Biochemistry Flashcards
6 recall points of enzymes
Definitions, Names and activation energy, Graphs, Rate, Clinical, Measurements
What is a cofactor (Enzymes)
the non-protein component needed for the reaction e.g. magnesium
What is a coenzyme (Enzymes)
the heat-stable substance that can aid enzyme reactions e.g. FAD from riboflavin
What is a isoenzyme (Enzymes)
an enzymes that catalyse the same reaction but vary in structure and other biochemical properties
Ways in which enzymes lower the activation energy
Entropy reduction
Desolvation
induced fit
What is Vmax and Km?
Vmax = The reaction rate when all enzymes are saturated Km = The substrate concentration when the reaction is at ½ the maximum velocity (Vmax)
Limiting factors for the rate of enzymes
Enzyme concentration
Substrate concentration
Temperature (limitation to conditions, there will be an optimum)
pH (limitation to conditions, there will be an optimum)
Inhibitors. There are two types of inhibitor competitive (Vmax unchanged, Km increases because it takes more substrate to overcome the inhibition) and non-competitive (Vmax decreased, Km remains the same)
Measuring enzymes allows us to ….
Detect suspected disease Confirm suspected disease Assess the response to therapy Assess organ function Detect inherited metabolic disease detection of vitamin deficiencies
Conditions that will alter the enzyme concentration in the plasma
Hypoxia Cellular damage Physical damage Immune disorders Microbiological agents Genetic defects Nutritional disorders
Challenges with working with enzymes
The measurements are not specific
They require particular conditions
Assays must be optimised
Recall points for carbohydrates
Functions Shape Monosaccharides Disaccharides Polysaccharides Glycogen and disease Glycoproteins Proteoglycans Metabolism
What are the functions of carbohydrates
- Metabolism. Sugar and starch is a major source of energy collected through catabolism.
- Potential energy store. i.e. in starch and glycogen
- Structural and protective i.e. cells walls (in plants) and extracellular matrices of animal cells.
- Communication, where they are found on the surface of the cell. i.e. blood types
Why are carbohydrates stored in polymers?
- Space saving
- Creates non-reducing ends allowing for ready synthesis and degradation
- exist as a hydrate gel which is not soluble and therefore isn’t able to leave the cell
Examples of monomers
Glucose
Galactose
Fructose
Bonds formed between monomers in carbohydrates
Glycosidic between the hydroxyl group and anomeric group of two monosaccharides
Bonds formed between proteins
Peptide bonds
What bond forms between nucleotides
Phosphodiester
What is an anomeric carbon?
Carbon with 4 different groups bonded to it
What does an anomeric carbon do ?
Stabilise the structure
Examples of disaccharides
Maltose
Lactose
Sucrose
What is maltose?
Mainly comes from the break down of starch however is found in beer and baby foods.
Reducing sugar as anomeric carbon is available for oxidation.
What is lactose?
Main sugar in milk.
Formed by one galactose and one glucose monomer.
Reducing sugar as anomeric carbon is available for oxidation.
What is sucrose?
Sugar in ‘table sugar’ and used as a sweetener in food.
Not a reducing sugar as anomeric carbon is not available for oxidation.
What are the two broad types of polysaccharide?
Homopolysaccharide and heteropolysaccharide
What is starch?
A polysaccharide made up from two types of glucose.
1. Amylose - straight chain linkage alpha 1-4 bonds.
2. Amylopectin - Branched chain linkage alpha 1-6 bonds.
Starch has many non-reducing ends.
Non-recuing sugar.
What is glycogen?
Polymer of glucose and contains alpha 1-4 and alpha 1-6 bons however is more extensively branches than starch.
Where is glycogen stored?
90% in liver and skeletal muscles
Describe the process by which glycogen is formed
Glucose to glucose 6 - Phosphate upon entering the cell
to glucose 1 - phosphate.
to UDP glucose
the glucose from UDP glucose is covalently bound to the glycogen chain.
