Section 2 Flashcards
(58 cards)
1
Q
What is the basic structure of an amino acid?
A
- tetrahedral alpha carbon
- neg charged carboxyl group (or uncharged)
- pos charged amino group (or uncharged)
- R group
- H atom
> charge of carboxyl and amino groups depends on
- alpha carbon is chiral
2
Q
Protein?
A
linear polymer built from amino acids
- > AA sequence determines 3D shape of protein
- > R groups allow for massive protein diversity
3
Q
complex
A
interaction of proteins with eachother or themselves
4
Q
chiral centre
A
an atom with arranged substituents such that the molecule is not superimposable on its mirror image
5
Q
enantiomers
A
- each AA except glycine has 2 enantiomers
- a pair of molecules each with 1 or more chiral centres that are mirror images on eachother
6
Q
are most amino acids L or D?
A
-> L amino acids exist in proteins and in living systems
7
Q
What does a Fischer projection of AAs in L and D forms look like?
A
L: COOH on top, H on bottom, NH2 group on left
D: NH2 group on the right of alpha carbon
8
Q
what is an intrinsically disordered protein?
A
- > doesn’t have a 3D (tertiary) shape
- > stays unfolded or only solds when bound to substrate
9
Q
what is a zwitterionic AA?
A
has both a + and - charge (@ neutral pH for most AAs)
- > COOH group loses H at around pKa of 2
- > NH3+ loses H at around pKa of 9 (and is neutralized)
10
Q
How many essential amino acids are there? What are they used for?
A
- 20 key AAs
- these (or slight modifications) are used in all living things to build proteins since they’re encoded by DNA
11
Q
what are the non-polar (aliphatic) AAs?
A
- Glycine (used for packing close) , Alanine, Valine, Leucine, Isoleucine (2 chiral centres), Methionine (nonpolar thioether), Proline
12
Q
What are some characteristics of hydrophobic AAs?
A
- pack closely at centre of protein to stabilize shape because of hydrophobic effect
- Different R groups allow for close packing to maximize VDW interaction
13
Q
What’s an S27D mutation?
A
Serine at the 27th position in the AA sequence has been turned into aspartate
14
Q
What are the aromatic AAs? What are some of their characteristics?
A
- phenylalanine (hydrophobic benzene), tyrosine (also has reactive OH to H-bond), Tryptophan (indol group with an N-H that can H-bond)
> largely participate in hydrophobic interactions but can be hydrophilic in some parts
contain aromatic phenyl ring
tend to be in core of protein
15
Q
what are some basic positively charged AA’s? what characteristics do they have?
A
- acid form has + charge (HIGH PKA)
- have high pKa’s and star acidic until very high pH
- basic because they don’t like to give protons
- positively charges at neutral pH since pKa of R groups is >10
- lysine (ionizable group), arginine (ionizable guanidinuim group), and histidine
16
Q
acidic negatively charged AA’s + characteristics?
A
- have carboxylic acid R groups
- pKa’s of R groups are < 4 so negatively charged @ pH 7 (LOW PKA)
- give up proton easily to become COO-
- aspartate, glutamate
- found of protein surface interacting with H2O
17
Q
Polar uncharged Amino Acids + characteristics?
A
- not charged
- can H-bond
- hydrophilic
- Serine, Threonine -> aliphatic hydroxyl groups, cysteine (thiol - disulfide bonds), asparagine and glutamine (derivatives of aspartate and glutamate -> contain terminal carboxyamide w/ uncharged terminal amine)
- more hydrophilic and reactive
18
Q
aliphatic
A
hydrocarbon chains mostly
19
Q
Are pKa’s of R-groups static?
A
Can change based on AA’s environment -> temp, ionic strength and microenvironment of ionizable group
20
Q
primary structure of proteins
A
linear sequence of amino acids linked by peptide bonds
21
Q
peptide bond
A
linkage of an alpha carbonyl of 1 AA to the alpha NH of another AA
- loss of H20 (condensation)
- not energetically favourable to form but STABLE
-> C(carbonyl) - N-H
22
Q
polypeptide
A
series of AA residues linked by peptide bonds
23
Q
residue
A
an AA unit in a polypeptide
24
Q
Why are proteins polar?
