Protein Structure And Function Flashcards
Characteristics of Amino Acids
Characteristics of a peptide bond
- building blocks of proteins
- linear chains via covalent bonds (peptide)
- water is lost in process of building proteins
- partial double bond character
- no free rotation about the bond
- rotation of single bonds gives flexibility to proteins
Amino Acid Basic Facts
1) All amino acids found in proteins are alpha amino acids
2) amino and carboxylate groups are bounded to the alpha carbon
3) pH 7.4 –> -NH3+ and -COO-
Amino Acid Structure
- Each of the 20 amino acids except glycine is chiral and can exist as D or L stereoisomers (enantiomers)
- Vertebrates: amino acids are in the L form
Nonpolar R Group Amino Acids
Glycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile) Proline (Pro) Phenylalanine (Phe) Tryptophan (Trp) Methionine (Met)
- found on protein interior
- do not accept or donate protons
- do not participate in hydrogen bonding or ionic bonds
Hydrophobic Interactions
Ala, Val, Leu, Ile –> cluster to stabilize proteins
Proline –> rigid conformation reduces polypeptide flexibility
–> proline is also the first amino acid in alpha helices; starts it off (beta sheets less frequent)
Glycine –> protein flexibility due to H R group
Polar Uncharged R group Amino Acids
Asparagine (Asn) Glutamine (Gln) Cysteine (Cys) Serine (Ser) Threonine (Thr) Tyrosine (Tyr)
- zero net charge at physiological pH
- hydrogen bonding with water
Cys & Tyr –> lose proton at high pH (basic pH)
Asn & Gln –> carbonyl and aside group participate in H bonding
Ser, Thr, Tyr –> polar OH group for H bonding and attachment for groups such as phosphate help with cell signaling
Asn, Ser, Thr –> sites of attachment for oligosaccharides in glycoproteins
Cysteine
- sulfur atoms can coordinate with certain metal ions and can be found at metal binding sites
- can be oxidized to form dimer thru disulfide bonds (important for stability)
Acidic Side Chains
-fully ionized at physiological pH
Aspartic Acid (Asp) Glutamic Acid (Glu)
Basic Side Chains
Lysine (Lys)
Arginine (Arg)
Histidine (His)
Lys and Arg fully proton acted at physiological pH
His is weakly basic (can be uncharged depending on environment) –> has the best buffering capacity at physiological pH
His also found in active sites of enzymes
Selenocysteine
Rare amino acid
Similar to cysteine but with an atom of Selenium in place of sulfur
Not coded directly by genetic code
Coded thru SECIS (Selenocysteine Insertion Sequence) and a UGA codon (in eukaryotes the 3’ untranslated region)
Not just floating around, specifically synthesized on special tRNA
Function: incorporate into nascent polypeptides
Stability of a Protein
- most important factor- sequence of amino acids*
1) Hydrogen Bonding
2) Van Der Waals Forces
3) Electrostatic attractions (ionic bonds can be either stabilizing or destabilizing)
4) Hydrophobic amino acids clump together (on the inside)
5) interactions between AA and AA-Environment
Proteins tend to fold into the conformation of lowest energy with the most hydrogen bonds
Primary Structure of Proteins
Sequence of Amino Acids in proteins –> determined by mRNA
Includes covalent bonds (peptide and disulfide)
Secondary Structure of Proteins- Alpha Helix
Recurring structural patterns
- 3.6 AA per turn of the helix
- forms spontaneously and is stabilized by hydrogen bonding
- H bonds b/w amide nitrogen and carbonyl carbon spaced 4 residues apart
- peptide bonds are parallel to the helix
- R group sticks out of the helix
AA that favor formation of Alpha helix (and do not favor)
Favor Ala Asp Glu Ile Leu Met
Do Not Favor
Proline –> steric constraints from R group
Glycine –> due to high conformational flexibility
[in large numbers] –> by electrostatic repulsion
Glu
Asp
His
Lys
Arg
Secondary Structure of Proteins- Beta Sheets
Composed of 2 or more regions of one polypeptide chain or 2 or more polypeptide chains
- each sheet contains 6+ AA residues
- R groups are above or below the plane of the beta sheet
- often depicted as arrows = blunt end is N terminus and pointed C terminus
-can be parallel or anti parallel
