples of polar uncharged AA

A

-GLY
-SER
-THR
-CYS
-TYR
-HIS
-GLN
-ASN

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8
Q

Examples of polar negatively charged AA

A

-GLU
-ASP

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9
Q

Examples of polar positively charged AA

A

-LYS
-ARG

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10
Q

solubility of AA?

A

-generally soluble in polar solvent & insoluble in organic solvents bcs contain polar group
-aliphatic AA soluble in organic solvents

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11
Q

melting point of AA

A

-high MP.
-have crystalline structure, highly charged, polar groups

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12
Q

AA absorbance of UV?

A

-aromatic AA absorbs UV light bcs of the conjugated double bonds in their R group
-proteins containing aromatic AA can be detected in colourless solution

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13
Q

why is AA considered amphoteric?

A

-considered amphoteric & called zwitterions bcs contain both +ve & -ve charges depending on the functional groups present in molecules

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14
Q

are AA affected by pH?

A

-they are affected by the pH of their surrounding environment and can become more positively / negatively charged due to the loss / gain of protons (H+)
- AA which make up proteins may be positive, negative, neutral or polar in nature n together give a protein its overall charge

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15
Q

how is peptide bond form

A

via condensation (elimination of water)

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16
Q

describe protein structure

A

-protein = biopolymers of amino acis
-vary in size
-divided into 2 classes : globular & fibrous
-f(x) : as enzymes / structure / transport / hormones etc
-conjugated proteins : those that posses a non protein moeity

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17
Q

what are the organizational levels in protein structure?

A

primary, secondary, super secondary, tertiary, quaternary

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18
Q

describe the primary structure of protein

A

the linear sequence of amino acids

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19
Q

describe the secondary structure of protein

A

local conformations of the
polypeptide chain formed as a result of the regular folding of
backbone atoms without participation of side chain groups
OR common folding patterns in protein structure OR
structure of the polypeptide chain resulting from a lot of H
bonding between neighboring peptide bonds.

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20
Q

describe the super secondary structure of protein

A

the arrangement of
secondary structures in a specific manner

21
Q

describe the tertiary structure of protein

A

the 3-dimensional structure of
the protein formed as a result of interactions between amino
acids far away from each other in the primary sequence.

22
Q

describe the quaternary structure of protein

A

the association or arrangement of
polypeptide chains (subunits) in an oligomeric protein.

23
Q

describe the alpha helix of secondary structure

A

-A lot of hydrogen bonding between C=Oand
-N-H groups of neighboring peptide bonds
-Helix is Right Handed
-In a globular protein, on average there are ~11 amino acid
(aa) in one helix (can be up to 53aa).

24
Q

describe the beta pleated sheet of secondary structure

A

-like the alpha helix, has many hydrogen bonds between
neighboring peptide bonds of the same or different chain.
-2 types; Parallel (chains in same direction) or Anti-parallel
(chain in different directions).
-Forms the -pleated sheet structure.
-In a globular protein there are 2-15 aa in this structure
(average = 6).
-the anti-parallel is more commonly found.
-there is a slight right-handed twist.
-usually found in the central core of globular proteins.

25
Q

what is tertiary structure

A

-The 3-D structure of a particular protein /polypeptide.
-Some include the arrangement of secondary structures –
Super secondary structures or motifs
-On average 27% are in alpha helix and 23% beta structures
-But there are exceptions – there is 75-80% alpha helix in
Myoglobin and Hemoglobin
-Concanavalin A has only beta structures and no alpha
helices. It is a lectin protein that binds selectively to
carbohydrates (sugars, glycoproteins) found in plants, human
etc.
-Usually all hydrophobic aa are found in the protein interior
(val, leu, met)
-Polar and charged aa (glu, asp, his, lys) are found on the
surface of the proteins – meets water molecules
-Polar aa with no charge can be found inside or on the surface
of globular proteins (ser, asn, tyr)
-Usually globular proteins that are large (>200aa) have
DOMAINs – for example, domain A & B (ex. Theenzyme
glyceraldehyde 3-P DH, phosphoglycerate kinase)

26
Q

what are the forces that influences protein structure?

A

-the peptide bond - its geometry
-the hydrogen bond
-hydrophobic interactions
-electrostatic interactions
-van der waals interactions
-disulphide bond

27
Q

why does the geometry of peptide bond influences protein structure?

A

-The C=O, C-N atoms are planar.
-Degree of rotation depends on the size of the R groups
of the amino acids in the peptide bond
-It has a double bond characteristic.
-The structure and geometry of the peptide bond limits
the degree of rotation or conformational coiling that
can take place.

28
Q

why does hydrophobic interactions influences protein structure?

A

-Occurs between side chains (R) that are hydrophobic in
nature
-Automatically/spontaneously avoids interaction with water
(more stable)
-Usually in the core of globular proteins

29
Q

why does electrostatic interactions influences protein structure?

A

Occurs between side chains that are charged (ex: between –
COO- with –NH+ groups)

30
Q

why does van der waals interactions (dipole-dipole) influences protein structure?

A

-Transient weak electrical attractions; electron clouds around
molecule fluctuate and forms temporary electric dipoles
-(ex: between two methyl groups, –CH3
)

31
Q

why does disulphide bond influences protein structure?

A

Between side chains of cysteine residues linking together
polypeptide chains (same or different chains)

32
Q

what is the quaternary structure?

