3 - Protein Structure And Function Flashcards
Function of a protein is determined by
Structure
Components of an amino acid
- amino group (H3N+)
- carbonyl group (—COO-)
- H atom
- R group (side chain)
Titration curve for weak acid
—COOH ——-> (—COO-) + H+
PKa =
PH at which the group is 50%:50% weak acid and conjugate base.
If pH is > 1 above or below the titration curve for weak acids, it means that
- If its above, it mostly conjugate base
- if its below, it mostly weak acid
At what pH will half the solution be of something, and the other half be of another form?
Ph= ~7
The ionization state of amino acids is altered by a change in
pH
At physiological pH, what form will carbonyl and amino be in?
Carbonyl = —COO-
Amino - —H3N+
Are amino acids achiral?
NO they are chiral
What kind of stereoisomer are amino acids? What properties
They are enantiomers,
- mirror images
- non superimposable
What does chiral mean
4 diff substituents
What are the three categories of amino acids
1) non polar/hydrophobic 8#
2) polar (H-bonding possible) 8#
3) charged (ionizable) 4#
What does it mean for an amino acid to be charged
It’s ionized
Are all the amino acids chiral
NO, glycine’s is the only one that isnt
What are the hydrophobic side chains properties
- Hydrophobic (C,H)
- aromatic
- non polar
- aliphatic And/or cyclic
What are the hydrophobic/non polar amino acid side chains?
1) alanine, Ala
2) valine, Val
3) phenylalanine, Phe
4) thyrophan, Trp
5) leucine, Lue
6) isoleucine, Ile
7) methionine, Met
8) Proline, Pro
Alanine
Ala,
- aliphatic
- non polar / hydrophobic
Valine
Val,
- highly hydrophobic
- aliphatic hydrocarbon
- impacted by hydrophobic effect and therefore hydrophobic
Leucine
Leu,
- 4 C atoms (large bulky)
- aliphatic
- non polar
- highly hydrophobic
Isoleucine
Ile,
- 4 C atoms
- aliphatic
- highly bulky and large
- highly hydrophobic
- 2 chiral carbons
Phenylalanine
Phe,
- very badly rigid
- aromatic, NOT aliphatic
- absorbs UV light at 260nm
- highly hydrophobic
Tryptophan
Trp,
- bulky, rigid
- aromatic
- absorbs U.V at 260nm
- hihgly hydrophobic
- the HN in the aromatic 5 membered ring can potentially be a H bond donor
- 5 membered ring + 6 membered ring
Methionine
Met,
- aliphatic, non polar
- hydrophobic
- contains thioether. (C-S-C)
- S could potential be a H bond acceptor
Proline
Pro,
- aliphatic, cyclic
- distorted geometry around alpha carbon
- non polar, hydrophobic
- internally cyclized
- amino is H2N and NOT H3N+.
What are all the polar side chains
1) serine, Ser
2) Theonine, Thr
3) tyrosine, tyr
4) cysteine, Cys
5) asparagine, Asn
6) glutamine, Gln
7) histidine, His
8) glycine, gly
Glycine
Gly,
- only amino acid that isnt chiral = its achiral
- smallest side chain
- good for small spaces for polar folding
- weakly polar - can be surface of protein (in contact with H2O)
Serine
Ser,
- polar
- H-bond donor
- contains primary alcohol
- OH can carry phosphate group sometimes
- not ionizable (can’t be —O-)
Threonine
Thy,
- polar
- H-bond donor
- secondary alcohol
- can have phosphate attached sometimes
- non ionizable (—O-)
Tyrosine
Tyr,
- primary alcohol on 6 membered ring (polar)
- the alcohol can be potential H bond donor
- absorbs light at 280nm
- highly hydrophobic (ring)
- can have phosphate group attached sometimes
- ionizable —> (—O-)
- PKa = 10,
What’s the pKa of tyrosine and what does it mean
PKa = 10
- therfore midpoint is 10 where 50% is ionized and the other 50% isnt ionized
- ionization more likely when buried in hydrophobic environment with no H2O
Cysteine
Cys,
- contains sulfur
- reactive cuz its ionizable
- thiolate ion
- pKa =8.5
- reactivity = formation of cystine
- HS— cna be both H bond donor and ecceptor
Cystine
Cysteine — S—S—cysteine
What kind of bonds does cystine held by
Disulphides bridge
Disulphides bridges are
- highly non polar
- entire side chain is now non polar when turns cystine
What happens to polarity when cysteine turns into cystine?
