Proteins Flashcards
1
Q
What percentage of cell dry mass is proteins?
A
Around 50%
2
Q
What is the size of proteins?
A
Macromolecular
10^3 - 10^6 atoms
3
Q
How many different types of proteins can the body generate?
A
2 million from 20,000 genes
4
Q
How many amino acids form a polypeptide that can fold?
A
> 40
5
Q
All amino acids except which have a chiral centre?
A
Glycine
6
Q
What 2 forms can amino acids exist in?
A
L and D enantomers
(L dominates D as D are rare in nature)
7
Q
From where was tyrosine first isolated?
A
Cheese
8
Q
Non polar R groups of amino acid result in?
A
Hydrophobic properties - 6 of these
9
Q
What R groups of amino acids make it hydrophilic?
A
Polar (6)
Acidic (2)
Basic (3)
10
Q
Learn the amino acids
A
Non polar - slide 13
Acidic - slide 15
Basic - slide 16
Polar - slide 17 and 18
11
Q
Where do disulfide bridges form?
A
Between cysteine –SH groups (Cys-S—S-Cys)
covelant crosslinks
12
Q
What reaction forma disulfide bridges?
A
Oxidation
(Reduction breaks them)
13
Q
Learn abbreviations for amino acids
A
Slide 20
14
Q
What is the name of bond between 2 amino acids?
A
Peptide
15
Q
Peptides with more than how many amino acids are regarded polypeptides?
A
10 (decapeptides)
16
Q
What are 2 properties of peptide bonds?
A
Rigid and planar
Caused by bond resonance
17
Q
The action of virtually all proteins involves what?
A
Binding of a ligand
18
Q
What is a ligand?
A
The substance that is bound by the protein.
Eg. Ion, small molecule or macromolecule
19
Q
What is the order of sequence of amino acids?
A
N-terminus to C-terminus
20
Q
What is sickle cell disease an example of?
A
Mutation in primary structure - single mutation in Hba haemoglobin gene
21
Q
How many amino acids per turn of an alpha helix?
A
3.6
22
Q
What are alpha helixis abundant in and absent in?
A
Abundant - haemoglobin
Absent - chymotrypsin (digestive enzyme)
23
Q
How many runs does beta pleated sheet have?
A
5 -10
24
Q
What are multiple B pleated sheets connected by?
A
Short runs or “hairpin loops”
25
Which one of B sheets or a helices are more flexible?
B sheets
26
What are characteristics of loops / random coils?
- Usually located on surface
- Rich in polar and charged residues
- Length = 2-20 residues
27
What typically causes differences between structurally similar proteins?
Loops /random coils
28
What is the name given to the groupings of structural elements?
Super secondary structures /motifs
(Occur in many globular proteins)
29
What is the beta-hairpin motif?
- Two antiparalell B strands joined by hairpin loop
30
What are the characteristics of beta-hairpin loop motif?
* Simplest supersecondary structure
* Common in globular proteins
* No specific function associated with this motif
31
What is the helix-loop-helix motif and its 2 functions?
Two α-helices connected by a loop
Functions as either DNA-binding (e.g. c-Myc) or Ca2+-binding motif (e.g. calmodulin)
32
Where is the helix-loop-helix motif commonly found?
- Transcription factors (helix-basic loop-helix)
- Cell signalling proteins that bind Ca2+ (EF-hand)
33
What is the greek key motif?
Particular arrangement of 4 beta-strands into an antiparallel beta-
sheet
Common in range of proteins (e.g. proteases [trypsin], cytokines [TNFalpha])
No specific function associated with this motif
34
What is the coiled coil motif?
2–7 alpha-helices are coiled together like the strands of a rope.
Usually contain repeats of a 7 residue pattern; heptad repeat (hxxhcxc)
h=hydrophobic, c=charged, x=any
35
Give examples of coiledcoil motif
- Leu zippers in transcription factors [e.g. c-Fos and jun]
- Structural proteins [Myosins]
36
What is the zinc finger motif?
Two anti-parallel beta-sheets followed by 1 alpha-helix, stabilised by a zinc ion
* May bind Fe, Zn or no metal at all
* Metal binding mediated by Cys (in beta-sheets) and His (in alpha-helix)
37
What are the fuctions of Zinc finger motifs?
Functions: Binding of DNA, RNA, lipid and protein substrates
38
What is the B barrel motif?
Multiple anti-parallel beta-sheets that twist to form a closed structure
First strand is hydrogen bonded to the last
39
What are the 4 types of beta barrel motifs?
– Greek key barrel
– Up-and-down barrel
– Jelly roll barrel (complex)
– Beta-helix barrel
40
What are the water channels in the pores of beta barrel motif called?
aquaporins
(learn 2 structures on slides 43 and 44)
41
What is a domain?
