Protein Structure Flashcards
What is the structure of proteins?
polymers of covalently joined amino acids
What are the components of amino acids?
- a central carbon atom
- an amino group
- a carboxylate group
- a side chain, which differs in each of the 20 types of amino acid
What is amphipathic?
having both hydrophobic and hydrophilic characteristics
What can sulfhydryl (-SH) groups form?
on cysteine can form covalent bonds with one another to make disulfide bridges
What do all amino acids exist as?
two stereoisomers, L and D, depending on the arrangement around Ca
What are found naturally in occuring proteins?
L-amino acids
T or F: glycine exist as two stereoisomers
false
What is the pKa of histidine?
close to the neutral pH of a cell, so it can act as a H+ donor or acceptor during biological reactions
What is a peptide bond?
results from a condensation reaction between the carboxyl group of one amino acid and the amino group of another amino acid
What are incorporated amino acids called?
amino acid residues
What forms the peptide backbone?
a repeating series of C and N atoms form the peptide backbone, with side chains protruding
What is the N-terminus?
the end of a polypeptide with an exposed amino group
What is the C-terminus?
the exposed carboxyl at the other end
How are residues in a polypeptide numbered?
from the N-terminus
Why do polypeptide chains have limited conformations?
resonance
What prevents free rotation of the peptide bond?
electrons shared between O, C, and N
What is the shape of a peptide bond?
planar
What are the parts of the polypeptide that can still rotate:
- the N-Calpha bond has rotation angle
- the C-Calpha bond has rotation angle
What do different angle combinations cause?
collisions of side chains or the polypeptide background: these angle combinations do not occur
What is the function of a Ramachandran plot?
indicates the restricted conformation
What does each point on the plot show?
a combination of angles
What do black regions on the plot show?
where clashes do not occur
What do gray regions on the plot show?
minimal clashes
What does the plot depend?
the amino acid residues in the polypeptide (e.g. glycine side chain is small (a single -H) so can tolerate many more angles combinations than other residues)
What is the primary structure?
the amino acid sequence
What is the secondary structure?
refers to localized regions of repeated regular structures such as beta-strands and alpha-helices
What are tertiary structures?
the final folded structure of a single polypeptide (3D)
What are quaternary structure?
the combination of multiple polypeptides in a single protein (many only have one)
What occurs in alpha-helices and beta-sheets?
H-bonding between the C=O group of one peptide bond and the N-H group of another
What are the characteristics of an alpha helix?
3.6 amino acids per turn and diameter of 12 A (similar to DNA major groove)
Where are the side chains of an alpha helix?
the side chains protrude outward from the alpha helix interact with proteins, nucleic acids, etc.
What disrupts an alpha helix?
proline
What does antiparallel mean?
N termini at opposite ends
What does parallel mean?
the same end
How are beta sheets formed?
when peptide backbones (beta strands) hydrogen bond to one another through their carbonyl and amino groups
What is the shape of beta sheets?
slightly twisted, largely planar
Where are side chains located in beta sheets?
above and below the plane of the beta sheet
Where are amphipathic sheets found?
at protein surfaces
What determines local secondary structure formation?
amino acid composition
What amino acids are often found in helices?
leucine, methionine, glutamine, and glutamic
What amino acids are often found in beta sheets?
valine, isoleucine, and phenylalanine
What amino groups often found in beta turns?
glycine and proline
Why does proline have an unusual structure?
introduces kinks in the polypeptide chain
Why does glycine have an unusual structure?
has a very small side chain (-H) and so is very flexible
What drives protein folding?
hydrophobic interactions
How do hydrophobic residues interact?
preferentially associate with each other and exclude water molecules; most polar residues are on the exterior of the folded protein
How can proteins be unfolded and refolded?
by changing conditions (e.g. heat, detergent, solvent), and when restored to native conditions
What is an example of a protein that cannot be re-nature?
albumin
T or F: secondary structures can be fairly reliably predicted
true
T or F: tertiary structures can be fairly reliably predicted
false, very complex and cannot be predicted from primary sequence de novo
How are protein structures predicted?
conservation of amino acid sequence enables prediction based on known structures
How do proteins share similar structures
proteins share similar and identical amino acids
What percent yields fairly similar structures?