Secondary Structure of Proteins- Turns (loops/coils)
Regions that connect alpha helices and beta sheets
- Do not have repetitive structure
- located on protein surface –> contain polar and charged residues
Tertiary Structure of Proteins
Folding of the secondary structure onto itself
3D form
Interacting regions of proteins can be stabilized by the net effect of many weak interactions and disulfide bonds
Hydrophobic residues bury within proteins
Quaternary Structure of Proteins
Arrangement of 2 or more polypeptide chains
I.e.: Hemoglobin
Quarternary Structure of Proteins- Motifs
STRUCTURAL
Occur in tertiary and quaternary structures
Include multiple secondary structures
Has function but cannot work independently like a domain
I.e.: transcription factors contain a variety of motifs: Helix-turn helix Helix-loop helix Leucine zipper Zinc finger
Quarternary Structure of Proteins- Domains
FUNCTIONAL- Hold different functions
Part of the polypeptide chains that can fold stably and independently with respect to the entire protein
Proteins can have multiple domains (with different functions)
Have biological functions i.e. Can phosphorylate proteins
More like a sequence, not like a physical structure seen in motifs 0
Fibrous Proteins- FUNCTION
Structural Support
External Protection
Flexibility
Shape
Fibrous Proteins- EXAMPLES
Collagen
Alpha-Keratin
Silk
Fibrous Proteins- Overall Arrangement
Polypeptide strands arranges in sheets or strands
Fibrous Proteins- STRUCTURE
One form of secondary structure (either alpha or beta)
Simple tertiary structure
Fibrous Proteins- SOLUBILITY
Contain hydrophobic residues for the most part therefore insoluble
Globular Proteins- FUNCTION
Enzymes
Motors
Regulation
Immunoglobulins
Transport
Globular Proteins- EXAMPLES
Hemoglobin
Myoglobin
Globular Proteins- Overall Arrangement
Globular (good)
Globular Proteins- STRUCTURE
Mixed secondary and complex tertiary structures
Globular Proteins- SOLUBILITY
Soluble due to mix of hydrophobic and hydrophilic residues
Disordered Proteins
Lack definable structure
Intrinsically disordered
Have a flexible structure –> easily interact with other proteins
Examples: Scavenger proteins Structural proteins Parts of protein interaction networks Versatile inhibitors
Ie: p53 tumor suppressant contains unstructured c-terminus region that can bind to at least 4 proteins and has a different conformation in each cases
Zwitterion
At neutral pH, an amino acid that lacks an ionizable R group dissolved in water exists as a zwitterion
Can act as either an acid or base –> ampholyte
Acid R Groups in Proteins (ionizable)
Lysine- NH2 terminal (NH3+ –> NH2 + H+)
Glutamate/Aspartate- COOH terminal (COOH –> COO- + H+)
Arginine Side Chain- Guanidinium –> Guanidino (+ charge on C –> one double bond and no charge on C)
Cysteine Side Chain- Thiol –> Thiolate ( SH –> S- + H+)
Histidine Side Chain- Imidazolium –> Imidazole (C=NH+ –> C=N + H+)
Tyrosine Side Chain- Phenol –> Phenolate (Ring-OH –> Ring-O- + H+)
Ka- acid dissociation constant (and pKa)
HA H+ + A-
- pKa= -logKa
- stronger the acid the smaller its pKa*
pKa Titration –> pH at which molecule is 50% acid form and 50% base form
pH pKa : BASE FROM PREDOMINATES
pKa part of the titration graph where the curve is nearly horizontal
Isoelectric Point (PI)
Proteins and some amino acids are electrically neutral
PI= (pKa1 + pKa2)/2
Maximal Buffering Capacity
When pH is close to the pKa value, the pH is most resistant to change
–> relatively large additions in the amount of base or acid produce only small changes in pH
Amino Acid Ionizable R Groups
Arginine Aspartic Acid Cysteine Glutamic Acid Histidine Lysine Tyrosine
COOH- usually around 2
NH3+ -usually around 8-9
Why are proteins important?
Disease- Most human diseases are related to malfunction of particular proteins (systemically or locally)
Diagnostic tests- Provide readout/assay for tests
Therapy- protein therapy along with antibody production and recombinant DNA help out everyday
Billy’s Case
Catabolism of Branched Chain Amino Acids
Val 1. 2
Ile —————-> a-keto acids————-> acetyl coA der.
