week 2 Flashcards
What is the primary sequence of protein structure?
This is the most simple level of protein organization; the linear amino acid sequence
What is the secondary sequence of protein structure?
This allows for local folding, specific and more common structures include the alpha helix and the beta sheet
What is the tertiary protein sequence
This concerns the long-range folding, and the 3D structure of the protein
What is the quaternary structure of protein?
This is when there is more than one polypeptide chain
Describe an amino acid structure
- Proteins are comprised of amino acids
- They have an amino group, a carboxylic acid group, and a side chain/R group all attached to an alpha carbon
What is an R group?
The R group can have a multitude of variations depending on the acid. It is what differentiates each of the 20 amino acids
What are the 4 major categories of amino acids?
- Acidic
- Basic
- Nonpolar
- Uncharged polar
Where are polar amino acids found?
These are important for enzymatic amino acids
Where are nonpolar amino acids found?
They are found in the interior of proteins, and sometimes in lipid bilayers
Describe the structure of cysteine
Cysteine is considered nonpolar; it has sulfhydryl groups and can form disulphide bonds
What is a disulphide bond?
These are bonds that can form between polypeptides or intrachain. They are also found in the keratin in your hair/skin, due to the fact that they can be exposed to external physical/chemical stress
Where does the peptide bond occur?
They occur within the ribosome, there occurs a reaction between the carboxyl group of the first amino acid, and the amino group of the second one
What are the terminus’ of proteins?
There is the N-Terminus, which is the amino group, and the C-Terminus, which is the carboxylic end. The peptide bond formation can be shown through C-C-N
What is a residue?
An amino acid when is it connected to another amino acid by a peptide bond/peptide chain
- Since they’ve lost a water molecule through the formation of the peptide bond, they are no longer a full amino acid
What is Leu-Enkephalin?
It is a pentapeptide, in which its reversed composition does not have any pharmacological effect. This is demonstrated to show that the linear orientation of a
peptide is essential for the function of an amino acid
What is the alpha helix in terms of structure?
The alpha helix is found in cell membranes with a strong cylindrical structure, and it is about 10 residues long with an amino and carboxyl end
What makes the cylindrical form of the alpha helix?
The hydrogen bonding within other molecules (NOT THE R GROUPS) in the molecule. There is hydrogen bonding between the H from the amino and the O from the carboxyl group.
How does bonding occur in the helix?
It occurs like position n with n+4
The second residue bonds with the 6th residue, and so on.
What are the differences between the alpha helix and DNA?
- DNA is usually double stranded, whilst protein is single stranded
- In DNA, the bases are also usually inward, whilst the amino acid bases are pushed to the outside in the alpha helix, and the R groups are pushed to the inside
How are beta sheets formed?
Hydrogen bonding occurs between the carbonyl oxygen and the amide hydrogen in neighbouring strands, whilst in Alpha helices it occured 4 residues away
Why is it now carbonyl and amide in the beta sheet/alpha helix?
Due to the condensation reaction done to form the polypeptide, it turns carboxyl to carbonyl, and amino to amine
What is a similarity between beta sheet and alpha helix?
Their bonding both occurs between non-adjacent molecules
What are the two types of beta sheets?
Parallel and Anti-Parallel
- Depends on the configuration of the amino acid and carboxyl ends and their orientations
What is an amyloid?
Beta sheets can form strong rigid structures, such as ribbon diagrams where the sheets are stacked ontop of one another
What is a coiled coil?
It is an amphipathic type of alpha helix; and it has both hydrophilic and hydrophobic parts to it
What is the purpose of a coiled coil?
These coils wrap around each other so that they can minimize the exposure of the hydrophobic parts, and increase exposure of the hydrophilic
What is the tertiary structure?
This is the overall 3D structure of the protein, and it is held together by hydrophobic interactions, non-covalent bonds, and covalent disulfide bonds
What ensures that proteins can fold into the most energetically favourable conformations?
- In the backbone, hydrogen bonds are between atoms of peptide bonds, and they can also be present within the side chains
What are chaperone proteins?
