Amino Acids and Protein Structure Flashcards
What are the two main functional roles of proteins in humans?
1.) Dynamic functions -ex: globular proteins (spherical) 2.)Structural proteins -ex: fibrous proteins (elongated)
The vast majority of types of protein
- small in abundance
- Spherical
Globular proteins
Small in number of types
- large in abundance
- Elongated
Fibrous (structural) proteins
What are three transport proteins?
1.) hemoglobin 2.) transferrin 3.) ion translocating ATPases
What are three types of gene expression proteins?
1.) Histones 2.) Polymerase 3.) Transcription factors
What are two proteins that function in the catalysis of Chemical Transformation?
- ) Glucose-6-phosphate dehydrogenase
- ) Pyruvate Kinase
- both are enzymes
Single base substitutions in DNA can cause disease by
Altering protein structure and function
What is the central dogma of molecular biology?
DNA —> RNA —> Protein
Sickle Cell disease is caused by a
Glutimate 6 is substituted with Valine
Amino acids can undergo post translational modifications to give far more than 20 types. What are some of the post translational modifications a.a.’s can undergo?
Methylation, formylation, adenylation, etc
Amino acids exist as zwitterions, meaning they are
Overall neutral, but have charges
What is the pKa of the amino group of an a.a.?
pKa = 9
What is the pKa of the carboxyl group of the a.a.?
pKa = 2
When pH = pKa, the ratio of protonated to deprotonated amino acid is?
[protonated] = [deprotonated]
Proteins are made up exclusively of
L-aminos
Generally toxic, but can exist in cell walls
D-aminos
To tell configuration, orient amino so you are looking down the H-C bond. For L-aminos, the R group should be
To the right of the COO-
What is the driving force in protein folding?
The Hydrophobic effect
The surface of a protein is not exclusively
Polar -will be a mixture of polar and nonpolar
The interior of a protein is almost exclusively
Hydrophobic side chains
A globular group of 100 to 300 amino acids
Domain
Out of the 100-300 a.a.’s making up a domain, how many are used for catalysis?
Typically less than a dozen.
-The rest serve structural purposes
The sulfur in Methionine is
Inert
The only achiral amino acid is
Glycine
Provides rigidity and stability to protein
-Only amino acid that occasionlly exists in the cis conformation (15%)
Proline
Proline is classified as an
imino acid
Aromatic a.a.’s can be on cell surface because of the enhanced stability resulting from
Aromaticity
In order to form, a hydrogen bond requires
- ) The right distance (3 Angstroms)
- ) The right geometry
The 6 neutral polar amino acids are perfect for
Post translational modifications
What three aminos are easily phosphorylated?
-readily reversible
Serine, Threonine, and Tyrosine
Add phosphate groups
Kinases
Remove phosphate groups
Phosphatases
Adding sugar to an amino acid
- creates hydrophilic surface of protein
- a great solubilizer
Glycosylation
What are the two types of glycosylation?
- ) O-linked (serine and threonine)
- ) N-linked (Aparagine)
Do not occur within cytoplasmic proteins because the cellular environment is highly reducing
-only occurs in oxidizing environments
Disulfide bonds
Disulfide bonds are not a driving force in
Protein folding
Disulfide bonds readily occur in
Extracellular proteins or domains
The inside of cells are reducing environments due to reducing agents such as
Glutathione
Has the only side chain that will cross-link protein chains together without the addition of post translational modifications
Cysteine
Contains 6 cysteines and three disulfide bonds
- 2 interchain
- 1 intrachain
Insulin
What is the pKa of the side chains of Glutamate and Aspartate?
pKa = 4
Great for the surface of a protein because they carry a -1 charge
Aspartate and Glutamate
What happens to the pKa of Asp and Glu’s side chains if it is unfavorable to deprotinate them?
-i.e. in the hydrophobic interior or if the two negative charges would be too close together
The pKa increases
-shows that pKa’s are actually variable
The pKa of glutimate increases when it is directly next to an
Aspartate
Which amino acid plays a role in metabolism as a nitrogen donor?
Glutamate
Why is Glutamate used to incorporate nitrogen into a molecule withing the cell?
Because ammonia is too toxic to be the donor
What is the functional group of the Histidine side chain?
imidazole
What is the functional group on the side chain of Lysine?
Amine
What is the Functional group on the side chain of Arginine?
Guanidinium
What aminos are always positively charged at physiological pH?
Lysine and Arginine
Amino with the only side chain whose pKa is close to physiological pH. Thus its protonation state varies in the physiological pH range
Histidine
A great way to regulate something by pH
-rare but a very important a.a.
Histidine
Occasionally involved in helping to scaffold the protein
Arginine (Arg, R)
Lysine’s and Arginine’s tend to pair with
Aspartate (Asp, D) and Glutamate (Glu, E)
Important for pH dependent regulation
Histidine’s
For an amino acid titration curve, the isoelectric point (IpH) is the
plateau between the two equivalence points
When looking at peptides, the biochemical unit is described as being made up of
a single amino acid
When looking at peptides, the structural unit is described as
The unit ranging from one alpha carbon to the next
What type of reaction is the peptide bond formation?
Dehydration
What are the characteristics of the peptide bond?
