Day 3: Amino Acids and Peptides Flashcards
What are the three options for the use of Amino Acids (AA) in our body?
- synthesis of protein and peptides. AA’s are the building blocks of proteins
- Synthesis of essential nitrogen containing biomolecules
- AA (protein) cant be used as fuel directly. During starvation, some AAs can be converted to glucose or ketone bodies to be used by cells as a source of energy
What is the bodies more perferred fuel?
Glucose: comes from carbs in diet like starch, sucrose, lactose
When low glucose the body burns fat as fuel
Can our brain use dietary fats as fuel?
No, it cant. so during starvation, some AAs are converted to glucose, fat and some AAs convert to ketone bodies to meet energy needs of the brain.
Can protein drugs be delivered orally?
No, it will get broken down into single amino acids by our GI system before being absorbed by our body
What are proteinogenic amino acids?
All the proteins in eukaryotes are composed of 20 different amino acids known as standard amino acids
**The name means that they are present in AA
What is the chirality of standard amino acids?
they are all chiral expect for glycine
what are human proteins composed of?
L-amino acids, no exeptions
What are proteases?
a group of enzymes whose catalytic function is to hydrolyze (break down) proteins by breaking the peptide bonds
also called proteolytic enzymes or proteinases
What are the two main groups and the subgroups of amino acids?
Main groups: Hydrophobic and Hydrophilic
Subgroups: Charged, Aromatic, Sulf-containing, branched-chain
What are the charged amino acids?
Negative: Aspartic acid, Glutamic acid
Positive : Lysine, Histidine,, Arginine
What are the polar amino acids?
Polar (hydrophilic): Tyrosine, Serine, Cysteine, Threonine, Asparagine, Glutamine
What are the Non-Polar amino acids?
Non-polar (hydrophobic): Glycine, Alanine, Valine, Leucine, Tryptophan, Methionine, Isoleucine, Proline, Phenyl alanine
What are the branched-chain amino acids?
Valine, Leucine, Isoleucine
BCAAs: May be useful supplement for muscle recovery and immune upregulation
What are the Aromatic amino acids?
Phenylalanine, Tyrosine, Tryptophan
What are the Sulfur-containing amino acids?
Cysteine, Methionine
What is Protein Phosphorylation? (Phosphorylation of amino acids)
One of the most important modes of regulation of protein function. (phosphoregulation)
almost all cases of phosphoregulation, the protein switches between active and inactive form.
What are the three amino acids that can be phosphorylated at hydroxyl residue
Serine, tyrosine (major), throenine
What are residues?
Amino acids that make up, or that are derived from a polymer
Direction is always N-terminal to C-terminal
What is a dipeptide?
Contains 2 residues
What is a tripeptide?
Contains 3 residues
What is an oligopeptide?
contains a few residues
What is a nonapeptide?
An oligopeptide containing nine amino acid residues
ex: oxytocin
what is a polypeptide?
Contains many residues
What is a protein (in terms of residues)
Has many residues (have defined 2D and 3D structure, usually ~40+
What are disulfide bonds?
These bonds between cysteine residues play a major role in the corsslinking folding and stability of the proteins
These protein crosslinking increases the rigidity, functions and proteolytic resistance
What is the ioselectric point (pI) of amino acids, peptides, and proteins
its when they carry no net electrical charge (equal numbers of + and - charges).
EX: if a peptide have 2 + and two - charges, overall charge is 0
What kind of charge do AAs / peptides / proteins carry at a pH value below the pI
A net postive charge
What kind of charge do AAs / peptides / proteins carry at a pH value above the pI
a net negative charge
Why do you want to know the values of peptides?
can be utilized for protein and peptide isolation, identificationa nd delayed absorption
When are peptides and proteins least soluble in water and whats the clinical implication of this?
At their isoelectric points
A peptide with pI 6 will be less soluble than a peptide with a pI 5 at pysiological pH (7.3)
Clinical implication: Long acting insuline Glargine; added modifications which lead to a shift of the pI from pH 5.4 to pH 6.7, making insulin glargine less soluble at physiological pH levels. This retarded its absorption and thereby extended its duration of action
What is an essential amino acid and which ones are they?
