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Flashcards in Protein Structure And Function Deck (59):
1

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

2

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-

3

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

4

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

5

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)

6

Acidic Side Chains

-fully ionized at physiological pH

Aspartic Acid (Asp)
Glutamic Acid (Glu)

7

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

8

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

9

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

10

Primary Structure of Proteins

Sequence of Amino Acids in proteins --> determined by mRNA
Includes covalent bonds (peptide and disulfide)

11

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

12

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

13

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

14

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

15

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

16

Quaternary Structure of Proteins

Arrangement of 2 or more polypeptide chains
I.e.: Hemoglobin

17

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

18

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

19

Fibrous Proteins- FUNCTION

Structural Support

External Protection

Flexibility

Shape

20

Fibrous Proteins- EXAMPLES

Collagen

Alpha-Keratin

Silk

21

Fibrous Proteins- Overall Arrangement

Polypeptide strands arranges in sheets or strands

22

Fibrous Proteins- STRUCTURE

One form of secondary structure (either alpha or beta)
Simple tertiary structure

23

Fibrous Proteins- SOLUBILITY

Contain hydrophobic residues for the most part therefore insoluble

24

Globular Proteins- FUNCTION

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