Protiens Flashcards
How many common amino acids are there?
20
What 3 categories can amino acids be divided into?
non-essential, conditionally essential, essential
What are non-essential amino acids?
the body is able to produce them
What are conditionally essential amino acids?
supplemented in the diet for young and compromised animals
What are essential amino acids?
the body is unable to produce them and they need to be acquired in the diet
Describe the chemical structure of an amino acid
central carbon atom, a carboxyl group, a hydrogen atom, an amino group and a variable side chain (R) group
How can the R groups vary?
structure, size and electrical charge
What does the variety in the R groups influence?
the solubility of the amino acids in water
Can amino acids act as both acids and bases?
yes
What does a doubly charged amino acid have?
one positive and one negative charge
What are doubly charged amino acids called?
zwitterion
How many structure levels do protiens have?
4
What are the structure levels of a protien called?
primary, secondary, tertiary and quaternary
What does the primary sequence of a protein determine?
its 3D conformation and function
What can changes in the amino acid sequence cause?
severely compromise the ability of a protien to carry out it’s function
How is a peptide bond formed?
when the carboxyl group of one amino acids reacts with the amino group of another amino acid
What is produced as a byproduct in the formation of a peptide bond?
water
What are two amino acids joined by a peptide bond known as?
a dipeptide
What is a chain of amino acids known as?
oligopeptide
What is a large chain of amino acids known as?
polypeptide
What does every peptide or protein have at each end of the chain?
a free amino group at one end and a free carboxyl group at the other end
Where do disulphide bonds occur?
between the R cystine group of cystine molecules
What is eliminated in order to form disulphide bonds?
2 hydrogens and 2 electrons
what effect does the removal of hydrogen and electrons in order to form disulphide bonds have on the protein?
stabilises the proteins structure
What does the secondary structure of a protien describe?
the local special arrangement of amino acids
What is the secondary structure of a protein formed by?
hydrogen bonds of the main chain atoms in the polypeptide backbone
What are the two types of protein secondary structure?
alpha helix and beta pleated sheet
How are the R groups arranged in an alpha helix?
on the outside of the helix in a right handed twist
How is the alpha helix stabilised?
by hydrogen bonds between the carbonyl oxygen of a peptide bond and the hydrogen bond of the peptide bond 4 amino acids away
What does the large number of hydrogen bonds in an alpha helix provide?
a stable rigid structure
How are R groups arranged in beta pleated sheet?
above and below the plane of the polypeptide backbone
Which bonds stabilise the structure of beta pleated sheet?
hydrogen bonds between carbonyl oxygen and hydrogen
What two forms can beta pleated sheet be in?
parallel and antiparallel
What is the name of the turns which connect the strands of an antiparallel beta pleated sheet?
beta turns
What does the tertiary structure of a protein describe?
the overall 3D conformation of the polypeptide chain.
What two protein structures do most proteins form in their tertiary structure?
extended fibrous structures and compact globular structures
What are the 3 methods of arrangement in tertiary structure of a protein?
reversable attractions/repulsions, hydrogen bonds, hydrophillic and hydrophobic R regions
What do hydrophobic and hydrophillic regions form from in protein tertiary structure?
arrangements from polar and non-polar R groups
How is globular proteins shape created?
different segments of the polypeptide chain fold bakc on each other, generating a more compact shape than seen in fibrous proteins
What does the folding in globular proteins provide for their structure?
structural diversity necessary for proteins to carry out a wide range of biological functions.
Name 5 examples of globular proteins?
enzymes, transport proteins, immunoglobulins, motor proteins, regulatory proteins
what does the quaternary structure of proteins describe?
the 3D arrangements of sub units in a multi-subunit protein.
What does the quaternary structure of a protein result from?
specific interactions between sub units
What is the name for 2 and 3 subunits?
dimer and trimer
How many sub units does haemoglobin have?