Becomes entirely non polar
What kind of bond binds S-S in cystine?
Strong covalent bond that formed between 2 ionizable cystines
Asparagine
Asn,
- amide
- hihgly polar
- non ionizable
- H-bond acceptor (carbonyl) and donor (amino)
Glutamine
Gln
- amide
- highly polar
- forms H-bonds
- non ionizable
- carbonyl (acceptor)
- amino (donor)
Histidine
His,
- aromatic
- absorbs UV at 280nm
- polar
- ionizable
- pKa = 6
- highly reversible ionization as charged/uncharged equilibrium
- can act as acid or base
Whihc polar amino acids contains alcohols?
Serine, threonine, and tyrosine
Whihc polar amino acids are ionizable?
Tyrosine, cysteine, histidine
Whihc polar amino acids contains amide group (H2N)
Asparagine, glutamine, histidine
What are the pKa values for the polar amino acids?
Tyrosine - pKa = 10
Cysteine - pKa = 8.5
Histidine - pKa= 6.5
Which amino acids contains sulfur atom?
Cysteine
What are the charged side chains
Acidic structure:
- aspartate, Asp
- Glutamate, glu
Basic structure:
- lysine, lys
- arginine, arg
Aspartate
Asp,
- salt bridge
- forms H-bonds
- hihgly polar
- charged (-)
- formation of conjugate base favoured at ph7
- pKa = 4
At ph = 1, aspartate will be in what form?
Weak acid form
Glutamate
Glu,
- very polar
- salt bridge
- charged (-)
- ## formation of conjugate base formed at ph=7
What form will glutamate be in ph=1
Weak acid form
Lysine
Lys,
- primary amide
- polar
- Hbonds
- salt bridge
- charged (+)
- pKa = 10.5
- formation of weak acid formed at ph = 7
Arginine
Arg,
- aliphatic, non polar region
- very polar
- H-bonds
- always (-) charged
- pKa = 12.5
- bulky
Is arginine ever not charged?
No its always charged (-)
What is primary structure?
The sequence of amino acids joined by peptide bonds and phosphodiester bonds
What kind of bonds are peptide bonds
Covalent bonds
Formation of peptide bonds occurs via
Nucleophilic attack between 2 amino acids to form peptide bond to bind them together,
Each amino acid in a dupe-tide is referred to as?
Residue
What is the sequence for a peptide bond?
O=C-N-H
A peptide bond is also an
Amide bond
Dipeptide, tropeptide, tetrapeptide
2,3,4 amino acid residues joined together via peptide bonds
N-terminus is always ____ and on the _____
C-terminus is always ____ and on the _____
N-terminus is always (+) and on the left
C-terminus is always (-) and on the right
( amide ) joines the
alpha carboxyl group of one amino acid to the alpha amino group of another amino acid.
• this sequence of amino acids is unique to each
gene product / polypeptide —-> unique function.
Peptide bonds have distinct chemical characteristics
- partial double bond character
Partial double bond character
Not a true double bond but has double bond character in that it cannot rotate.
- polar
- H Bonding
The amino group is always the H bond _____
The carbonyl group is always the H bond ____
The amino group is always the H bond donor
The carbonyl group is always the H bond acceptor
Peptide bonds are flexible or rigid
rigid and planar
Polypeptide backbone strucure sequence
N-Ca(R)-C(=O)-N
Whihc bonds in the polypeptide backbone can and cannot rotate
N-Ca = can rotate
Ca-Cc = can rotate
Cc-N = polypeptide bond and had partial double bond character so CANNOT ROTATE
In the polypeptide backbone, whihc bond is the peptide bond?
Cc-N
Why is the rotation of polypeptide backbone limited?
Because of the steric hindredness and O atoms.