A
- not a charge
- have an amino end on LEFT
- have a carboxyl group on RIGHT
eg.) SGYAL
25
What's a polypeptide backbone?
- repeating NC(alpha)C(carbonyl) linked by peptide bonds with variable side chains
- all carbonyls and amine groups in backbone can H-bond (except Proline because of ring)
- equilibrium favors separation of peptide bonds but activation E to do that is too great
26
how is the weight of a protein expressed?
- weight in Daltons
- kDa
- 1 Da = mass of 1 H atom = 1g/mol
27
what should knowing the AA sequence of a polypeptide allows us to do?
1. determine 3D shape (except we can't)
2. understand the function of proteins
3. understand disease
4. understand evolutionary history
28
what is meant by "polypeptides are flexible but conformationally restrained"?
- peptide bond has double bond characteristics (trigonal planar lockin due to resonance - no free rotation)
- resonance between peptide bond and carbonyl
- peptide bond planar, with C(alpha)-C(carbonyl)-N(H)-C(alpha) -> locked in trans conformation where R groups face away from eachother (except X-Pro - has both cis and trans)
-> BUT bonds between N-C(alpha) and C(alpha)-C(carbonyl) CAN rotate
29
what is a dihedral angle and how do they work?
amount of rotation about N-C(alpha) bond - PHI
OR
C(alpha)-C(carbonyl) - PSI
- ranges from -180 - 180 degrees
- provides flexibility to AA sequence
- not all combos of phi and psi are permitted due to steric hindrance -> combinations possible shown in Ramachandran plot
> glycine and proline have different plots (glycine is more flexible and proline is more hindered so less angles are permitted)
> dark blue -> favourable
> light blue -> borderline
> white -> non-permissible
ONLY 25% of all angle combos are permissible (flexibility is only 1/4 of what it would be for a single bond)
because of these limitations, proteins usually fold into one conformation each time
30
when do molecules assume random coils?
when large molecules can freely rotate among many bonds (mixture of many structures)
31
What is secondary structure?
The local spatial arrangement of AAs close together in linear sequence
> some proteins don't have a defined secondary structure
eg) Alpha helix or B sheet
32
Alpha Helix
- polypeptide backbone forms inner part of right-handed helix, and R groups stick outwards
- stabilized by intra-chain H-bonds between N-H and C=O
33
What are some characteristics of an alpha helix?
1. ) ideal dihedral angles of PHI = -60 and PSI = -45
2. ) C=O forms H-bond with N-H of a residue (i+4) (4 residues ahead of i)
- all N-H and carbonyls in backbone are H-bonded except first and last
3. ) helix will grow in length 1.5 Angstroms/residue added to helix (residues normally 3-4 Angstroms long)
4. ) R groups i+1 and i+2 are NOT close to i and point in the opposite direction
5. ) R groups i+3 and i+4 are close to i and point roughly in the same direction
6. ) left-handed helices rare because of steric hindrance
7. ) shown as ribbons or rods
34
How does an alpha helix form?
-> by entropy and R group favourability to water -> held together by H-bonds
35
Can an alpha helix be ampiphatic?
YES! can have polar groups on one end and hydrophobic groups on other end
36
How does keratin look like?
- series of 2 coils coiled around eachother -> helix wrapped around other helix
37
How long is an alpha helix usually?
around 45 Angstroms long
38
B sheet
two or more B-strands (polypeptide stands usually from the same molecule) associated as stacks of chain in an extended zigzag from, stabilized by H-bonds
-can be parallel, anti parallel or mixed
> shown by broad arrows pointing towards C terminal
39
anti-parallel beta sheet
N-H and C(carbonyl) of residue i on one strand bonds to single residue j on other strand
- PHI -139 and PSI of 135 optimal angles
each strand added to B sheet increases length by 3.5 Angstroms
- a little more stable since groups not too clusteres together
40
parallel beta sheet
C(carbonyl) of residue i on one strand bonds to single residue j on other strand
AND N-H on residue i also bonds to C=O of residue j+2
Accordion folds as a result
- PHI -119 and PSI 113
each strand added to B shet increases length by 3.25 Angstroms)
> slightly more tightly packed
41
What's a Beta barrel?