4
What is the common precursor of all amino acids
glucose
What 3 seperate pathways does glucose undergo?
pentose pathway, glycolysis and citric acid cycle
How is amino acid synthesis regulated?
feedback inhibition of the first reaction by the end product of the pathway
What other, non-protein, biomolecules do amino acids make?
hormones, coenzymes, nucleotides, alkaloids, cell wall polymers, porphyrins, antibiotics, pigments and neurotransmitters
What is a precursor of porphyrins?
glycine
What structure do porphyrins have?
cylindrical
what are porphyrins?
nitrogenous biological pigments
What is one of the best known porphyrins?
haem
What is haem the pigment in?
red blood cells
What is haem a cofactor of?
haemoglobin
What digestive aid is haem the source of?
bile pigments
What is haem released from?
dying erythrocytes (RBC)
What happens when haem is degraded?
free Fe2+ (iron) and bilirubin (ultimately)
What is used to convert haem to biliverdin?
haem oxygenase
What catalyses the conversion of biliverdin to biliruben?
biliverdin redactase
How can you view the reaction of haem to bilirubin?
observing a change in colour (e.g. bruising), black or purple from damaged erythrocytes, green from biliverdin and yellow from bilirubin
How does bilirubin travel in the bloodstream?
as a complex with serum albumin.
What happens to bilirubin in the liver?
it is transformed to the bile pigment bilirubin diglucuronide.
What happens to bilirubin diglucuronide?
it is sufficiently soluble to be excreted with other components of bile into the small intestine.
What happens to bilirubin diglucuronide in the small intestine?
it is converted predominantly into urobilinogen by microbial enzymes
What happens to urobilinogen?
some is reabsorbed into the blood and transported to the kidney where it is converted to urobilin. the remaining urobilinogen in the intestine is converted to stercobilin.
What is urobilin?
the compound that gives urine its yellow colour
What is stercobilin?
the compound that gives faeces its red brown colour
What are colorimetric assays and what can they be used to infer?
reactions which cause a colour change to infer protein presence or activity
What sort of data does a colorimetric assay provide?
semi-quantitative as the results are visually assessed
What compound is often used in colorimetric assays?
bromophenol blue
What happens to bromophenol blue when it is exposed to proteins?
they change colour
What diagnostic technique are colorimetric assays used in?
urine dipsticks
What does SDS-PAGE stand for?
sodium dodecyl sulphate polyacrylamide gel electrophoresis
What does SDS-PAGE do to proteins?
separates them according to size
What happens during SDS-PAGE?
gel forms pores which trap proteins, bigger proteins are less able to pass through it. An electrical current is applied across the gel and proteins which become negatively charged (follow the current)
What happens once the proteins are separated by size in SDS-PAGE?
they can be transferred to a thin membrane and specific proteins detected using an antibody
Why may secondary antibodies be added to the proteins?
they allow them to be visualized
What is this process of transfer to a membrane and visualization of the proteins known as?
Western blotting
What happens during ELISAs?
cells are fixed with a fixative (e.g. acetone), the primary antibody is added and allowed to bind to the protein of interest. The labeled secondary antibody is then added to the primary. The secondary antibody is bound to a florescent marker.
When are ELISAs useful diagnostic techniques?
when a protein location rather than quantity is informative
Give an example of when ELISA may be useful
feline infectious peritonitus, feline coronavirus is commonly found in cats guts but if it is found in an abdominal fluid aspiration it is indicative of FIP. This would be detected using ELISA
What is immunohistochemistry?
using an enzymatic colour-changing reaction to detect proteins of interest in fixed tissue samples from pathology samples
What is immunocytochemistry?
similar to immunohistochemistry but uses cells rather than tissues
What are the advantages of protein testing?
identify host or pathogen proteins, can show location (immunohistology), qualitative or quantitative. Convenient, rapid in-house assays (of variable accuracy) available
What are the disadvantages of protein testing?
variable sensitivity (false negative results), variable prices depending on test. Variable sample stability depending on protein structure and test requirements
What happens during protein catabolism?
proteins are broken down to amino acids
What process do amino acids undergo in order to generate energy?
oxidative deanimation
What are the 3 metabolic circumstances that oxidative deanimation happens under?
normal synthesis and degradation of cellular proteins (protein turnover), when the diet is rich in protein and ingested amino acids exceed the body’s need for protein synthesis, the surplus is catabolised. During starvation or uncontrolled diabetes mellitus, when carbohydrates are either unavailable or not properly used, cellular protein are used as fuel.