The binding of the first 8 glucoses is done glycogenin and there after by glycogen synthase
Describe how glycogen is broken down
Terminal monomer is removed by glucose phosphorylase from the non-reducing ends.
The other monomers of this branch are then removed by transferase and attached to the end of a neighbouring chain.
The last monomer on the brain is removed by glucosidase and releases this monomer.
When does degradation of glycogen occur?
When blood glucose concentration falls, glycogen from the liver is converted back into glucose and released into the blood.
This is not possible in the skeletal muscle here glycogen is converted into ATP.
Diseases that effect the synthesis and degradation of glycogen
Von Giekes disease - Glucose 6 -phosphatase deficiency
McArdle’s disease - Glycogen phosphorylase deficiency
What is a glycoprotein?
Proteins with carbohydrates attached.
What is the function of the carb attached to a protein in a glycoprotein?
These carbohydrates increase solubility, influence folding and confirmation, protect it from degradation and assist in communication.
Examples of glycoproteins
GAGs which are found in mucus and synovial fluid, they consist of layers that slip over each other.
Medical conditions involving glycoproteins
Mucopolysacchardoses. Lack of enzymes causes a build up of GAGs this can cause dementia etc. i.e. hurler, hunter syndrome
Hurlers syndrome is a developmental defect. Development stops at 4 years and death occurs at 10. Causes arterial wall thickening, dementia, clouding of the cornea etc.
What are proteoglycans ?
Carbohydrate with a protein attached
Examples of dietry carbs
Starch Glycogen Cellulose and hemicellulose Oligosaccharides lactose sucrose maltose glucose fructose
Describe the metabolism of carbohydrates
Salivary amylase in the mouth
Pancreatic amylase in the duodenum
Digestion in the Jejunum
Digestion result in the break up of carbs into glucose, fructose and galactose
How is glucose absorbed ?
Glucose is absorbed through the glucose symport. ATPase pumps Na out of the cell and it falls back into the cell pulling with it Glucose through the symport.
Upon entry to the epithelial cell glucose is converted into glucose 6 -phosphate to prevent it from leaving.
Enzymes which convert Glucose to glucose 6-Phosphate
In the liver glucokinase. Low affinity (high Km), so only takes glucose when blood glu levels are very high. It has a very high Vmax so it converts the glucose very fast.
In the other tissues Hexokinase has a high affinity (Low Km) and so glucose is absorbed even at low blood glu levels however it has a low Vmax.
How are fructose and galactose absorbed ?
Glactose - Very similar to glucose
Fructose - Bind to GLUT5 and moves down its concentration gradient
Enzymes found in carbohydrate section of the course
Glycogenin Glucose synthase Glucose phosphorylase Transferase Glucosidase Glucose 6 - phosphatase Glycogen phosphorylase
The function of a protein can be …. or ….
Structural or functional
By what process are proteins made ?
Transcription (DNA to mRNA)
Translation (mRNA to amino acid chain)
What is denaturation?
When there is a loss of chemical bonds within a protein. It disturbs the secondary and tertiary structure but not the primary stricture.
It causes a loss in function.
What are the functions of proteins?
Structural Contractile Defence Storage Enzymatic Receptor Hormonal Transport
Describe the structure of an amino acid
Amino acids are chiral (apart from glycine). They have a R group, Carboxylic acid group (COOH), Amine group (NH2) and a C-H bond.
What alters the acidity of a amino acid ?
The charge
Name and briefly describe the amino acid classifications
Aliphatic amino acid - R group is a hydrocarbon
Aromatic amino acid - R group is a hydrocarbon ring
Sulphur-containing amino acid - R group contains sulphur
Acidic amino acid
Basic amino acid
Polar amino acid - Amino acid with a charge
Miscellaneous - Strong
What is the primary structure of a protein
Sequence of amino acid monomers bonded together with peptide bonds.
What is the secondary structure of a protein
Folding of the polypeptide chains and production of hydrogen bonds between non-adjacent monomers to from alpha helixes and beta pleated sheets.