25% sequence identity
What are similar amino acids?
amino acids that have small changes (letter changes) in amino acid sequence
How is the function of newly identified genes predicted?
based on the amino acid sequence it encodes
What percent of similarity indicates similar structure and function?
> 25%
What is a strong indicator of similar function?
conservation of critical amino acids
What is a domain?
a compact region of a polypeptide than can fold on its own
T or F: proteins can have multiple domains?
true, domains fold independently and carry out specific functions
What are proteins comprised of?
domain “modules”
What is the structure of proteins?
modular
What are motifs?
stereotypical combinations of 2 degree structures
What are motifs associated with?
specific amino acid sequences that make specific contacts with each other or ions that coordinate charges
What is the structure of secondary amphipathic structures?
having a hydrophilic and hydrophobic surface, enabling interactions with other such structures
Where is the “recognition” helix located?
lies in the major groove of DNA and makes H-bonds with base groups
What is the function of other parts of a protein binding to DNA?
make non-specific contacts with the DNA backbone that facilitate finding the specific sequence, and stabilize binding
What do many proteins bind to DNA as?
dimers that interact with DNA sequences separated by approximately one turn of the NA helix
What forms a zinc-finger?
two cysteines and two histidines coordinate a Zn ion to form a finger
What does each finger recognize?
~3bp of DNA in a sequence-specific manner
Why do chemical groups vary more in the major groove than in the minor groove?
because T-A and A-T are the same, and G-C and C-G are the same, so these can’t be distinguished by binding proteins
What type of bonds do DNA-binding proteins form?
non-covalent interactions with exposed groups
What varies in different DNA sequences?
different combinations of hydrogen, bond acceptors, hydrogen donors, and methyl groups available
What is interaction specificity determined by?
specificity between protein and DNA is determined by the DNA sequence and the protein shape/ available binding groups
How many bonds can Asparagine form with an A?
two hydrogen bonds with an A
What covalent modification of amino acid side chains can act as a “switch”?
phosphorylation, acetylation, and methylation
What happens when covalent modification of amino acid side chains act as a switch?
results in allosteric change in the protein. Alternatively, the modification may directly effect ligand binding cooperative interactions
What is ubiquitin?
small protein (7 kDa) that may be covalently linked to lysine
What is the function of mono-Ub?
regulates activity
What is the function of poly-Ub?
targets the protein for rapid degradation
What is SUMO?
small ubiquitin-like modifier
What is the function of glycosylation?
adds bulky carbohydrate groups, altering their surface structures. Very common in membrane and secreted proteins
Are hydrophobic groups reactive?
No, hydrophobic groups are essentially non-reactive
What is the function of the sulfhydryl (S-H) group in R group covalent formation?
can form disulfide bond with another cysteine (usually in the same protein)
What is the function of hydroxyl groups (serine, threonine, tyrosine) in R group covalent formation?
react to form O=-linkages, including phosphorylation and glycosylation
What process can the amine group of asparagine undergo?
glycosylation
What process can the amino group of lysine undergo?
methylation, acetylation, or ubiquitylation
What is phosphorylation?
a reversible modification that alters the protein function
What is the major donor for phosphorylation?
ATP
What is the function of protein kinases?
catalyze phosphate addition
What is the function of protein phosphatases?
catalyze phosphate removal
What is the role of hydrolysis of the phosphoanhydride bonds of ATP?
as pyrophosphate, it provides much of the free energy needed for many enzymatic reactions
What are the three characteristics of ATP?
- major phosphate and adenylate dono in the cell
- building block in RNA and the precursor of dATP
- major allosteric regulatory of many proteins. May involve binding of ATP only, or binding and hydrolysis of ATP