Proteins will fold into the shape dictated by their amino acid sequence, but chaperone proteins make the process more efficient and reliable in living cells – they make sure that proteins fold in a reliable way
What is a protein domain?
These are regions of sequences that are able to fold up independently and create their own tertiary structure; they usually have their own specialized functions that can operate in a semi-independent matter
How many domains do eukaryotic proteins have?
Two or more domains connected by intrinsically disordered sequences
What are kinases?
These can phosphorylate proteins, and attached to them are kinase domains
What is a protein family?
They are groups of proteins with a common evolutionary origin; overall their functions are very similar, but they have evolved to have slightly different functions within a cell
What is the quaternary structure?
They consist of different polypeptide chains called subunits, and within a peptide, there can be a domain
What differs between a subunit and a domain?
A domain is a discrete function and/or structural section of a polypeptide. These are regions of sequences with their own functions.
This differs from a subunit, which is a single polypeptide in a protein which is in turn composed of multiple polypeptides. It is important to note that subunits can have domains.
What are scaffold proteins?
These are examples of multiprotein complexes; sometimes you need a scaffold protein as an entity that will bind different proteins and get them in close enough proximity for them to react
What is proteomics?
This is the large-scale study of proteins; how they interact and their locations etc. etc.
What exactly is a polypeptide?
The resulting chain of amino acids from linking them with peptide bonds
What are the L & D isomers of amino acids?
These are two isomers of existing amino acids. In the L isoomer, the carboxyl is on the right and the amino is on the left, whilst it is the opposite in the D isomer.
Which amino acids do proteins exclusively contain?
L-amino acids
What is special about cysteine?
A disulfide bond can form between two cysteine side chains in proteins
What is the polypeptide backbone made of?
A repeating sequence of C-C-N
How do electrostatic attractions assist in polypeptide formation?
It aids in protein folding
How does the hydrophobic force assist in determining the shape of a protein?
In an aqueous environment, hydrophobic molecules tend to be forced together to minimize their disruptive effect on the hydrogen bonded network of the surrounding water molecules; thus, a polypeptide is able to face polar amino acid side chains on the surface, whilst nonpolar ones are buried on the inside to form a tightly packed hydrophobic core on the inside
What helps a molecule stabilize its folded shape?
- Large numbers of hydrogen bonds within a protein molecule (backbone-backbone, backbone-sidechain, sidechain-sidechain)
What is renaturation?
A process whereby denatured proteins can refold spontaneously into its original conformation once the denaturing solvent is removed from a denatured protein
What is the role of an isolation chamber?
Some chaperone proteins act as isolation chambers that help a polypeptide fold; chamber caps are used so that the polypeptide chain can fold without aggregating with the crowded conditions of the cytoplasm
What is the role of a chamber cap?
This provides an enclosed chamber in which the newly synthesized polypeptide chain can fold without the risk of aggregating with other polypeptides in the cytoplasm
What are amyloid structures?
When proteins fold incorrectly, they sometimes form amyloid structures that can damage cells and even whole tissues; they are thought to contribute to a number of neurogenerative disorders such as Alzheimers
What are prions?
These are misfolded proteins that are able to convert the properly folded version of a protein in an infected area into the abnormal folded version
What is the difference between globular and fibrous proteins?
Globular proteins are which the polypeptide chain folds up into a compact shape, like a ball, with an irregular surface
Fibrous proteins have elongated, three dimensional structures that are long and narrow
What is alpha keratin?
Keratin filaments are fibrous proteins that are extremely stable, they are dimers of coiled coil regions
What are intermediate filaments
A component of the cytoskeleton that gives cells mechanical strength
Describe the formation of collagen
Collagen molecules consist of three long polypeptide chains, each containing the nonpolar amino acid glycine at every third position.
This allows the chains to wind around one another to create a triple helix with glycine at the core.
Collagen fibrils are very strong and help tissues hold together
What are covalent cross-linkages?
These linkages can either tie together two amino acids in the same polypeptide chain or join together many polypeptide chains in a large protein complex
What is a disulfide bond?
The most common covalent cross-links in proteins are sulfur-sulfur; they form disulfide bonds
These bonds help stabilize a favoured protein conformation
