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Protein Structure And Function Flashcards

1
Q

Characteristics of Amino Acids

Characteristics of a peptide bond

A
  • 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
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2
Q

Amino Acid Basic Facts

A

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-

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3
Q

Amino Acid Structure

A
  • 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
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4
Q

Nonpolar R Group Amino Acids

A 
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

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5
Q

Polar Uncharged R group Amino Acids

A 
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)
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6
Q

Acidic Side Chains

A

-fully ionized at physiological pH

Aspartic Acid (Asp)
Glutamic Acid (Glu)
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7
Q

Basic Side Chains

A

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

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8
Q

Selenocysteine

A

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

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9
Q

Stability of a Protein

A
  • 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

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10
Q

Primary Structure of Proteins

A

Sequence of Amino Acids in proteins –> determined by mRNA

Includes covalent bonds (peptide and disulfide)

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11
Q

Secondary Structure of Proteins- Alpha Helix

A

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
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12
Q

AA that favor formation of Alpha helix (and do not favor)

A 
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

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13
Q

Secondary Structure of Proteins- Beta Sheets

A

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

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14
Q

Secondary Structure of Proteins- Turns (loops/coils)

A

Regions that connect alpha helices and beta sheets

  • Do not have repetitive structure
  • located on protein surface –> contain polar and charged residues
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15
Q

Tertiary Structure of Proteins

A

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

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16
Q

Quaternary Structure of Proteins

A

Arrangement of 2 or more polypeptide chains

I.e.: Hemoglobin

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17
Q

Quarternary Structure of Proteins- Motifs

A

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
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18
Q

Quarternary Structure of Proteins- Domains

A

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

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19
Q

Fibrous Proteins- FUNCTION

A

Structural Support

External Protection

Flexibility

Shape

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20
Q

Fibrous Proteins- EXAMPLES

A

Collagen

Alpha-Keratin

Silk

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21
Q

Fibrous Proteins- Overall Arrangement

A

Polypeptide strands arranges in sheets or strands

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22
Q

Fibrous Proteins- STRUCTURE

A

One form of secondary structure (either alpha or beta)

Simple tertiary structure

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23
Q

Fibrous Proteins- SOLUBILITY

A

Contain hydrophobic residues for the most part therefore insoluble

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24
Q

Globular Proteins- FUNCTION

A

Enzymes

Motors

Regulation

Immunoglobulins

Transport

25
Globular Proteins- EXAMPLES
Hemoglobin Myoglobin
26
Globular Proteins- Overall Arrangement
Globular (good)
27
Globular Proteins- STRUCTURE
Mixed secondary and complex tertiary structures
28
Globular Proteins- SOLUBILITY
Soluble due to mix of hydrophobic and hydrophilic residues
29
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
30
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
31
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+)
32
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
33
Isoelectric Point (PI)
Proteins and some amino acids are electrically neutral PI= (pKa1 + pKa2)/2
34
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
35
Amino Acid Ionizable R Groups
``` Arginine Aspartic Acid Cysteine Glutamic Acid Histidine Lysine Tyrosine ``` COOH- usually around 2 NH3+ -usually around 8-9
36
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
37
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
38
Essential Amino Acids- Billy's Case
Val, Ile, Leu ---> cannot be synthesized by the body
39
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 ```
40
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
41
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 -->
42
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
43
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
44
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
45
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
46
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
47
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
48
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
49
What's wrong with JM?
high levels of IRT- immunoreactive Trypsinogen IRT normally produced by pan crease and elevated levels --> CF
50
Female Student Case
2 week history of severe frontal headaches, high fever, non productive cough, bone and muscle pain, abdominal discomfort
51
What's wrong with the female student?
Typhoid?? Elevated ALT and AST --> potential liver damage + for Salmonella No Change in patients conditions
52
Proteins for diagnostic tests- ALT
Alanine aminotransferase Liver enzyme Healthy Range 8-37 IU/L
53
Proteins for diagnostic tests- Albumin
Protein made by the liver Healthy Range: 3.9-5.0 Can indicate liver or kidney damaged
54
Proteins for diagnostic tests- A/G ratio
Albumin/globulin ratio Healthy ratio: bit over 1 Both found in the blood
55
Proteins for diagnostic tests- Alkaline phosphatase
Healthy range: 44-147 Enzyme involved in both liver and bone
56
Proteins for diagnostic tests- AST
Aspartate aminotransferase Healthy Range: 10-34 Enzyme found in heart and liver
57
Proteins for diagnostic tests- Bilirubin
Healthy Range: 0.1-1.9 Provides info about liver, kidney, bile ducts, anemia
58
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
59
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

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