What is Secondary structure
Folding of polypeptide backbone
Regular patterns of secondary structure
Alpha-helixes
Beta-sheets
Within each peptide bond there is a
H bond Acceptor (O=C) and donor (N-H)
What bond connects two peptides together
H bond between H form (N-H) and O form (O=C)
Secondary structure is all about folding of the
backbone and putting the peptide bonds in positions so that they can form H-bonds with one another.
Alpha - helixes
- right handed
- H-bonding between peptide bonds
- H-bond between carbonyl atom of C1 and H of amino of N5.
- H-bond between carbonyl atom of C2 and H of amino of N6.
- H-bond between carbonyl atom of C3 and H of amino of N7.
- first 4 amino groups and last 4 carbonyl groups are excluded from H-bonding. Because peptide has limited length.
Side chains of alpha helix
- sidechains outside
- ## backbone polypeptide (right handed)
Why are side chains in alpha helix outside?
Because they of the right handed polypeptide backbone
Alpha helix secondary structure is stabilized by
H-bonding of the polypeptide backbone and not in the side chains
Proline is
Cyclic
Why is proline alpha helix different
- cuz of distorted backbone geometry = doesnt allow for regular structure to form in alpha helix
Because proline has distorted backbone structure its known as a
Helix disrupter = backbone turns
Polypeptide chains have a sense of
direction
N————> C
Right —-> left
What are the two different ways of aligning polypeptide backbone?
Parallel and anti parallel
Antiparallel
N—->C
CC
C
Parallel
N—> C
N—> C
N—> C
N—> C
- long irregular loops connecting C to N going all the way around
Parallel B-sheets
- donor and acceptors alternate throughout sequence
- held together by H-bonds between peptide bonds
- very long irregular loops
- stabilized by H-bonding b/w peptide bonds
- H-bonds in parallel B-sheet are at an angle.
Antiparallel B-sheets
- Have 180 degree irregular loops
- perpindicular H-bonds (upright, no angle)
Between the polypeptide backbones going in opposite directions for B-sheets, what bonds are between them?
H-bonds
Irregular secondary structure
loops
- not flexible, have specific position
-
In alpha helix and B-sheets, where are the H-bonds located
- alpha helix: it’s between groups IN THE SAME HELIX.
* beta-sheets: it’s between backbone groups of neighbouring strands.
Both alpha helixes and b-sheets have conformations that require specific
angles of rotation around the peptide bond.
Both a-helices and B-sheets form only from sequential
amino acid residues in the polypeptide.
What is tertiary structure?
3D, space filling arrangement of all the atoms in space
Tertiary structures feature what?
- 3d arrangement of ALL atoms to all other atoms
- arrangement of secondary structure
- arrangement of sidechains
- prosthetic groups arrangement
Proteins can be either
Fibrous or globular
Fibrous proteins
“Filaments”
- connective tissue, tendon, muscle, bond
- B-sheets layered on top of each other
- alpha helixes
Globular proteins
Spherical
- functional proteins
- enzymes
- transporters
- receptors
Secondary structure within globular proteins is
varied.
Meaning they could have helixes only or B-sheets only or both, with or without irregular loops.
Hydrophobic residues are generally located
“inside” soluble-globular proteins
In proteins, where are hydrophilic R groups located, and where are hydrophilic R groups located
- Hydrophobic R groups (aliphatic, aromatic) located inside structure
- hydrophilic R groups (polar, charged) located on surface
a-helix and B-sheet secondary structure is generally located in the
interior of folded proteins
Where are irregular loops located and why
The H bonding capacity of the polypeptide backbone in irregular loops is not fully satisfied, and so these sequences interact with water at the surface.
In the polypeptide, whihc groups aren’t involved in H-bonding
The first 4 amino and last 4 carbonyl
Regular secondary structure is generally found in the
interior of folded proteins
Are a-helixes amphipathic or aliphatic?
Amphipathic
The polar and non polar sidechains in the a-helix are where in the secondary structure?
Non polar sidechains stay inside, and polar sidechains stay outside
Why is it important for non polar side chains to remain inside protein structure and polar to remain outside?
To keep hydrophobic interaction inside protein to keep it stabilized
What drives protein folding?
