AAs and Proteins Flashcards

1
Q

Functional Group

A

Amino
carboxyl
R

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2
Q

R group

A

determines
the biochemical
properties of the
amino acids.
* Charge
* Polarity
* Size
POLAR, and
POLAR, and
and uncharged

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3
Q

Chiral Carbon

A

4
different groups/atoms
attached to it

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4
Q

amino acid
DOES NOT
have a chiral centre?

A

GLYCINE

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5
Q

naturally occurring amino acids

A

classified as left-handed or L-amino
acids.

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6
Q

D Amino Acids

A

found in bacterial cell
walls and in some secondary
metabolites.

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7
Q

Properties of Core Region

A

At the pH levels
typically found in
cells (usually pH
7.0–7.4 - neutral
pH), both the
carboxyl and amino
groups of amino
acids are ionized

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8
Q

What happens at the carboxyl end?

A

the carboxyl group loses a hydrogen ion -COOH -COO- + H+ ACID

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9
Q

What happens at the amino end?

A

the amino group
gains a hydrogen ion

-NH2 + H+ -NH3+ BASE

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10
Q

What happens at the overall core region?

A

Amino Acids exist as ZWITTERIONS.

They show the properties of acids and bases at the same time!
At neutral pH, the core of an amino
acid has no net charge.

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11
Q

Non Polar AAs (10)

A

Glycine (Gly,G)
Cysteine ( Cys, C)
Alanine (Ala, A)
Proline ( Pro, P)
Isoleucine (Ile, I)
Leucine (Leu, L)
Methionine (Met, M)
Tryptophan (Trp, W)
Valine (Val, V)
Phenylalanine (Phe, F

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12
Q

Polar Uncharged AAs (5)

A

Serine (Ser, S)
Threonine (Thr, T)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Tyrosine (Tyr, Y)

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13
Q

Positively Charged Polar AAs

A

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

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14
Q

Negatively Charged Polar AAs

A

Aspartic acid (Asp, D)
Glutamic acid (Glu, E)

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15
Q

Non-polar amino acids - hydrophobic

A

They have hydrocarbon
chains and/or rings.

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16
Q

Non-polar amino acids – special amino acid

A

Cysteine contains a thiol group
(SH)
Glycine is the smallest amino acid
and is not chiral
Proline forms a ring – which is
NOT a benzene ring

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17
Q

Polar – uncharged amino acids

A

They all have a C-O or C=O bonds

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18
Q

Primary protein structure

A

 Specified by the genetic code of the organism.
 The sequence in which amino acids are linked by
peptide bonds in a protein.

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19
Q

Peptide bonds

A

Two amino acids are joined by condensation reaction
forming a peptide bond

20
Q

Oligopeptide

A

2 -25 amino acids

21
Q

polypeptide

A

More than 25 amino acids

22
Q

Short oligopeptides have specific names

A

2 amino acids – dipeptide
3 amino acids – tripeptide
4 amino acids - tetrapeptide

23
Q

Linear arrays of amino acids can make a huge number of different molecules

A

Consider a peptide with
two amino acids (AAs) AA1 AA2 20 × 20 = 400 different molecules
Consider a peptide with
three amino acids AA1 AA2 AA3 20 × 20 × 20 = 8000 different molecules
For any protein that is made of 100 amino acids, the number of possibilities is:
20100 = 1.267 × 10130

24
Q

Secondary protein structure

A

 Secondary structure refers to 3D form of local segments
of proteins, stabilised by intramolecular and sometimes
intermolecular hydrogen bonding.
 Hydrogen bonds form between the R groups of amino acids.
 This bonding causes coiling or folding of the polypeptide.

25
Coiling
Coiling results in formation of alpha (a) helices – spiral, cylindrical (helical) shape.
26
Folding
in formation of almost flat, but kinked sheet of amino acids called beta (b) pleated sheets.
27
Tertiary protein structure
 Tertiary structure is the overall 3-dimensional shape formed from a single protein chain.  Arises due to interactions between amino acids that are far away (usually 10 aa or more).  These amino acids come in to contact with each other through the process of protein folding.
28
Hydrophobic interactions
amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules
29
ionic bonds
Salt Bridges
30
Disulfide Bridges
Covalent bonds between the sulfur- containing side chains of cysteines. They are much stronger than the other types of bonds that contribute to tertiary structure.
31
Importance of protein folding in biological systems
Changing an amino acid in the primary sequence will change the structure of the protein. This change in the structure may produce a change in protein function (depending on where the change occurs). The amino acid change can have damaging effects if the new amino acid has different biochemical properties
32
Quaternary protein structure
 Quaternary structure is formed from the association of more than 1 polypeptide chain.  It is very common for proteins to consist of multiple subunits.  Quaternary structures are stabilised by the same bonds that stabilise tertiary structures.
33
In a dimer When both polypeptides are the same =
homodimer
34
polypeptides are different
heterodimer
35
Protein Folding in the cell
 Protein folding takes place in the Endoplasmic reticulum  Special proteins called chaperones ensure that newly made proteins do not interact with each other randomly  Important types of chaperone proteins are the Heat Shock Proteins (HSPs).  Chaperone proteins come in many shapes and sizes.
36
What happens if a protein is misfolded?
 Misfolded proteins can cause disease.  Example: Mad cow disease (prions) Creutzfeldt-Jakob disease (CJD) and Bovine Spongiform Encephalopathy (BSE) Correctly folded name: PrPC function: maintain the myelin sheath in nerve cells. Misfolded name: PrPSc abnormality: cannot be degraded - form large aggregates – destroy nerve cells.
37
Globular
 vast majority of proteins  function:  catalysis of reactions (enzymes)  transport  hormones  amino acid order: irregular
38
Fibrous
 less common type  function:  structural support  amino acid order: repetitive sequences
39
Globular Proteins
40
Insulin
One of the smallest proteins. Functions as a hormone. A complex of 2 polypeptides connected with disulfide bonds.
41
Haemoglobin
Has quaternary structure – formed from 4 polypeptides (called a tetramer). Each polypeptide has a heme molecule containing an iron atom. Oxygen atoms bind to histidine amino acids close to the iron atoms, for transport in the blood.
42
SCA
example of a disease caused by a single base mutation in the nucleotide sequence. The change causes the hydrophilic amino acid, glutamic acid (E) to be substituted for a hydrophobic amino acid, valine (V). Sickle blood cells live 10-20 days instead of 90-120 days.
43
Histone
Proteins involved in supercoiling (storage of DNA). The surface of histones is very positively charged – remember DNA is negatively charged.
44
Fibrous Proteins
45
Collagen
>25% of the total body protein. Found in skin, tendon, bone, dentin, cartilage, vitreous humor, muscle, blood vessels. There are at least 16 types. Most common are types I, II and III. Excellent example of repetitive amino acid sequence Most common alternating sequence: Gly-Pro-Hyp (Hyp is hydroxyproline)
46
Hydroxyproline
a version of proline with an extra OH (hydroxyl) group.  This extra OH group allows for many hydrogen bonds between collagen molecules = holds collagen molecules together.  Formation of hydroxyproline from proline is assisted by vitamin C (ascorbic acid).
47
Vit C deficiency
Vitamin C Deficiency Lack of Hydroxyproline Defective collagen structure