A

-The fourth level of protein structure is concerned
with the interaction of 2 or more polypeptide
chains to associate to form a larger protein
molecule.
-Proteins with more than one polypeptide chain are
said to be oligomeric, and the individual chains are
called subunits or monomers of the oligomer.
-The geometry of the molecule is its quaternary
structure. Two subunits forms a dimer, three a
trimer, four a tetramer etc.
-The subunits (polypeptide chains) may be identical
(homogeneous) e.g. muscle creatine kinase is a
dimer of 2 identical subunits or non-identical e.g.
haemoglobin is a tetramer and contains 2 alpha + 2
beta subunits (heterogeneous).

33
Q

what is the central dogma of protein?

A

-The central dogma of protein folding – “The primary structure determines the tertiary structure”
-Protein folding is spontaneous and probably starts with a local secondary (α-helix or β-structure) structure, which forms the nucleus/centre, around which the rest of the coil folds around.
-Recently proteins called molecular chaperone or chaperone proteins have been discovered (originally called heat shocked proteins) which help in protein folding – although exactly how not known.
-Probably protect certain exposed non-polar regions of developing polypeptide

34
Q

what is the structure of fibrous protein

A

keratin and collagen

35
Q

what is the globular protein

A

myoglobin and hemoglobin

36
Q

what is fibrous protein

A

formed from parallel polypeptide chains held together by cross links. these form long, rope-like fibres, with high tensile strength and are generally insoluble in water

37
Q

what is collagen

A

the main component of connective tissue such as ligaments, tendons, cartilage

38
Q

what is keratin

A

the main component of hard structures such as hair, nails, claws and hooves

39
Q

what is silk

A

forms spiders’ webs and silkworms cocoons

40
Q

explain keratin in depth

A

-Main structural component of hair (also nail, skin and horns etc).
-Its basic unit is the a-helix polypeptide.
-Two a-helices are twisted together to form a coiled-coil.
-Two coiled-coils twist together to form a protofilament/protofibril.
-Protofilaments are arranged in 9+2 fashion to form a microfibril
-Many microfibrils are packed together form a macrofibril
-Many macrofibrils pack together to form a fiber (a single hair)

41
Q

what are the characteristics of the a-keratin polypeptide

A

-Rich in hydrophobic amino acids that promote a-helix formation.
-Because R-groups are directed toward the outside of the helix,
keratins are highly insoluble in water.
-Lack helix-breaking proline residues.
-Structure of protofilaments is stabilized by intermolecular hydrogen bonds and disulfide bridges.
-The disulphide bonds can be reductively cleaved by
mercaptans (ex. Ethyl or methyl mercaptans).
-Hair so treated can be curled and set in a “permanent wave” by an oxidizing agent which reestablishes the disulphide bonds and the hair in a new conformation.

42
Q

explain collagen in depth

A

-Most abundant protein in vertebrates – 25% of all protein in body
-Structural component of extracellular matrix, bone, teeth, tendons and blood vessels.
-Basic structural unit is a collagen polypeptide that
forms a left-handed helix
-No α-helix or β-pleated sheet structure possible
-The collagen molecule is a triple helix of three
collagen polypeptides – ~ 3000A long

43
Q

what is the example of fibrous protein

A

-structural protein with tensile strength
-glycine-proline-alanine
-3 polypeptide chains, each in the shape of helix
-3rd amino acid is glycine (allows the coils to lie close to e/o)
-triple strands wind around each other forming fibres
-molecules within the fibre are joined by cross linkages

44
Q

what is globular proteins

A

-usually have a spherical shape caused by tightly folded polypeptide chains
-the chains are usually folded so that hydrophobic groups are on the inside, while the hydrophilic groups are on the outside. this makes many globular proteins soluble in water

45
Q

what is the examples of globular proteins

A

-transport proteins ( haemoglobin, myoglobin, those embedded in membranes)
-enzymes (lipase, DNA polymerase)
-hormones (oestrogen, insulin)

46
Q

what is myoglobin

A

-Myoglobin structure was elucidated by John Kendrew & Max
Perutz (late 50s) using x-ray crystallography techniques.
-Small in size (153 amino acid residues) and crystallizes easily
– easy to study.
-Has the ability to carry oxygen because it has a prosthetic
group – haem (a tetrapyrrole – see below).
-Myoglobin is extremely compact.
-75% of polypeptide is in alpha helix – 8 helix segments, A, B, C, D, E, F, G & H.

47
Q

what is hemoglobin

A

-Hemoglobin (or haemoglobin, frequently abbreviated as Hb), which is contained in red blood cells, serves as the oxygen carrier in blood.
-Hemoglobin also plays a major role in the transport of carbon
dioxide from the tissues back to the lungs.
-Each heme group contains an iron atom, and this is responsible for the binding of oxygen.
-Has 4 polypeptide chains; 2 α chains (141aa – minus D helix); 2 β chains (146aa – shortened H helix) chains (i.e. has 4 subunits; 574 aa; M.Wt. 63,500)
-Each subunit almost spherical.
-Each subunit can carry 1 oxygen molecule
-Thus the capacity to carry oxygen is high:
Hb4 + 4O2 → Hb4(O2)4 oxy-hemoglobin
-Fe2+ in the protohaem can bind to 6 atoms (like myoglobin).
-The β subunits has 8 helical segments (A,B,C ….H) – just like myoglobin. The α subunits have 7 helical segments (minus the D segment).

48
Q
A

SIJ1003 (6 decks)

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