It is Rigid, Planar, and Polar
-has partial double bond character
Refers to the two alpha carbons of a structural unit being on opposite corners of the plane
trans configuration
15% of prolines are in the
cis configuration
Why is the trans configuration preffered in peptides?
cis configurations lead to steric hindrance
Specify the path of the polypeptide backbone
phi and psi angles
How many sets of phi and psi angles can repeat without steric collisions?
Two
The result of the fact that only two sets of φψ angles can be repeated without steric collisions is
The generation of the repetitive secondary structures:
- ) alpha helix (coiled chain)
- ) beta strand (extended chain)
Defined by covalent bonds including disulfide bridges
Primary structure
Defined by H-bonds
-alpha helix, beta sheet
Secondary Structure
The alpha helix is an example of a
Coiled coil
All of the carbonyls of an alpha helix point in the
Same direction
-give a net dipole
In an alpha helix, what is the charge of the
- ) C-terminus
- ) N-terminus
- ) negatively charged
- ) Positively charged
Help to minimize the polarity of an alpha helix
H-bonds within the backbone
In an alpha helix, every carbonyl oxygen and amine nitrogen are involved in an H bond. Where the nth atom binds to the
n+4th atom
What are the dimensions of an alpha helix
- 6 residues/turn
- 4 Å / turn
- 5 Å rise / residue
What are the three types of helices?
- ) hydrophobic
- ) Amphipathic
- one side of helix is hydrophobic and the other is polar - ) Polar
What are the three perpendicular directions of the beta sheet?
1.) directions of strands (polypeptide chain) 2.) H-bonds between strands 3.) Side chains above and below the plane of the sheet
Beta strands are connected with one another to form beta sheets by
H-bonds between strands
What are the dimensions of a beta sheet
~3.5 Å / residue
Cover twice the distance of an alpha helix
beta strand
What are the two types of beta sheets
Parallel and anti-parallel
Made up of alpha-beta motifs, where the beta sheets are connected by alpha helices
-this burries them in the interior
Parallel Sheet
What is the polarity and location of the Parallel beta sheet?
Hydrophobic and burried in the protein interior
What is the polarity and location of the anti-parallel beta sheet?
Amphipathic and exposed on the surface of the protein
Point alternatively above and below the plane of the beta sheet
Side chains
Non-repetitive secondary structures
- usually located at the proteins surface
- 50% of residues in globular proteins
Turns and Loops
Turns and loops often serve as
Binding surfaces and active sites
What are the most common secondary motifs in proteins?
1.) helix-loop-helix 2.) Greek key 3.) beta-alpha-beta
A very stable secondary fold
-direction of arrow points to C-Terminus
Greek Key
How can we connect two beta strands that lie parallel to one another?
With an alpha helix (beta-alpha-beta motif)
What forces stabilize proteins?
- ) Hydrophobic interactrions
- ) van der Waals Interactions
- ) Hydrogen Bonds
- ) Ionic Interactions
- ) Disulfide Bridges
What is an example of an ionic interaction that could help stabilize a protein?
Lysine interacting with an Arginine
The energy difference between a proteins folded and unfolded state is very
Small -
they are susceptible to denaturation
In order to function, proteins need to be
Dynamic (able to move)
Structural/functional units of 100-300 amino acids
- Typically globular units
- 10-30 kDa
- often contiguous in primary structure
Domains
Carries iron in a heme
-it’s helices are packed anti-parallel to one another
Cytochrome b562
Hard to classify as either hydrophobic or hydrophilic
Glycene’s
A popular example of the perpendicular packing of helices -1st protein structure to be successfully determined
Myoglobin
Made up of anti-parallel beta sheets which fold to create a hydrophobic interior and a hydrophilic surface
-it gets its name from its continuous wrapping sequence
Up-down beta barrel
Carries vitamin A around the body because vitamin A is completely insoluble in water
Retinol (an up-down beta barrel)
What is the difference between a transmembrane up-down barrel and a cellular up-down barrel?
The transmembrane barrel will be hydrophobic on the outside and hydrophilic on the inside
Found in the lense of your eye
-an example of a stable protein, it is not synthesized, so if you lose it, you go blind
γ-Crystallin
y-Crystallin is an example of a
Greek key barrel
Get’s rid of oxygen radicals in the body
Superoxide dismutase
What is the most common fold in the human body?
- a parallel beta barrel in the center
- layer of protective Amphipathic alpha helices on the outside
- goes beta-alpha-beta-alpha
α/β Singly Wound Barrel
In the α/β Singly Wound Barrel the helices are
Amphipathic, outside is polar, inside is non polar
Don’t really form barrels
-Stay as flat/twisted sheets with alpha Helices on either side
Doubly Wound α/β
What is this structure?
Up-Down β Barrel
What is the difference between these two Up-Down β Barrels?
Retinol is cellular, Phosphorin is transmembrane
Which motif is represented here?
Greek Key Barrel
Which structural motif is represented here?
anti-parallel beta barrel
Which structural motif is represented here?
α/β Singly Wound Barrel
Which structural motif is represented here?
α/β Singly Wound Barrel
Which structural motif is represented here?
Doubly Wound α/β
