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Protein Structure and Function: Biochemistry Exam 1
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1Levels of protein folding
Primary- amino acid sequence
Secondary- alpha helicies and beta sheets
Tertiary- domain made up of subunits of alpha and beta sheets bound together
Quarternary- one or more domains form a single polypeptide chain
Protein- two or more domains forms an active protein molecule
19 amino acids excluding ([blank_start]glycine[blank_end]) have the same structure other than their R groups
In nature, all amino acids are [blank_start]L[blank_end]-isomer amino acids
CORN rule- with Hydrogen coming towards you
clockwise= [blank_start]D[blank_end]
Counterclockwise= [blank_start]L[blank_end]
All reactions in the human body are [blank_start]stereospecific[blank_end] meaning stereochemistry is crucial
example is Thalidomide which gave birth defects in Germany due to R enantiomer
In the body's neutral 7.4 pH, amino acids exist as [blank_start]dipolar[blank_end] ions or Zwitterions
Aliphatic amino acids have no reactive groups in their R group and are therefore [blank_start]hydrophobic[blank_end]
Hydroxyl Amino acids [blank_start]Serine[blank_end] and Threonine can both act as H- bond donors and also acts as a nucleophile
Aromatic Amino Acids Phenylalanine, Tyrosine, and Tryptophan (largest AA) have three general properties
1. Very [blank_start]hydrophobic[blank_end]
2. A methylene spacer
3. Give rise to UV absorbance around [blank_start]280[blank_end] nm
Sulfhydryl Amino Acids Cysteine, and Methionine
cysteine can be a H-bond donor or acceptor. In extracellular proteins Cysteine can form a covalent bond with another Cysteine making a [blank_start]disulfide[blank_end] bond (only one capable of doing this)
Met is predominantly hydrophobic and therefore unreactive
Acidic Amino Acids Apartic Acid and Glutamic Acid
-Can act as hydrogen bond donors or acceptors
Amide Amino Acids Asparagine, Gluatmine
-Can act as hydrogen bond donors or acceptors
Basic Amino Acids Lysine and Arginine
Can form [blank_start]salt bridges[blank_end] with Aspartic and Glutamic Acid
Essential Vs. Non-Essential Amino Acids
Essential AA- are [blank_start]required[blank_end] in the diet because they cannot be made by the body naturally
Non-Essential- 11 amino acids are made naturally in the body if not in the diet
Amino Acids are linked via [blank_start]peptide[blank_end] bonds (bond from Nitrogen to carbonyl)
Peptide bonds are formed via a dehydration reaction
Peptide bonds have a partial [blank_start]double[blank_end] bond character due to resonance and are geometrically [blank_start]planar[blank_end]
A peptide bond is [blank_start]shorter[blank_end] than a normal C-N bond
Due to repulsion, many peptide bonds favor the [blank_start]trans[blank_end] conformation
Angles phi and psi are dihedral [blank_start]torsional[blank_end] angles which determine the conformation of the polypeptide
Which bonds can be synthesized with little cost to the body and are very stable thus giving better fitness evolutionarily?
-[blank_start]Amide[blank_end] bonds
Ramachandran and colleagues plotted the values of phi and psi on their Ramachandran plot
What effect does proline have on the conformation of a polypeptide and the AA adjacent to it?
-Proline is good for accommodating [blank_start]bends[blank_end] and turns in proteins making a compact and extended form which are similar energetically
Proline is the only amino acid that favors the [blank_start]cis[blank_end] conformation due to less steric hinderance
Secondary Structure of Proteins
1. Alpha helix
35% of all AA in globular proteins are Alpha helix
Peptide bonds have a dipole and when in Alpha helix the dipoles form a larger dipole called the [blank_start]Macrodipole[blank_end] which allows for the aloha helix to bind charged molecules
In the Alpha helix the ([blank_start]i+4[blank_end]) rule indicates that the backbone carbonyl Oxygen H-bonds with the NH of the residue 4 up.