Beta sheets twisted around eachother to forma barrel-like structure (Twisted vs. flat)
42
How can a peptide chain reverse direction (like in anti-parallel beta sheet)?
- B turns (secondary structure)
| - larger loop with no structure
43
Tertiary structure
spatial arrangement of AA residues that are FAR APART in primary sequence + disulfide bonding
(polypeptide chain or many chains coming from originally 1 polypeptide)
44
describe myoglobin
> O2 storage protein in mammalian muscle
- single polypeptide chain of 153 AA residues
- has huge loop -> iron in a protopophyrin ring where O2 binds
- 70% alpha helices and rest in loops and turns
- alpha helices nice in core of protein since R groups can be made to face outside
- > core made up of hydrophobic residues ( except 2 histidines helping to coordinate heme iron and H2O)
45
What is a structural domain?
multiple compact regions in a protein linked by flexible sections of polypeptide that usually don't have defined tertiary structure
-> part of the polypeptide chain (a subunit is a separate piece)
46
describe fibroblast growth factor
Has many beta sheets, some alpha helices and twists/turns where secondary structure is undefined
47
quaternary structure
spatial arrangement of multiple subunits (polypeptides) and the nature of their interactions
-> 3D shape of many chains together
48
homomer
quaternary protein with identical polypeptide chains
49
heteromer
different polypeptide chains in quaternary structure
Hemoglobin is 2 x 2
50
describe hemoglobin
- O2 transporter in mammalian blood
- composed of 4 subunits (2 alphaglobins and 2 betaglobins)
- > tetramer
- dimer of dimers
51
describe minute virus of mice
made of 9 VP1 units and 51 VP2 protein units to form an isohedral capsid with just enough room to fit viral DNA
52
What drives protein folding?
- thermodynamics (delta G negative, although free energy difference between folded and unfolded is small)
- entropy (hydrophobic effect)
- enthalpy
53
What destabilizes protein secondary structures?
- unpaired charged or polar groups (not H bonded)
| - proline and glycine destabilize 2dary structures
54
What is meant by folding is an all or none process?
- protein is either folded or not in its DOMAIN
| - either intrinsically folded domain or intrinsically disordered domain
55
What is meant by protein folding is cooperative? How is protein folding proxied?
- one part of structure
(eg. alpha helix) will influence how the rest of the protein folds
- folding is depicted as a FREE ENERGY FUNNEL
- in unfolded state there are many different possible structures with high free energy, but as these species fold and the free energy decreases, # of possible structures decreases until the folded state is reached
56
Does every protein have a single 3D structure?
No, some proteins have multiple folded structures, or exist in equilibrium between two folded structures since delta G is too small
57
What are 3 ways to determine the structure of intact folded proteins?
1. ) NMR (nuclear magnetic resonance) -> measures location of nuclei
2. ) X-ray Crystallography -> myoglobin structure 1st -> measures electron density
3. ) Cryo CM -> cryo-electron microscopy -> taking many pictures of proteins
>can combine methods
58
How can we modify amino acids post translationally?
1. ) hydroxylation -> adding OH group (usually to proline)
eg. ) fibre connective tissue stabilization
2. ) carboxylation -> adding carboxyl group to glutamate
eg. ) required for clotting
3.) glycosilation -> attachement of 1 or more sugars to a residue like asparagine, threonine or serine (surface labelling)
4. ) phosphorylation -> attachement of phosphate group to OH of R group from serine, threonine, or tyrosine
eg. ) signal translation
5.) acetylation -> adding acetyl group to an NH3+ group (ei lysine tp protect from degradation)
> proteins can be cleaved or trimmed after synthesis -> can activate or inactivate them
eg. ) cleaving polypeptide into many proteins
eg. ) fibrinogen is inactive until cleaved into fibrin which clots
