Lecture 1: Levels of Protein Structure Flashcards
Key Types of Proteins
- Enzymatic
- Defensive
- Storage
- Transport
- Hormonal
- Receptor
- Contractile/motor
- Structural
Primary Structure is based on…
Amino acid sequence
Structure of amino acids
- central tentrahedral carbon (alpha carbon)
- linked to:
1. amino group
2. side chain, r group
3. hydrogen atom
4. carboxylic acid
Most common form of amino acids
L form
*this means that the amino group is on the left, H on the right in fischer projection
*doesnt say anything about rotation of light!
(except glycine)
Enantiomers vs Diastereomers
(as it relates to amino acids)
enantiomers = mirror images
diastereomers = not mirror images but same connective order
This matters because there are L and D forms of amino acids
- L is more common, D is less common
- enantiomers are not interchangeable, usually one version is used/important and another version is not
Classifications of amino acids
(categories)
what are their characteristics at pH7?
- non-polar, aliphatic (alkyl groups)
- aromatic (ring)
- polar, uncharged
- positively charged (Basic)
- negatively charged (Acidic)
Nonpolar Aliphatic Amino Acid R Groups (acronym?)
- Glycine
- Alanine
- Proline
- Valine
- Leucine
- Isoleucine
- Methionine
Aromatic Amino acids
- Phenylalanine
- Tyrosine
- Tryptophan
Spectroscopic Properties of aromatic amino acids
Absorb in the 280-300 range
Can Id/measure proteins in samples
*Different ones absorb more, but that general range is wehre absorption is seen
Polar, uncharged amino acids
STCAG
- serine
- Threonine
- cysteine
- asparagine
- glutamine
cysteine and reversible disulfide bond formation
Cysteine forms disulfide bonds because has a -Ch2-SH R group
- C - CH2 - S - H
Positively charged amino acids
LAH
- lysine
- arginine
- histidine
Unique Property of Histidine
- Good to have at an active site to both stabilize and destabilize a substrate
- side chain has a pKa of 6.5 –> near a physiological pH
- exists in the protonated and deprotonated form at the same time
- R groups are what make the protein reactive, but it is still only reactive if it is reactive at a physiological pH
Negatively charged amino acids
- aspartate (-CH2 - COO)
- glutamate (- CH2 - CH2 - COO)
Zwitterion form of amino acid
- protonated amino group (NH3+)
- deprotonated carboxyl group (COO-)
*both are protonated at low pH
*both are deprotonated at high pH
Zwitterion formation based on ph
- 0-2: both protonated, NH3+ and COOH
- 2-9: zwitterion, NH3+ and COO-
- 9-14: both deprotonated, NH2 and COO-
Henderson Hasselbeck Equation
Describes the shape of the titration curve of any weak acif or amino acid
Ka = [H+] [A-] / [HA]
–> in terms of H+
–> negative of both sides
–> -log = ph or pKa
pH = pKa - log ([HA]/[A-])
Titration Curve of amino acid
Buffer regions
Equivalence point/PI
pKa
Key Pieces of info from Titration curve
- quant measure of the pKa of each of the two ionizing groups
- buffering regions
- relationship between net charge and pH of solution
PI (Isoelectronic point)
- characteristic pH at which net charge is zero
- equal amounts of + and - charged acid and zwitterions
- can be arithmetic mean of the two pKa values
Peptide Bond Formation Structure? Reaction?
two amino acids can be covalently joined through a substituted amide linkage (peptide bond) to yield dipeptide
loss of a water molecule, dehydration an form multiple –> oligopeptides, polypeptides
Properties of peptide bonds:
- resistant to hydrolysis and kinetically stable (high Ea and reverse Ea makes it unfavorable/difficult to go in reverse)
- planar due to partial double bond character of C-N bond
- contain a hydrogen bond donor (NH) and hydrogen bond acceptor (CO)
- uncharged, allowing proteins to form tightly packed globular structures
Resonance of Peptide bonds
- carbonyl is partially negative
- amide is aprtially positive
trans and cis
In what form are peptide bonds in proteins?