Cannot be synthesized in our body
valine, lysine, typtophan, leucine, methionine, phenylalanine, isoleucine, threonine, hisidine
9 of them
What is a nonessential amino acid and which ones are they?
We can synthesize in our body
Alanine, Arginine, Asparagine, Aspartic acid, Cysteine, Tyrosine, Glutamic Acid, Glutamine, Glycine, Proline, Serine
11 of them
What is the recommended daily allowance of protein for a healthy individual?
0.36 g “high quality” protein per lb body weight
1 lb = 0.45 kg
What is a high quailty protein source?
one that contains all the essential amino acids
comes from animal sources ( milk, eggs, and meat)
What are “low quality” protein sources?
Protein source that is deficient in one of essential amino acids.
Most vegies are low quality but they can be made up for by eating differant types to gain the ones you need
During starvation what happens to AAs in the liver?
The liver can convert them into glucose to be used by the brain and RBC. they are called glucogenic amino acids.
What are ketogenic amino acids?
they are AAs that are converted into ketone bodies which can be used as an energu source during starvation.
What is a non-standard amino acid?
AA naturally present in cells but does not participate in protein synthesis. Some are consituents of peptides, but thye are generated by modification of standard amino acids in the peptide molecule by post-translational modification
What is Carnitine?
Non-standard amino acid
Our body synthesizes carnitine from lysine. It shuttles fatty acids to the mitochondria for energy production
What is creatine?
non-standard amino acid
Produced from three standard amino acids (arginine, glycine and methionine)
Its found in muscle; creatine phosphate is high energy molecule, breaks down to produce ATP when needed.
Its secreted in the urine as creatinine
High levels in serum is maker of compromised kidney function; high creatinine kinase in serum is maker of muscle damage
What is Hydroxylysine and Hydroxyproline?
Non-standard amino acid
Derived from lysine and proline by hydroxylation
these are required to maintain collagen structure.
ONLY non-standard AAs present in peptide
What is Taurine?
Non-standard amino acid
Derived from cysteine, synthesized in the liver, component of bile salt
Common composition of energy drinks
What is the relationship between lysine and cold sores?
Lysine suppliments and diets high in lysine and low in arginine have been used to discourage herpes outbreaks
What are the pros of peptide drugs?
Higher potency: generally very active on their target receptor = high effect at low dose
High Selectivity: Very tight fit into their receptors makes them much more selective than smaller molecules; which means they tend to bind only to their target receptor and therefore are less likely to be associated with serious adverse side effects
Naturally occuring biolgics: better safety. since they are nautrally they are broken down much eaiser and have less accumulation in body tissue and fewer toxicity
What are cons of peptide drugs?
Short-lived: Short half-life, means that they generally act in the body for only a very short time, 2-30 minutes before being broken down by proteases
Immunogenicity: can induce antibody production in the body
Difficult to administer orally: Most via injection, oral admin leads to degradation and destruction by the digestive system
Low Product stability: Cannot be stored in aqueous solution more than a few days
What is the incretin system?
When glucose is taken orally, intestinal cells secretes two peptides called incretins
Glucagon-like peptide-1 (GLP-1)
Glucose-dependent insulinotropic peptide (GIP)
What does GLP-1 (glucagon-like peptide-1) and GIP (glucose-dependent insulinotropic peptide) do after they are screted
they bind to their own receptors in the pancreatic beta cells to induce insulin secretion
only have a half-life of 1 minute because they are broken down rapidly by protease DPP-4
why wouldnt you want to modify or hide specific sequences to imporve peptide drug stability?
it can lead to immunogenicity
What are the biological barriers associated with the oral delivery of peptide drugs?
Oral route is challenging, due to HCL and proteases being designed to break down these polypeptides into small pieces prior to absorption; snake venom generally doesnt work if swallowed because its peptide based and these barriers break it down unlike when it is injected into the skin.
The 2nd barrier is the intestinal absorptive epithelium. most oral drugs given by oral route are absorbed by intracellular passive diffusion. Most of the cell is phopholipid bilayers, with passive diffusion is limited by lipophilic drugs with MW below 700 Da. most peptide drugs are hydrophilic molecules with MW above 3000, making it hard for them to traverse the membrane
What is vasopressin and how does it work in diabetes insipidus
A peptide antidiuretic hormone, which stimulates re-absorption of water in the kideny, leading to the formation of more concentrated urine
Diabetes insipidus leads to deficit in vasopressin, so people excrete large volumes of urine and always thirsty
What is desmopressin?