What is deanimation?
the process by which amino acids are broken down
Why do amino acids need to go through deanimation?
amino acids can’t be stored
What is produced when animo acids are deanimated?
they produce a carbon skeleton and ammonia
Why must ammonia be detoxified before excretion?
it is highly toxic
What can the carbon skeleton be broken down into and used for?
3-4 carbon units used to build fatty acids or glucose
What happens to the amino group of many amino acids so they form glutamate?
they are transfurred to alpha ketoglutarate
What is yielded from oxidatively deanimating glutamate?
ammonium
What do aminotransaminases do?
catalyse the transfer of an amino group from an amino acid to an alpha - ketoglutarate
What is left behind once the amino group has been transfurred to alpha - ketoglutarate?
the corrosponding alpha-keto acid analog of the amino acid
Why is there no net loss of amino group (deanimation) during the transfer of amino acid to alpha-ketogluterate?
alpha-ketoglutarate becomes animated as the amino acid is deanimated
What happens to the nitrogen atom that is transfurred to alpha-ketoglutarate in the transmission reaction?
it is converted to a free ammonium ion by oxidative deanimation
What enzyme catalyses the conversion of nitrogen to a free ammonium ion by oxidative deanimation?
glutamate dehydrogenase
What does glutaminase catalyse?
the production of glutamate from glutamine
Where does glutamine come from in the body?
muscle and other tissues
What ion does the production of glutamate from glutamine produce?
an ammonium ion
What happens to ammonium ions before entering the urea cycle?
converted into carbamoyl phosphate
What happens in the first step of the urea cycle?
citrulline is formed from ornithine and carbomyl phosphate (entry of first amino group)
What happens during the second step of the urea cycle?
formation of argininosuccinate by addition of aspartate to citruline
What does the third step of the urea cycle involve?
formation of arginine and by-product fumerase from argininosuccinate
What does the formation of arginine from argininosuccinate release?
fumarate
What does fumarate do?
enter the citric acid cycle
What happens in the 4th step of the urea cycle?
urea is formed and can be excreted
How do aquatic species dispose of nitrogen?
release ammonia into the surrounding water as this dilutes it
How do birds and reptiles dispose of nitrogen?
in the form of uric acid
What involvement do enzymes have in reactions?
biological catalysts which alter the rate of s reactio but are not changed by it.
what is an enzymes active site made from?
amino acid residues
What parts of an enzymes structure are essential to the function of the active site?
primary, secondary, tertiary and quaternary
What do some enzymes require to form substances with the correct active sites?
cofactors
What do co enzymes act as?
carriers or donors of functional groups
What are enzymes classified by?
the type of reaction they catalyse
how are many enzymes named?
by adding the suffix -ase to the name of their substrate or a word or phrase describing their activity
What do oxidoreductases do?
transfer of electrons
What do transfurases do?
group transfer reactions
What do hydrolases do?
hydrolysis reactions (transfur of functional groups to water)
What do lyases do?
cleavage of C-C, C-O, C-N or other bonds by elimination, leaving double bonds or rings or addition of groups to double bonds
What do isomerases do?
transfur of groups within molecules to yield different isometric forms
What do ligases do?
formation of chemical bonds between two macromolecules by condensation reactions coupled to hydrolysis of ATP
How do enzymes help with the reaction they are involved with?
lower the activation energy for the reaction they catalyse, they therefore can speed up reactions
What does the rate of enzyme action depend on?
the reaction being catalysed and the concentration of the substrate
What does the Michaelis-Menten equation do?
relates the rate of product formation (V0) with enzyme affinity (Km)
What are the two types of inhibition that enzymes are subject to?
competitive and non-competitive
What happens during competitive inhibition?
an inhibitor molecule blocks the active site of the enzyme
What happens during non-competitive inhibition?
inhibitor molecule binds to another part of the enzyme and changes the shape of the active site
What can be done to control enzyme activity?
controlling the supply of substrate, controlling the amount of enzyme, controlling the catalytic activity of regulatory enzymes
How can the supply of substrate be controlled?
keeping substrates in vacuoles
how can the numbers of enzymes in use be controlled?
enzymes are tagged to be degraded after use
What 3 ways can catalytic activity of regulator enzymes be controlled?