H-bonds in the alpha helix are almost straight and parallel to helix axis
Side R group Chains project [blank_start]out[blank_end] from alpha helix
Where does alpha helices fall in the Ramachandranplot?
-very [blank_start]bottom[blank_end] two spots
2. Beta Sheets
15% of AA in globular proteins are beta sheet structure
Beta strands are only stable when incorporated into a Beta sheet so that it can hydrogen bond to peptide groups on the other Beta strand
2 Types of Beta sheets however both have Hydrogen bonds that occur in Pairs & have side R groups pointing out
[blank_start]Parallel[blank_end] Beta sheets
Antiparallel Beta sheets
Bends and Turns in Secondary Structure of Proteins
To connect alpha helices to Beta strands and alpha to alpha you need a bend or a turn
These bends and turns follow the ([blank_start]i+3[blank_end]) rule where the C=O H-bonds to the H-N up 3 residues
Which amino acids are found in turns?
-[blank_start]glycine and proline[blank_end] (alphabetical order)
3. Tertiary structure
the Tertiary structure is essentially a Domain which is specific Alpha helices and Beta sheets connected that for a distinct unit
Domains are stable and can fold independently
Example of a Domain would be the [blank_start]NAD[blank_end] bind site domain
The using gene fusion and gene [blank_start]duplication[blank_end] and theNAD binding site, allows for making a variety of proteins with differing functions
4. Quarternary Structure of Proteins
-Made up of one or more domains which makes a single polypeptide chain which is called a [blank_start]subunit[blank_end]
-2 or more polypeptide chains makes an active protein
The subunits can be identical "[blank_start]homo[blank_end]" or different "[blank_start]hetero[blank_end]"
Post Translational Modification of Proteins
Glycosylation- describes adding a sugar to an Amino Acid
ABO blood groups differ in their type of linked glycosylation
Blood Type [blank_start]O[blank_end]- does [blank_start]not[blank_end] elicit Antibody formation
Blood Types A & B- do elicit Antibody formation
Phosphorylation- describes adding a phosphate group to an Amino acid via an [blank_start]ester[blank_end] bond linkage
Blood Clotting: Carboxylation of Glu Residues
Vitamin [blank_start]K[blank_end] is needed solely for this carboxylation to allow for Blood clotting in the body
Warfarin and Cumanin are carboxylumineles which act as anticoagulants by decarboxylating the Amino Acid
Collagen- found in ligaments and blood vessels, insoluble.
Hydroxylation- describes the addition of an OH group to an Amino Acid (Proline or [blank_start]Lysine[blank_end])
-hydroxylation is important for [blank_start]stabilizing[blank_end] the triple helix of collagen
-To hydroxylate the Proline and Lysine the body must have ascorbic acid aka. Vitamin [blank_start]C[blank_end] which makes collagen [blank_start]insoluble[blank_end] by making crossed linked and staggered fibers of protein
-Improper hydroxylation of Proline and Lysine causes a rare [blank_start]stretchy[blank_end] skin disorder- Aglycine
- BL
- CD
- DL
- Estereospecific
- Fdipolar
- Ghydrophobic
- HSerine
- Ihydrophobic
- J280
- Kdisulfide
- Lsalt bridges
- Mrequired
- Npeptide
- Odouble
- Pplanar
- Qshorter
- Rtrans
- Storsional
- TAmide
- Ubends
- Vcis
- WMacrodipole
- Xi+4
- Yout
- Zbottom
- AAParallel
- ABi+3
- ACglycine and proline
- ADNAD
- AEduplication
- AFsubunit
- AGhomo
- AHhetero
- AInot
- AJO
- AKester
- ALK
- AMLysine
- ANstabilizing
- AOC
- APinsoluble
- AQstretchy
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- Quiz on Protein Structure and Function: Biochemistry Exam 1, created by Paul Videau on 27/09/2016.
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- Paul Videau
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