Hydrophobic effect
How does the hydrophobic effect drive protein folding?
It causes the hydrophobic side chain to cluster so they dont interact with H2O. Causing the structure to fold keeping the non polar regions inside.
Sometimes during protein folding, what is put sindie besides non polar sidechains
Polar side chains
Salt bridge occurs between
O(-) and N(+) of the O-O(-) and H3N(+)
- between charged amino acids
Disulphides bridges are
Covalent
Disulphide bridges enhance the stability of
3D tertiary structures in extracellular proteins ONLY (NOT cytosolic)
Disulphide bridge occurs between what amino acids ?
Cys-84 and Cys-26
CH2-S-S-CH2 (cystine) has Disulphide bridges
Polar amino acids in the hydrophobic core of a globular protein are usually involved in either
H-bonding or ion pairs.
H-bonding and formation of salt bridges are enhanced when
Amino acids are buried in hydrophobic environment so that no H2O gets in.
Having polar regions inside the protein sometimes is good or bad? Why?
GOOD
Because it magnifies the ionization of certain amino acids
Which Amino acids are ionized when polar regions are inside the hydrophobic core?
Cys and thr, both becomes (-) charged
Tertiary structure may include
- domains
- motifs
- prosthetic groups
Domain:
an independent folded 3D structure within a single polypeptide
Each domain has its own
Hydrophobic core
What kind of bonds are between Domains?
Covalent bonds
What stabilized domains ?
Hydrophobic effect
Pyruvate kinase
Has 3 domains within its tertiary structure
- 3 hydrophobic cores.
A domain is entirely dependant on the
unique amino acid sequence of any given protein.
Prosthetic group:
a non protein, organic molecule,
• Permenant part of the 3D structure tertiary structure.
• Absolutely required for function.
• Provide additional chemical reactivity.
MOTIF:
A short region that is a recognizable, common pattern or arrangement of secondary structure elements and/or specific amino acid side chains within a domain
Example of a motif ?
Zn finger
Zinc finger
- Common transcription factor for binding
- contains a-helix and antiparallel b-sheets with 180 irregular loops
- central cavity with Zn2+ ion held tightly in with coordination bonds
Example of prosthetic group
Heme in hb and Mb
What drives tertiary structure
Hydrophobic effect?
Which of the following do you think affects the stability of protein tertiary structure the most? A. salt concentration B. pH C. temperature D. detergent
D. detergent
Why does detergent have the most impact on the stability of tertiary structure?
Because it solubilized the hydrophobic groups and sit-ups the hydrophobic effect.
How does salt concetration effect tertiary structure
effecting the formation of salt bridges
How does temperature effect tertiary structure
Effects the possibility of forming hydrophobic interactions (van der waal), H-bonds, and salt bridges
How does ph effect tertiary structure
Effects the possibility of forming H-bonds and salt bridges.
What determines the tertiary structure?
Sequence of amino acids (primary structure)
Prion Folding & Misfolding
Prion is infectious protein that induces misoflding
Prion effects
- increases B-sheets
- decreases a-helixes
- loops change
- flips into infectious state
- causes mad cow disease
A NORMAL prion protein has mostly what’s
A-helixes and irregular loops
Disulphide bonds are covalent and it requires a _______ to break them
reduction reaction
WHAT KIND OF REACTION FORMS DISULPHIDE BRIDGES?
OXIDATION
What is Quartenary structure
Required more then 1 polypeptide subunit
What is quartenary strcure stabilized by?
Non covalent bonds
Heterodimer and homodimer
Heterodimer: has two different kinds of polypeptide units, therfore 2 different genes
Homodimer: single kind of polypeptide unit, so identical gene
Which of the following statements about quaternary structure is TRUE?
A. Quaternary structure is defined as the arrangement of polypeptide backbones in proteins with four subunits.
B. Quaternary structure exists where a protein contains more than one domain.
C. Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
D. Quaternary structure requires covalent interactions such as disulphide bridges between polypeptide chains
C. Quaternary structure is stabilized by the same types of noncovalent interactions as tertiary structure.
In the quartenary effect, what drives the association of the subunits?
Hydrophobic effect.