Allosteric control, proteolytic cleavage, covalent modification
How does allosteric control control the catalytic activity of regulator enzymes?
allosteric regulators act as non-competitive inhibitors and alter its activity
How does proteolytic cleavage catalytic activity of regulator enzymes?
many enzymes are produced in an inactive precursor (zymogen) form which is then activated by proteolytic cleavage.
What sort of enzymes are often produced in zymogen form to stop them damaging the cells they are made in?
digestive enzymes to stop them from digesting the cells that make them
How does covalent modification control catalytic activity of regulator enzymes?
Phosphorylation by a kinase or dephosphorylation by a phosphatase are common modifications which can increase or decrease enzyme activity.
What level is serum concentration of cellular enzymes at?
low
Why may enzyme activity in plasma be increased?
cell proliferation or damage (e.g. cancer, cell death, trauma)
What does the amount of enzyme in serum depend on?
the amount of enzyme in the damaged tissue, the organ or tissue mass, the degree of damage and the rate at which the enzyme is cleared from the plasma
What can analysis of serum enzymes provide?
information about which tissue has been damaged
Why can activity of diagnostic enzymes increase or decrease?
Increase: Proliferation of cells which normally produce it, Death of cells which contain it, Trauma or over-use (especially muscle)
Decrease: Reduction in the number of cells which produce it, Presence of inhibitors
Why is correct protein folding important?
misfolded proteins cannot perform the functions they were intended for and can accumulate in cells or tissues
When does protein folding occur?
very rapidly in newly synthesised cellular proteins
What happens to those proteins which cannot fold correctly when surrounded by a polar solvent?
they need help from a pre-formed chaperone protein
What happens to these proteins without the assistance of chaperone proteins?
they can become misfolded
What re misfolded proteins called?
prion proteins
What can prion proteins cause?
other proteins to misfold and create aggregates
What happens if misfolded proteins are not downgraded in the cell?
aggregates can form deposits that cause disease
What can these aggregate deposits present as in humans?
alzheimers
What do misfolded protein aggregates form in animals?
spongiform encephalothopy. Can be present as bovine, feline or transmissible.
what is spongiform encephalothopy colloquially known as?
mad cow disease
What does loss of protein structure lead to
loss of function
What is the destruction of the 3D shape of a protein known as?
denaturation
What does denaturation involve?
the disruption of the interactions responsible for secondary and tertiary structure and reduces the polypeptide to a random coil
What are some denaturing agents?
heat, pH, organic solvents, urea and mercaptoethanol, detergents
What happens if a protein denatures?
enzyme active site can no longer work to catalyse reactions, co-enzymes and carrier proteins are unable to bind to substrate, reducing transportation of other biomolecules throughout the cells and organs, receptor sites of signalling protein molecules become denatured so cell signalling is affected.
can enzymes refold after the denaturing agent is removed?
very few can, most are irreversibly damaged
What is pancreatitis?
inflammation of the pancreas
What effect can inflammation of the pancreas have on zymogens?
can activate them prematurely
When are zymogens usually activated?
once inside the GI tract
Why are zymogens activated inside the GI tract?
prevents them from breaking down tissues outside this area
Where are zymogens often stored?
zymogen granules
What are the main causes of pancreatitis?
very high fat diet, with or without concurrent obesity. Can also be caused by medical treatment or steroids. It can happen spontaneously without obvious cause (idiopathic)
What are the consequences of pancreatitis?
digestive enzymes spill into abdominal cavity, digestive enzymes begin to digest tissues in the body and can case lasting damage to surrounding organs (liver, bile ducts, gall bladder, intestines
How can pancreatitis be treated?