- trans
- steric clashes arise from cis
(proline is exception)
Peptide bonds that are cis
- X-pro
- Proline: nitrogen is bonded to two tetrahedral carbon atoms so steric differences between cis and trans are less significant
- Glycine: R group is just an H so it is very flexible
Single Bonds vs Peptide Bonds
Phi and Psi
- in contrast with the peptide bond, the bonds between the amino group and the a-carbon are purely single
- freedom of rotation about the bonds (torsion angles phi and psi) allows proteins to fold in many dofferent ways
–> many rotational combinations are forbidden because of steric collissions
–> Ramachandran diagram reveals there are only three regions physically accessible
Ramachandran Diagram of Peptide Bonds
What does it reveal?
Defines what is possible to build in the secondary structure
What is the secondary structure of a protein?
regular spatial arrangement
What is regular Spatial Arrangements?
- “local spatial arrangement of the main chain atoms in a selected segment of a polypeptide chain”
Most common secondary structures
- a- helix
- b-strand (b sheets, pleated sheets)
- b-turn (b-bend, reverse turn or hairpin turn)
- o-loop (loop or omega loop)
Characteristics of helices
p = pitch (angle it is at)
n = number of repeating units per turn
(>0 right handed/clockwise, <0 left handed/counterclockwise)
d = helical rise of repeating units per turn (p/n)
Most common rotation of helix
Right handed
Left handed are rare
Interactions between helices (how do helices come together to make super helices?)
- form superhelices
1. helical coiled coils (alpha keratin) - 2 alpha helices wound left handed
2. triple helices (collagen) - three left handed helices wound right handed
Where do superhlieces exist
Fibrous proteins
- protective, connective or supportive material (hair, skin, tendon, bone)
- motility (muscles, cilia)
Disulfide bonds determine curliness of hair
a-Keratin:
What is its structure?
- coiled-coil proteins
- 2 a-helixes in Right handed rotation, coiled around eachother in left handed rotation
- two helices wind around one another to form a super helix as part of higher order structures
- result of hydrophobic interactions with water (whenever you repel water two molecules get close to eachother)
Heptad repeats of a-keratin
- every 7th residue within each of the two helices is leucine
- held together by van der waals interactions primarily between the leucine residues
Collagen
Where is it?
What is its structure?
- 3 special helices coiled left handed, coiled together in a right handed structure
- main fibrous component of skin, bone, tendon, cartilage and teeth
- coiled coil proteins but three separate polypeptides supertwisted about eachother
- every cell is connedcted via collagen
Glyceine in Collagen
- every third residue in the amino acid sequence
- glyceine - proline - hydroxyproline pattern recurs frequently
Hydroxyproline
derivative of proline that has hydroxyl group in place of one of the hydrogen atoms on the pyrrolidine ring
Secondary structures: Strands and sheets
- b-strands are almost fully extended rather than being tightly coiled as in a-helices
- two or more can be arranged in parallel or antiparallel b-sheets
Parallel b-sheets
Antiparallel b-sheets
loops between each strand
Types of connections of b-strands in b-sheets:
- hairpin
- right handed crossover (clockwise, top - if looking at starting sheet)
- FORBIDDEN: left handed crossover (counterclockwise, bottom)
Fatty Acid Binding in b-sheets
- all adjacent b-strands run in opposite direction, b sheets are purely antiparallel
- sheets twist and arrange in a barrel shape
Structure of silk
antiparallel b-sheets
Secondary structure: Turns and loops
- proteins have globular shapes owing to the reversals in the direction of their polypeptide chains
- connecting elements that link runs of a-helices or b-strands
- less regularly structured
- invariably lie on the surface of proteins and thus often partiicpate in interactions between proteins and other molecules
- most common forms are b-turns and o-loops
*some of the most important parts a protein are the turns and loops which interact with other molecules
Proline b-turns
cis structure
natural kink
Glycine b-turns
small, minimizes steric hindrance
Loops and role in interactions
Loops become the location of interactions, mediate them
Secondary Structure: Propensities of amino acids to form secondary structures
- how amino acid sequence of a protein specifies its tertiary structure depends on whether specific sequences form structures such as a-helices of b-strands
1. some amino acids occur at higher frequencies in certain secondary structures
2. some amino acids have steric constraints
3. prediction is difficult though
Single sequences with multiple structures
- same peptide sequence can be in a-helices or b-sheets
- alter overall protein structure
Tertiary Structure
General amino acid distribution
Features of tertiary structures of water soluble proteins:
- an interior formed of amino acids with hydrophobic side chains
- a surface formed largely of hydrophilic amino acids that interact with the aqueous environment
Hydrophobic interactions
- driving force for the tertiary structure formation of water soluble proteins
Membrane proteins and tertiary structure
- proteins existing in a hydrophobic environment (such as cell membrane) display the inverse distribution of hydrophobic on the outside and hydrophilic interior
- form channels through which cations and anions pass
Tertiary structure: Interactoins stabilizing protein shape
- interactions between amino acid side chains along backbone
Based on:
- hydrophobic forces (atraction of hydrocarbon side chains by LDF)
- hydrogen bonds
- ionic bonds (charged side chains +/-)
- covalent bonds (disulfide bridges)
Tertiary Structure: motifs, folds and domains
describe structural pattern in a polypeptide chain
Motif
Recognizable pattern involving two or more elements of secondary structure and the connections between them
fold
combinations of motifs
domain
structural unit within a polypeptide chain that folds independently and is independently stable
Common motifs
bab
b-hairpin turn
aa motif
Greek Key motif
1,2 on inside 3 and 4 on either side
Hairpin turns in between
Longer between 3 and 4
domain classificaitons
- a-domains
- b-domains
- a/b-domains
a-domains
topologies
- 4 helix bundle
- globulin fold?
