Biochem GEM 201 Flashcards
What is biochemistry
Which branch of biochem focuses on reactions occurring in us that involve carbon, hydrogen and oxygen?
Which branch of biochem focuses on the rate of reactions ?
Which branch of biochem focuses on Essential trace metals, metals incorporated into biomolecules e.g. iron in haemoglobin and cofactors for enzymes?
Which branch of biochem focuses on how fast or slow reactions occur and the energy barriers that must be overcome for the reactions to proceed?
Which branch of biochem focuses on The use of instrumentation in medical laboratories to determine amounts of biomolecules in body fluids?
Which branch of biochem studies the cause of diseases at the molecular level ?
It is simply defined as the study of the chemical reactions that occur in biological organisms. It encompasses all aspects of the chemistries when dealing with living organisms.
2.Organic chemistry - since we are organic and most of the reactions occurring in us involve carbon, hydrogen and oxygen.
3.Physical chemistry - how fast or slow reactions occur and the energy barriers that must be overcome for the reactions to proceed .
4.Inorganic chemistry - Essential trace metals, metals incorporated into biomolecules e.g. iron in haemoglobin and cofactors for enzymes.
5.Analytical bio-chemistry - The use of instrumentation in medical laboratories to determine amounts of biomolecules in body fluids.
6.Molecular biochemistry - Studying the cause of diseases at the molecular level
Biochemists study the reactions to understand the processes that keep us alive
What’s the relationship between med biochemistry (or physiology) and Chem pathology
Note:
Biochemistry in our lives
1.Look around - see all living things around you. The process that allows them to grow, multiply, stay healthy, become diseased, age and die are all biochemical in nature.
2.The different events in our lives is due to variant biochemical reactions taking place within our bodies at any point in time.
3.Such differences create variation within and without the human race
4.See what a little difference in biochemical reactions can do to living things
We look similar, but we are actually different with respect to the biochemical reactions
Medical biochem and physiology focus on the normal reactions in the body
Chem path: Abnormal reactions or chemical reactions in the body.
With regards to the relationship between medical biochem and clinical practice, note this:
Practicing medicine depends on understanding chemical reactions that promote health and its linkage to the diseased state.
➢Biochemistry explores the normal chemical reactions in humans and diagnosis of diseases is based on knowing how these reactions are altered.
➢Treating the diseased state is knowing how to restore the altered process back to the normal. Thus, you must know the biochemical attributes of the medication you are administering.
➢Medicine will eventually become individualized. Your genome will eventually determine the type of treatment that should be applied. Such biochemical advances will overtake you if your molecular biochemistry/molecular medicine foundation is not solid.
➢A parallel direction of future medicine nano-medicine. Again, you will be dependent on your biochemical knowledge to move forward.
Goals of the course: Understand the language of Biochemistry and important biochemical principles.
2.Use these principles to explain the chemical and molecular aspects of health-related problems.
3.Accept the fact that disease and plans for treatment depends on knowledge of the normal process and how these normal processes are altered at the basic science level.
4.Appreciate that biochemical principles are involved in day-to-day professional practice.
5.The practice of every day medicine depends mostly on Biochemistry, Physiology, Chemical Pathology, Microbiology and Pharmacology.
Note: It is impossible to understand disease without first understanding health. For example, you cannot understand how bleeding is controlled naturally without first understanding mechanisms of coagulation.
2.Though most medics will outwardly disagree, deep down they know that in the consulting room, you will be applying your knowledge in the basic sciences for every day practice of medicine.
3.Biochemistry forms a relationship with all the life sciences - genetics, immunology, microbiology, pharmacology, pathology, physiology and toxicology amongst others. All these are essential for the practice of medicine.
4.You need to make every effort to connect all these pathways in order to be a better physician than your predecessors.
Explain the biochemical mindset behind this presentation or explain briefly the biochemical pathways that cause this clinical presentation
Adult with acetone on breath (fruity smelling or nail polish smell) in the morning
Why do you smell It strongly in the morning
Why will an ammonia smell be smelled in extreme starvation? State two other ways the ammonia smell can come.