IV fluid therapy, anti-emetics, analgesia, resting the pancreas (24h starvation), longer term dietary changes and weight loss management
What is hyperammonaemia?
when ammonia is not converted to urea and remains in the body in excess
What are the signs of ammonia excess?
neurological e.g. vomiting, ataxia, headpressing, seizures, coma and death
What is the most common cause of hyperammonaemia?
portosystemic shunt, where an extra blood vessel bridging between the vena cava and the portal vein allows blood to avoid being filtered by the liver
Why must blood be filtered by the liver?
that is where protein deanimation and the urea cycle occur. blood is filtered through the liver by the portal vein so that ammonia and other waste products can be detoxified before being sent to the kidneys for excretion
What are other causes of hyperammonaemia?
lack of enzymes for urea cycle resulting in reduced rate of urea production
How can hyperammonaemia be treated?
surgery can close PSS but the patient must be stabilised first. This is done by restricting dietary protein intake to reduce nitrogen in the diet and medical management to help excretion of ammonia. If the cause is lack of urea cycle enzymes, enzyme precursors and substitute molecules can be supplemented
Where are many exocrine enzymes produced and what is their function?
in the pancreas and they catalyse the breakdown of fats, carbohydrates and proteins
What happens if the pancreas is not able to produce enough of these enzymes?
the body is unable to digest the molecules they break down and they cannot pass out of the digestive tract. This usually results in weight loss despite a normal/increased food intake
What other causes can weight loss despite an increased appetite have?
lymphoma, parasites, infectious agents
What is very important in diagnosing EPI?
clinical history and trypsin-like immunoreactivity
What does trypsin-like immunoreactivity test?
the levels of trypsin (an enzyme that digests protein) and trypsinogen (the precursor to trypsin) in the blood.
What disease is indicated by levels of trypsin and trypsinogen below normal range?
diagnostic for EPI
How is EPI treated?
supplemented with pancreatic enzymes (powders or tablets.) Switched on to highly digestible, low fat diets to compensate for the reduced levels of exocrine enzymes. Important to treat the cause of the EPI, which can be chronic pancreatitis.
What do coenzymes act as?
Carriers and donors of functional groups
Why do coenzymes usually have dietary precursors?
They cannot be fully synthesised by the body
What happens if the body is unable to synthesise coenzymes that require dietary precursors?
If they are not readily present in the diet this will cause issues
What are two of the most common coenzymes deficiencies?
Thiamine (vitamin B1) and cobalamin (vitamin B12)
What is thiamine the precursor to?
Thiamine pyrophosphate
What molecule does thiamine form a compound with to create thiamine pyrophosphate?
ATP
What functional group is thiamine pyrophosphate a carrier for?
Aldehyde ( -CHO)
What reaction is thiamine pyrophosphate a coenzyme in?
Catabolism of sugars and amino acids
What happens if thiamine is not present in the diet?
There is incomplete breakdown of sugars
What are the early signs of thiamine deficiency?
Non specific such as lethargy and anorexia
What are the signs in the later stages of thiamine deficiency?
Neurological signs such as in coordination, circling, head tilt, and abnormal gait which can progress to tremors or seizures
What is a way to test for thiamine deficiency?
Administer thiamine and see if the patient improves
What is cobalamin a coenzyme for?
Enzymes in three different classes
What 3 classes of enzyme is cobalamin a coenzyme for?
Isomerases, transfer hydrogens to create different isomers.
Methyltransferases, transfer methyl.
Dehalogenases, only in bacteria
What are the enzymes that cobalamin is a coenzyme for, involved in?
DNA synthesis and amino acid metabolism
What clinical signs are shown if there is a deficiency in cobalamin?
Poor body condition, inability to gain weight, weakness, lethargy, vomiting and diarrhoea
For what reason may signs of cobalamin deficiency be seen in the very young?
It can be congenital
How is cobalamin deficiency treated?
Cobalamin supplementation