What is the tertiary structure of a protein
Folding of the chains even further so that bonds form between the R groups of amino acids forming Van der Walls forces, ionic, hydrogen, disulphate bridges, and hydrophobic interactions. This level gives rise to the proteins function.
What is the quaternary structure of a protein
Where different polypeptide chains join together. Not all proteins have this. i.e. Haemoglobin
Quaternary structure can be conjugated where there is a non protein group added to the protein.
What are the types of conjugated protein
Glycoproteins - Protein with a carb attached.
Lipoproteins - Proteins with a lipid attached. They are found in cell membranes and transport hydrophobic molecules. They transport fats, fat soluble vitamins, and fat soluble hormones.
Metalloproteins - Proteins with metal ions attached i.e. Haemoglobin.
What is a oligosaccharide?
A number of glycoprotein carbs joined together in a chain
What is a apolipoprotein?
A number of lipoproteins in a complex together
What are the functions of a metalloprotein
enzymatic
Signal transduction
transport
storage
What are the different types of proteins?
Globular - Spherical proteins (very common)
Fibrous - Elongated
Membrane
What are globular proteins used for ?
Storage Enzymes Hormones Transport Structural
Where are fibrous proteins found?
In muscle fibres and connective tissue
What are membrane proteins used for?
Enzymes
Transport
Cell adhesion
Describe the lipid disorder Fh
Individuals have a high LDL cholesterol in blood due to genetic pre-disoposition.
This can result in cholesterol being deposed around the eyes and tendons (shown in image) this is known as Xanthelasma and Xanthoma respectively.
What are lipids?
Heterogeneous organic molecules
What are the functions of lipids?
- Stored energy
- Membranes
- Enzyme co-factors
- Steroid hormones
- Vitamins (ADEK)
- Signalling molecules
What are the classes of lipid ?
- Fatty acids
- Triacylglycerol’s
- Phospholipids
- Glycolipids
What does it mean for a fatty acid to be saturated or unsaturated?
Unsaturated - Double bonds
Saturated - No double bonds
What is the structure of a fatty acid ?
Carboxylic acid with long non-polar tail.
Give examples of fatty acids that are essential
Linoleic and linolenic acids and arachidonic acid.
Describe the different types of fatty acid i.e. Good
Good - for our cardiovascular health, polyunsaturated i.e. veg oils
Bad - for out cardiovascular health, saturated however they are essential for myelination
Really bad - Trans fatty acids, formed in the hydrogenation of veg oil.
What are omega 3 and 6 fatty acids?
Omega 3 are from linolenic acid. they lower plasma cholesterol and prevent atherosclerosis, lower TAGs, prevent obesity and reduce inflammation.
Omega 6 are from linoleic acids but don’t have the same benefits of Omega 3.
How are omega 3 and 6 named?
- From there methyl end. I.e. the double bond is on the 3rd or 6th carbon from the methyl end
- From there carboxyl end i.e. 18:9 where there are 18 carbons but the double bond is on the 9th one.
What are triacylglyerols?
Esters of fatty acids and glycerol. Important in insulation.
What are phospholipids?
Glycerol bonded to two fatty acids and a phosphate group.
What are glycolipids ?
Carbohydrate + lipid. Antigens in blood groups.
What is our main source of lipid?
triacylglycerol
Describe digestion of triacylglycerol
- Enters mouth and is mixed with inactive lingual lipase
- Enters the stomach and lingula lipases are activated. Gastric lipase is added and the break down of lipids starts.
- Enter small intestine and are emulsified (spilt into small beads of fat called micelles) by bile salts.
- Pancreatic lipase is added and completes the breakdown into monoglycerol and fatty acids.
Peristalsis aids the digestive process
Give examples of other lipids that are digested and describe there digestion
- Cholesterol
- Free fatty acids
- phospholipids
Hydrolysed to fatty acids and lysophosphatidic.
What can happen if lipid malabsorption occurs?