Examples: globin fold in myoglobin or hemoglobin, 4-helix bundle in cytochrome b562 or HGH
- up, down, up, down
- up, up, down down (up. loop. up. turn. down. loop. down)
b-domains
topology
- containing only b-sheets
Examples: immunoglobulin fold in most immune system proteins
- Immunoglobulin fold
- up and down b-barrel
- jelly roll barrell
a/b-domains
topology
- both a-helices and b-sheets
examples: a/b barrels and open b sheets
1. a/b barrel = 8 tandem b/a units
2. Rossman Fold/Open B sheets
Unstructued domains
- molten globule
- unstructured
Open b-sheet domains
Topology
Rossman fold
babab arrangement
- able to bind mono or dinucleotides such as NAD= or NADP +
- founds in nearly all dehydrogenases and many other enzymes
Quaternary Structure
subunit interaction
Subunit interaction
- proteins consisting of more than one polypeptide chain display quaternary structure
- each individual polypeptide chain is called a subunit
- multiple interacting subunits: dimer, trimer, tetramer, oligomer, polymer
- interacting subunits can be identical/homomers or different/heteromers
- protomers: repeating structural units in multimeric proteins (single or groups of subunits)
Hemoglobin
a2b2 heterotetramer
(4 subunits)
Quaternary Structure: symmetric patterns
- identical subunits of multimeric proteins are generally aranged in one or a limited set of syemtric patterns
Types:
- rotational
- helical
Rotational Symmetry
-subunits pack around the rotatoinal axes to form closed structures
rotatinal symmetry: cyclic
Nomenclature is “c”
- twofold
- threefold
Rotational symmetry: dihedral
“D”
- twofold
- fourfold
Rotational synnetry: icosahedral
fivefold, threefold and twofold
Importance of icosahedral symmetry
- only need three different proteins to make a ball structure
- a few genes
- structure can carry genome
Helical symmetry
- makes tower, house structure
- “brick” subunits
tobacco mosaic virus
Proteins behave like amino acids because…
1) the R groups are charged
2) terminal ends
Why does histidine have 3 pKas?
1) R group (+ charged)
2) carboxyl group charged
3) amino group
*Histidine is part of LAH in “positively charged R group”
What causes scurvy?
- vitamin c/ascorbic acid is required for hydroxylation of proline and lysine in collagen
- humans are missing ascorbate which is an enzyme needed in the process
- glycine - x/Cy endo proline = y/Cy exo hydroxyproline
- coupled enzymatic reaction in which: x does not get hydroxylated and Y does
- w/o ascorbate, X gets hydroxylated and Y does not
–> leads to an unstable structure
- Need the * coupled reacion, otherwise the the wrong structure results
Phi vs Psi
Phi is between Carbon and Nitrogen
Psi is between Carbon and Carboxyl Carbon
Special amino acid in Keratin
Leucine
Every 7th residue
Special amino acid in collagen
Glyceine
Every third residue
Gly-Pro-Hydroxyproline sequence occurs frequently
4 Special Amino Acids
Histidine: protonated and deprotonated form, pKa is near physiological pH
cysteine: disulfide bond formation
Proline: In b-hairpin turns, cis conformation is favored
Glycine: in b-hairpin turns, flexible to swivel into cis conformation
Main Bonds in primary structure
- peptide bonds
Main bonds in secondary structure
- hydrogen bonds
