8: proteins Flashcards
(23 cards)
What is translation?
– Translation is the process of translating the mRNA “language” into something the cell can use - that of a protein.
What is a proteome?
– The proteome is the full complement of proteins expressed by an individual’s tissue, cell, or organism at a particular time
What is the structure of proteins?
- Proteins are polymers (chains of repeating, similar subunits called monomers)
- the monomers are amino acids
- chains of amino acids are called polypeptides
What is the structure of amino acids?
- functional groups: an amino group (NH2), a carboxyl group, and a variable R group that varies from one amino acid to the other
- the centre of the amino acid is an asymmetric carbon called the alpha (a) carbon with a H attached
How are amino acids bonded?
– peptide bond: a dehydration reaction that extracts a water molecule as it joins the amino group of one amino acid to the carboxyl group of another amino acid
What determines the function of proteins?
– The order and properties of amino acids (R side chains) determine the shape which determines function.
What are the different types of amino acids?
- Non-polar amino acids: have hydrophobic R groups
- Polar amino acids: have hydrophilic R groups
- Charged amino acids: have positively charged (basic) or negatively charged (acidic due to carboxyl group) R groups
What is the native confirmation of a protein?
- The shape into which a protein naturally folds is known as its native conformation.
- When a protein is in its native shape, it’s in a low energy state –it can go into a higher energy state by unfolding or interacting with a phosphate group, acetyl group, etc (post-translation modifications). It can also go into a higher energy state by misfolding (prion)
What are prions?
- Errors in finding a native conformation, due to heat or interference from other molecules can occur
- Proteins naturally go through confirmational changes, as long as they can return to their low energy native conformation. If they get stuck into higher energy state, it will lose its normal activity and can become pathological
- These often result in at best non-functioning proteins, and at worst dangerous prion-like proteins or Alzheimer’s-like plaques.
- Abnormal proteins causes normal proteins to refold into an abnormal confirmation and they can accumulate and cause damage.
- Over time, the clumps grow larger and destroy nerve cells leading to progressive neurological symptoms
What is the PrPc protein and its prion?
- One that is largely a-helical (PrPC) -native
- One that is largely b-sheet (PrPSc) - infectious
- When a protein becomes pathological, those a-helical shapes will go to largely b-sheets and make the proteins thermodynamically unstable
- PrPSc can induce an identical b-sheet conformation in PrPC and, in doing so, begins a self-perpetuating propagation process that results in pathology (PrPSc will alter other, native confirmation proteins and cause it to misfold)
- thus, PrPSc results in a disease state due to the change in secondary structure (from mostly alpha to mostly beta)
What is the primary structure of a protein?
- Based on sequence of amino acids
- Sequence is important because it will determine the types of interactions seen in the protein as it folds
- Not only are the amino acids important but also the order in which they are sequenced
What is the alpha-synuclein protein and its mutation?
- A 140-amino-acid protein
- Two mutations have been discovered contributing to early-onset (EOPD) Parkinson’s
- In the A53T mutation, threonine is substituted for alanine at residue 53 (alanine is non-polar and is switched out to threonine which is polar)
- Alpha-synuclein protein misfolds and accumulates in neurons leading to pathology.
What is the secondary structure of proteins?
– Secondary structure includes α-Helixes and β-sheets.
» a-helix (H-bonding between every fourth amino acid) and b-pleated (H-bonds between two or more segments of the polypeptide chain that lay side by side)
» α-helices are the most common secondary structure in proteins
– Secondary structure gives stability to the protein and will help beget the tertiary structure its native conformation (the a-helices will help maintain the hydrophobic and hydrophilic amino acid side chains in a particular order that will allow it to be thermodynamically stable)
What is the tertiary structure of a protein?
– Has a single polypeptide chain “backbone” with one or more protein secondary structures
– The interactions and bonds of side chains within a particular protein determine its tertiary structure.
» Amino acid side chains may interact and bond in a number of ways
– Most proteins take on a globular structure once folded
» The globular proteins generally have a hydrophobic core (amino acids with non-polar side chains forming van Der Waals attractions in the middle of protein) surrounded by a hydrophilic outer layer (amino acids with polar or charged amino acid side chains that form ionic bonds and disulphide bridges)
» Disulfide, (S-S) covalent linkages between adjacent cysteine monomers with sulfhydryl (SH) R group
» ionic bonds between the negatively charged carboxyl group and positively charged amino group
What is the structure of inter membrane channels/receptors?
- Tertiary structure with hydrophobic core and hydrophilic surface and quaternary structure with hydrophilic core and and hydrophobic surface
- Hydrophobic part of the protein (quaternary) imbedded in the lipid bilayer and hydrophilic part of protein sticking out and interact
- When a NT binds to its receptor, it causes the protein to open up –in this case it opens up a water liking channel and water flows through and carries an ion with it (causing change in membrane potential)
What is the quaternary structure of proteins?
- The quaternary structure refers to how these protein subunits in their tertiary structure interact with each other and arrange themselves to form a larger protein complex.
- These subunits may be the same (as in a homodimer) or different (as in a heterodimer).
- Many proteins are made up of multiple polypeptide chains, often referred to as protein subunits.
- The final shape of the protein complex is once again stabilized by various interactions, including hydrogen-bonding, van Der Waals and salt bridges
What is the structure of the GPCR?
– Three-dimensional structure of a G protein-coupled receptor (GPCR) embedded in a cell membrane, with its loosely attached G protein, consisting of three subunits: alpha, beta and gamma
What happens when a ligand binds to GPCR?
- When a neurotransmitter, hormone or other ligand binds, the receptor changes shape to catalyze the exchange of guanosine diphosphate for guanosine triphosphate (GTP) from the alpha subunit.
- When GTP (guanosine triphosphate) binds, the alpha subunit breaks apart from the beta and gamma subunits
- The subunits then interact with other intracellular proteins to transmit signals down two independent pathways.
How do proteins fold?
- Many proteins fold unassisted (through the chemical properties of their amino acids)
- Others require the aid of post-translational modifications or molecular chaperones to fold into their native states
What are posttranslational modifications and the different types?
– Increases the functional diversity of the proteome by the covalent addition of functional groups or proteins, proteolytic cleavage of regulatory subunits or degradation of entire proteins
» Phosphorylation
» Glycosylation
» Disulphide bridge
» Acetylation
– A NT binding to a receptor kind of serves like a post translational modification
What is acetylation?
– adds an acetyl group to the N-terminus of a protein or at lysine resides
What is phosphorylation?
- adds a phosphate group to serine, threonine, or tyrosine
- regulation of cell cycle, growth, apoptosis and signal transduction pathways
- Phosphorylation causes conformational changes in proteins that either activate or inactivate protein function.
- Protein kinases mediate phosphorylation (via ATP) and phosphatases reverse protein phosphorylation by hydrolyzing the phosphate group
- ex. when CREB is phosphorylated, it undergoes a confirmational change (turns on)
What is glycosylation?
- attaches a sugar, usually to an “N” or an “O” in an amino acid side chain
- effects on protein folding, conformation, distribution (will dictate where the protein will go -delivery mechanism), stability and activity
- In the ER, glycosylation is used to monitor the status of protein folding, acting as a quality control mechanism to ensure that only properly folded proteins are trafficked to the Golgi
- Sugar moieties on soluble proteins can be bound by specific receptors in the trans Golgi network to facilitate their delivery to the correct destination
- If a protein is misfolded, it can be glycosylated and help fold the protein in its proper confirmation
- If a protein is phosphorylated into a higher energy state, glycosylation can help return it to its proper native confirmation