Steatorrhea.
Describe what happens after the lipids are absorbed
After absorption they are resynthesized and packaged in chylomicrons for transport.
What solubilising protein are lipid packaged with ahead of transport ?
ApoB-48
Describe the path of chylomicrons (carrying lipids) in the body
They are released into the lymph, move to the blood. This means you can tell if someone has recently eaten by measuring there blood fat content. They are then delivered to the tissues.
What happens when TAGs get into tissue cells?
Hydrolysed into fatty acids by lipoprotein lipase.
Where will the chylomicrons (carry lipid) go after they drop off there lipid ?
Liver
How are fatty acids removed from storage?
Hormone sensitive lipase
Name the different types of lipids
- Chylomicrons. TAG rich.
- VLDL. TAG rich (but less rich than chylomicrons)
- LDL. Cholesterol rich (less dense again)
- HDL. protein/ cholesterol rich and least dense.
What condition is caused by too much LDL?
Atherosclerosis
What is B-oxidation ?
Conversion of fatty acids inside the cell to acetyl CoA, + FADH + NADH. This is done two fatty acids at a time.
Where does B-oxidation occur ?
Mitochondrial matrix
Describe how the fatty acids move from the cytosol to the mitochondrial matrix
Carnitine shuttle.
- In the cytosol fatty acid is converted to fatty acyl-CoA which allows it to cross into the mitochondrial membrane.
- In the mitochondrial membrane it is converted to fatty acyl-carnitine by CAT 1 this allows it to cross the rest of the membrane. This step is regulated by malonyl CoA.
- Once’s into the mitochondria it is converted back to fatty acyl-CoA and carnitine by CAT 2 and then back to fatty acids.
Can very long chain fatty acids use the the carnitine shuttle ?
No they must be broken up into smaller chains however this is less energy efficient.
What condition is caused if there is a CAT 1 enzyme deficiency?
Hypoglycaemia.
Once inside the mitochondria describe the process of fatty acid break down (B oxidation)
- Dehydrogenation to produce FADH2
- Hydration
- Dehydrogenation to produce NADH
- Thiolysis to produce Acetyl CoA
Do fatty acid or glucose degradation produce more ATP ?
Fatty acids
If glucose levels are low what happens to fatty acids?
B oxidation increases and then ketogenesis occurs to produce ketones that can be used by the brain and other key organs to keep them functioning.
What does the amount of ketogenesis rely on ?
- Availability of acetyl CoA
- Activity of rate limiting enzyme HMG CoA synthase
Where are ketones formed?
Liver
What happens if ketone levels get too high?
ketonemia, ketonuria and academia occur
How can you tell if someone has a very high ketone level?
Fruity odour in breath due to acetone.
Describe fatty acid synthesis
Acetyl CoA can be converted to fatty acids. This means that anything which can be broken down into acetyl CoA can be used to form fatty acids (i.e. carbs, protein etc).
Acetyl CoA goes through the citrate shuttle and then is converted to Malonyl CoA by Acetyl CoA carboxylase. Malonyl CoA is then converted to palmitate a fatty acid.
Where does fatty acid synthesis occur ?
Cytosol
What energy requirements are there for fatty acid synthesis?
ATP and NADPH
How does Acetyl get out of the cell?
Citrate shuttle. Acetyl CoA is converted to citrate which can cross the membrane and then is converted back into Acetyl CoA on the other side
What are the four steps in the conversion of Malonyl CoA to palmitate?
Elongation
Reduction
Dehydration
Reduction
What are three examples of steroids?
Cholesterol
Steroid hormones
Bile salts
What are statins ?
They are essential in cholesterol synthesis.
What are eicosanoids ?
Hormone. Anti-inflammatory drug inhibit eicosanoid synthesis.
What are the three types of eicosanoids ?
Prostaglandins
Thromboxane
Leukotrienes
What is the function of eicosanoids ?
Regulation of inflammation, pain, blood pressure, blood clotting, reproductive functions etc