A polypeptide chain (or part of chain) that folds independently into a stable
structure with its own hydrophobic core
42
What is a doimain formed from?
Several simple motifs and secondary structure elements
43
How many domains can a protein have?
1-7 domains
each is associated with a distinct biological function
44
Give an exaple of a domain
Src homology 2 (SH2) domain – binds phospho-Tyr residues
Important in insulin signalling
45
What do Ionic bonds in the tertiary structure form?
Between CO2- and NH3 of R Groups
electrostatic attraction
46
How do hydrophobic interactions occur?
Hydrophobic R Groups cluster inside proteins to shield themselves from water
Van der Waals interactions
47
Which structure is a fibrous protein?
Secondary. Forms long parallel fibres and sheets. These are usually insoluble in water
48
What is the important role of fibrous proteins? 2 examples?
Provides support and strength
- Collagen
- Keratins
49
What are the 2 types of keratin?
Alpha keratin - in mammals hair and nails
Beta keratin:
- invertebrate silks, reptile scales, and claws
- Avian feathers, beaks and claws
50
What is the structure of collagen?
Super-helices of Gly-rich triple alpha-helices (tropocollagen)
Assembles into fibrils
51
What is collagen for?
Main protein in connective tissue
Supports, connects or separates tissues and organs
52
What are the properties of collagen?
- Strong and elastic
- very abundant (25% of total protein)
53
What is collagen found in?
Bone
Cartilage
Ligaments
Tendons
Teeth
Blood vessels
Skin
Eyes (cornea and lens)
54
What is the name of the syndrome associated with collagen?
Ehlers Danos Syndrome (EDS)
55
What can EDS affect?
1. Skin
2. Musculoskeletal
3. Cardiovascular
56
What is the structure of alpha keratin?
Coiled coils of two alpha-helices that assemble together to form large fibres
57
What are the properties of alpha keratin?
(Found in hair and nails)
- Strong and inextendable
- insoluble and chemically inert
- disulphide bridges cross link coiled-rings
58
What is beta keratin aka? Where is it found?
Fibroin
Found in silk and spider webs
59
What is the structure of Fibroin?
Layers of antiparalell beta sheets rich in Ala and Gly residues
Small side chains interlock allowing close packaging of B sheets
Sheets joined by amorphous streches - This gives elasticity and stregnth
60
What is a globular protein?
A mixture of irregularly folded secondary elements that form a 3D shape.
These are usaully soluble in water -Inner hydrophobic cor and transported easily in body fluids
61
Give 3 examples of globular proteins
– Myoglobin
– Haemoglobin
– Immunoglobulins
62
What is haemoglobin made of and what is its function?
4 haem molecules (polypeptide chains) - porphyrin ring +Fe2+ (binds to O2)
Transports oxygen from lungs to rest of body for aerobic respiration
63
What ere 2 mutations in Hb DNA that cause disease?
- Sickle cell disease
- Thalassaemias
64
What is sickle cell disease?
– Single mutation in DNA coding within beta-globin gene
– Non-sense mutation = changes primary sequence
65
What are the effects/symptoms of Sickle cell disease?
- Changed RBC shape (sickle shaped)
- RBCs rigid, become bloced by capillaries
- Increased haemolysis (RBC destruction) - Anaemia/spleen damage
66
What is the mutation in Sickle cell disease?
Single mutation in beta-globin gene
(T to A) changes 10 sequence (Glu to Val)
67
What is an Immunoglobin?
Y-shaped proteins of the immune system which
identify and combat invading foreign organisms
68
How are the 4 chains in immunoglobins linked?
By disulfide bridges
– 2 large H (heavy) chains
– 2 short L (light) chains
69
What gives each immunoglobin a speciic binding site shape (antigens)?
VAriable structures in heavy and light chains
70
What engages an immunoglobin for attack?
Constant portions of the heavy chains
71
What happens to Ionic bonds in altered pH?
– Break ionic bonds
– Disrupts tertiary structure
– Can render proteins insoluble in water and precipitate out of solution
72
What does low pH do to an Ionic bond?
– Low pH = high H+ concentration (acidic)
– Adding H+ neutralises the COO- part of the ionic bond removing its charge
73
What does a high pH do to Ionic bonds?
– High pH = low H+ concentration (alkaline)
– Removes H+ - neutralises the NH3+ part of the ionic bond removing its
charge making it NH2
74
What is pyrexia?
increased body temperature, fever
(used as ancient anti-viral defence mechanism)
75
Which organic solvents can denature a protein?
Ethanol, acetone, phenol