A synthetic modified analog of the missing hormone, vasopressin.
Is given orally and is degraded much more slowly than vasopressin in the body. But why?
- relatively small peptide size it can pass thro intestinal epithlium
- D-arginine has been introduced in desmopressin to evade protease attack
If you have 1 free AA how many ionizable groups will it have?
It will have 2 (the amino + charge) and the carboxy - charge
Which AA is called Immino and what does it mean?
Proline; it means that its side chain inter acts with the amino group to form a ring
What does it mean to have a chiral center
The alpha carbon has 4 SINGLE BONDS to 4 different things
What is the one AA which has no chirality?
Glycine
What is the chirality of all the AAs in the human body?
they are all in the L (left) postion
What is the indication if you find D amino acids in a persons poo?
it could mean they have a bacterial infection due to the fact humans can not cleave or breakdown D AAs.
Where are the D amino acids of bacteria found in the bacteria and why do the bacteria need them?
They are found in bacteria cell walls and it allows them to escape digestive enzymes (proteases) = more resistant
What does some research show about BCAAs (branched-chained amino acids)
It shows that they might be helpful in muscel recovery and immune upregulation
What is Selenocysteine?
The 21st amino acid. Has anti-oxidant activy.
Unlike the other amino acids this one does not have a free pool in the cell
What is pyrrolysin?
22nd amino acid. NOT IN EUKARYOTES (PROTEINOGENIC AA)
What AA is the most effective as a buffer at physiological pH?
Histidine
Where does an AA act as a buffer in terms of the pH and pKa value?
An AA will act as a buffer at a pH close to their pKa value
How many bonds would there be in a 3 peptid bond?
2 bonds between 3 amino acids!
Where is the start of a peptide bond and what is its name?
It starts at a free amino group which is termed the N-terminal
What is at the end of a peptide bond and what is the name of it?
Free Carboxyal and the name is C-terminal
Can all sulfur containing AAs create disulfide bonds?
NO!!! only cysteine can
Cysteine can form bonds with itself
EX: if you have 3 cysteine bonds, how many disulfide bonds can there be?
A: 1.
Can cystein bind to more than 1 AA chain?
Yes, happens with Insulin where chain A links to chain B and helps with stabilization
If you have two peptides; which one would be more soluble at phys pH?
A: pI = 5.2
B: pI= 6.3
It would be A, the lower the number means how soluble it would be
pI below pH means + charge (water likes it so it disolves)
pI above pH means - charge
What is the clinical importance of changing a drugs pI?
If you can increase a pI and bring it closer to the pH of the body it will increase the amount of time the drug lasts (Glargine = long acting insulin)
What is the recommended daily allowance of protein for a person?
0.36 g of “high quailty” protein per pound
What is a glucogenic amino acid?
one that gets converted into glucose to be used as fuel in the body
What incretins?
When a person eats or has glucose in the system they release two peptides Glucagon-like peptide-1 (GLP) and Glucose-dependent insulinotropic peptide (GIP) causes insulin to be released in pancreas
What is bad about GLP-1
It get broken down by protease - dipeptidyl peptidase-4 (DPP-4) really quickly so you dont get much of an effect
Where does DDP-4 cut GLP-1?
Will cut after alanine or proline which will cause GLP-1 to be inactive
What is exendine-4?
A peptide found in gila monster venom, it showed similar biological property of human GLP-1, but was resistant to DPP-4
What is Exenatide?
Byetta, bydureon. Synthetic Exendine-4
Used to treat type two diabetes and allows for pancrease to release more insulin.
The change to the N-term of GLP-1 allowed it to be longer acting beacuse it was not cut by DDP-4
What is the problem with Exenatide?
It can lead to an immune reponse within the pancreas and cause inflammation
**still has gila monster amino acids
What is liraglutide?
Victoza; was created to circumvent the immunogenicity of byetta
Used once daily; and contains an acetylatyed form (Fatty acid), this makes it nonpolor and have hydrophobic effects and the DDP-4 is unable to remove it as eaily allowing for it to be long acting
