Chapter 2, Structure of Protein Flashcards
The N-terminal of a peptide chain is written to the (L/R) and the free carboxyl to the (L/R).
N-terminal – Left
free carboxyl – Right
Formation of the peptide bond is a _________ reaction, as it entails the loss of a water molecule.
condensation
Peptide bonds are examples of amide bonds and cleavage of them requires a molecule of water (hydrolysis). Peptide bonds are considered strong _________ bonds (not easily cleaved).
covalent
Peptide bonds can be seen as how many resonance isomers?
2
(C=O double bond with a C-N single bond) or
(C=N double bond with partial charges at NH and O)
Describe the rotation around the peptide bond.
There is a restriction of rotation.
Describe the polarity and charge of the -C=O and the -NH groups of the peptide bond.
Polar, but uncharged.
If you have 10 amino acids attached by peptide bonds, the 8 in the middle would be ________ and the 2 on the ends would be ________.
(charged or uncharged)
8 in the middle - uncharged
2 on the end - charged
*The minimum number of charged will be 2, but the maximum depends on the R groups.
Each individual amino acid in a peptide is called a….?
residue
Peptides with 10 to 100 amino acid residues are called _________ while those with greater than 100 amino acid residues are called ________.
10-100, polypeptides
>100, proteins
What is the largest human protein?
titin
Which structure is defined as different types of local confirmations, stabilized by hydrogen bonding?
Give two examples.
Secondary (alpha helix and beta sheets)
What is the average length of an alpha helix?
10 residues
Naturally occurring alpha helices are coiled in a ______-handed manner with each turn corresponding to how many residues?
Right-handed, 3.6 residues per turn
Which structure is the linear sequence of amino acids?
Primary
The alpha helix is stabilized by intrachain _________ bonds between the carbonyl of a peptide bond and the -NH of a peptide bond located how many amino acid residues along the polypeptide chain?
hydrogen bonds
four amino acid residues
Which amino acid is often known as the “helix breaker” because of it’s size and chemistry which induces distortion in the direction of the helical axis?
Proline (amino and imino acid!)
In beta sheets, all peptide bonds participate in hydrogen bonding, which run _________ to the axis of the polypeptide.
perpendicular
In beta sheets, separate neighboring polypeptides are aligned in a _________ or ________ orientation.
parallel or anti-parallel
Pleating of the beta sheets (accordion folding) serves to optimize inter-chain or intra-chain ________ bonding.
hydrogen
Alpha helices and beta sheets are found in what two types of proteins?
fibrous and globular
What is the typical length of a beta sheet?
3-10 amino acid residues
Non-repetitive secondary structures include bends, forms, and loops which possess a less regular structure relative to alpha helices or beta sheets. Disordered regions can assume a more organized structure upon the binding of a specific ________.
ligand
Supersecondary structures, which are referred to as \_\_\_\_\_\_\_\_\_, are protein structures that contain at least 2 adjacent units of secondary structure. Examples include: Helix-loop-helix Beta-meander Beta-barrel Alpha-helix-hairpin Beta-hairpin
Motifs
Peptide bonds in proteins:
- _________ double-bond character
- Rigid and planar
- ______ configuration
- Polar uncharged
*Partial
*
*Trans
*
The folding of the protein domains into a 3-dimensional formation.
Tertiary structure
Basic functional and 3-dimensional units of a polypeptide that are constituted from combinations of super-secondary structural motifs to create independently folding, self-stabilizing regions of the polypeptide chain.
Domains
Which regions of the gene can domains be associated with?
exons
What are the four types of chemical interactions that can cooperate in the stabilization of tertiary structures?
- Disulfide bonds
- Hydrophobic interactions
- Hydrogen bonds
- Ionic interactions
* Disulfide are the only covalent bonds
The significance of relatively weak noncovalent interactions, is that they allow for both easy _________ and _________ of bonding.
association and disassociation
If a protein will remain in the cytoplasm, it will not have this. But if the protein is in the ER, lysosome, membrane, or being secreted, it probably will have this. What are we referring to?
disulfide chains
EXTRAcelluar mammalian proteins generally contain disulfide bonds (________), while INTRAcellular proteins contain _________.
EXTRA - cystine
INTRA - cysteine
Protein folding is an “all or none” process characterized by _________ transitions.
cooperative
Protein folding occurs by what?
progressive stabilization of intermediates
Proper folding can also be dependent upon other factors such as surrounding water or lipid molecules or molecular chaperones which are also known as what?
heat shock proteins
Protein folding is extremely fast, occurring spontaneously, even in test tubes. What are the problems associated with this?
- High intracellular protein concentration creates problem of hydrophobic aggregation.
- Unfolded proteins also susceptible to proteinases.
Protein denaturation is caused by the disruption of which structures of the protein?
secondary and tertiary
Denatured proteins adopt a confirmation known as a _______ _______. These proteins are usually (soluble/insoluble).
random coil, insoluble
The structure of a protein that involves the association of 2 or more polypeptide chains, either identical in sequence, or different, to form a protein complex.
Quaternary structure (When the tertiary chains come together) *This is the actual, functional protein
What type of structures are found in chromosome and viruses?
Supra-quaternary
In hair curling, the keratin molecules are first ________ which ruptures the stabilizing disulfide crosslinks. Then, the addition of ________ agents, reforms the disulfide bonds into their new (curled) position.
- first reduced
* then oxidized
The thiol (sulfhydryl) group in cysteine can bind different _________.
metals
Protection against intracellular insults offered by:
- Protein disulfide isomerases
- Ubiquitin-proteasome… Proteins selected for degradation are tagged with ________, a small globular protein. They are recognized by the cytosolic proteasome, which will initiate their degradation.
- Chaperones (heat shock proteins)
a. Prevent premature _________.
- ubiquitin
3a. folding
Unnecessary, damaged, misfolded, or dysfunctional proteins originating from inside the cell are usually degraded by the _________.
proteasome
Another class of chaperones, known as _________, are barrel-like structures in which the nascent protein is situated as it folds. The inner wall of this barrel-like structure is actually lined with hydrophobic amino acids. Both of these are known as heat shock proteins.
chaperonins