Leu
Enzyme 1: branched chain aminotransferase
Enzyme 2: branched chain a-keto dehydrogenase complex
Billy’s Case: no enzyme 2, leading to Maple Syrup Disease
Essential Amino Acids- Billy’s Case
Val, Ile, Leu —> cannot be synthesized by the body
Examples of Diseases that can be Causes by a Change in a single Amino Acid
Sickle Cell Anemia Osteogenesis Imperfecta Tay Sachs Fabry's Disease Polycystic Kidney Disease Hereditary no polyposis colorectal cancer Von Hippel-Lindau Disease (VHL) Phenylketonuria Lesch-Nyhan Syndrome Hemochromatosis
Features of Cystic Fibrosis
- caused by single mutation in CFTR gene
- over 1500 mutations identified
- CFTR: encodes a chloride channel protein that regulates anion movement across epithelial membranes
- -> membranes include: lungs, pancreas, other organs
1) inactive CFTR –> impaired Cl transport and increased Na absorption across epithelial cells –> net increase in water absorption
2) mucus becomes more sticky due to less volume of liquid on the surface
3) bacterial growth favored in sticky mucus and dry airways
4) Chronic infection and inflammation
Examples of Cystic Fibrosis Mutations
Class 1
W1282X mutation causes premature stop at expense of Tryptophan
–> shortened protein
–> 7% common
Class 2
F508 Phenylalanine is deleted
–> protein fails to reach cell membrane
–> 85%
Class 3
G551D Glycine replaced by Aspartate
–> channel not regulated properly
–>
Protein Therapy for CF- Dornase Alfa (Pulmozyme)
A Mucolytic used to improve lung function
Extra cellular DNA from white blood cells work to fight the thick and sticky mucus infection
Dornase Alfa is a DNase that destroys DNA and helps to thin out the CF mucus so it’s easier to cough out of the body
Protein Therapy for CF- Ivacaftor
A CF transmembrane conductance regulator (CFTR) potentiator
CFTR mutation –> cannot regular channels
Ivacaftor improves transport of chloride through the ion channel by binding to the channels directly to induce a non conventional mode of gating –> increases probability that the channel will be open
Protein Therapy for CF- Orkambi
- used for F508 mutation (phenylalanine is deleted –> proteins do not fold properly –> not enough CFTR gets to the cell surface –> targeted for degradation)
- Lumacaftor improves the conformational stability of CFTR increasing processing and trafficking of mature proteins to the plasma membrane
Billy’s Case
Began with normal breast feedings
8th day of life- had sepsis, couldn’t suck
Continued breast feeding for nutrition but started on antibiotics
Condition worsened with seizures, weight loss, hypertonic limbs, and maple syrup smelling diapers
What’s wrong with Billy?
Failure to metabolize certain AA
-Billy’s urine tested positive for keto acids and had elevated levels of branched chain amino acids
What should be done with Billy?
Breast feeding should be stopped and intake of nourishment that contains high amounts of Val, Ile, Leu should be restricted
JM’s Case
Low weight and frequent respiratory illness
Low weight despite switching to formula and then solid foods
Has a normal appetite and always hungry
Poor height, weight, abdominal distention, wasted buttocks
What’s wrong with JM?
high levels of IRT- immunoreactive Trypsinogen
IRT normally produced by pan crease and elevated levels –> CF
Female Student Case
2 week history of severe frontal headaches, high fever, non productive cough, bone and muscle pain, abdominal discomfort
What’s wrong with the female student?
Typhoid??
Elevated ALT and AST –> potential liver damage
+ for Salmonella
No Change in patients conditions
Proteins for diagnostic tests- ALT
Alanine aminotransferase
Liver enzyme
Healthy Range 8-37 IU/L
Proteins for diagnostic tests- Albumin
Protein made by the liver
Healthy Range: 3.9-5.0
Can indicate liver or kidney damaged
Proteins for diagnostic tests- A/G ratio
Albumin/globulin ratio
Healthy ratio: bit over 1
Both found in the blood
Proteins for diagnostic tests- Alkaline phosphatase
Healthy range: 44-147
Enzyme involved in both liver and bone
Proteins for diagnostic tests- AST
Aspartate aminotransferase
Healthy Range: 10-34
Enzyme found in heart and liver
Proteins for diagnostic tests- Bilirubin
Healthy Range: 0.1-1.9
Provides info about liver, kidney, bile ducts, anemia
Proteins for diagnostic tests- Creatinine
Healthy Range: 0.5-1.1 for women and 0.6-1.2 for men
Waste product processed by the kidneys
Resistance to Therapy
Quionolones
- family of synthetic broad-spectrum antibacterial drug
- used to treat wide variety of infectious agents
- bind to DNA gyrase (topo II) or topo IV via a water Mg2+ bridge
- inhibits topo ligase domains leading to DNA fragmentation