Why will ammonia smell from breath come due to liver issues?
●Straight away, you know that this patient is not obtaining enough energy from carbohydrates than required.
●Therefore, the person is breaking down fatty acids for energy production and the liver is synthesizing ketone bodies from these fatty acids.
●The ketone bodies are acetoacetate and β-hydroxybutyric acid. Acetoacetate breakdown yields the acetone, which is the fruity smell.
●The patient therefore has ketosis (elevated levels of ketones in the body). Could be the patient is starving, is fasting, is on a low carbohydrate diet or may be suffering from diabetes.
So reduced getting of energy from carbs leads to fatty acids breakdown via beta oxidation by the liver and this leads to production of acetyl co A. But there is accumulation of acetyl co A cuz of the reduced low carbs so this leads to ketone bodies synthesis(ketogenesis) by the liver from the excess acetyl co A. The ketone bodies produced are acetoacetate and beta hydroxybutyric acid and the acetoacetate produced acetone which is the fruity smell.
Why Acetyl-CoA accumulates when carbohydrate metabolism is low:
1. Acetyl-CoA comes from fatty acid breakdown (beta-oxidation). When the body is low on carbohydrates (glucose), it breaks down fat for energy instead — producing a lot of Acetyl-CoA in the liver.
2. Normally, Acetyl-CoA enters the Krebs cycle (TCA cycle) to produce energy — but this cycle needs oxaloacetate to run.
3. In carbohydrate deficiency, oxaloacetate is diverted away from the Krebs cycle because:
• It is used for gluconeogenesis (to make glucose).
• So there’s less oxaloacetate available to combine with Acetyl-CoA, which means the Krebs cycle slows down.
4. Now, since there’s plenty of Acetyl-CoA from fats, but not enough oxaloacetate to process it, Acetyl-CoA builds up in the liver.
5. The liver then converts this excess Acetyl-CoA into ketone bodies — which the rest of the body (especially the brain during starvation or diabetes) can use for energy.
●How dangerous is the ketosis. This is where the use of a dipstick – Ketostix can be dipped in urine to ascertain urinal excretion of ketone bodies.
Adult with acetone on breath (fruity smelling) in the morning.
Diagnosing and forming an opinion is the first step to successful medical practic
●If about ++++, then you do a physical examination and apply knowledge of biochemical principles to ask specific questions to rule out or include some conditions.
●Type I diabetes - lack of insulin means that glucose is not taken in by cells to produce energy. The cells resort to burning fat for energy leading to production of ketone bodies.
●Look out for other possible symptoms of diabetes for example, excessive urination, excessive thirst and losing weight despite a huge appetite. This can lead to diabetes ketoacidosis – a more serious ketosis.
●Do not overlook other possibilities even if you are almost certain of the diagnosis.
●Smelling ammonia in addition to acetone can be an indication of liver disease.
But to make these connections we must know and understand the basic facts of the biochemical pathways involved
Great observation!
You can still see fruity-smelling breath (acetone) in the afternoon or evening, but it’s often most noticeable in the morning, especially in certain conditions. Here’s why:
Why it’s stronger in the morning:
• Overnight, your body is fasting, so carb stores (glycogen) are getting depleted.
• Your body shifts more to fat breakdown, leading to increased ketone production.
• Acetone (a volatile ketone) builds up and is exhaled, causing the fruity breath in the morning when the person wakes up.
But it can still be present later if:
• The person has prolonged fasting or skipped meals.
• The person has uncontrolled diabetes (esp. Type 1).
• The person is on a low-carb/keto diet.
• There’s a metabolic disorder causing persistent ketosis.
Summary:
• Most noticeable in the morning, but not exclusive to mornings.
• The more prolonged the fasting or ketosis, the more pronounced the breath smell can be throughout the day.
Ammonia smell: Caused by excess protein breakdown or poor kidney function. Ammonia forms from excess protein breakdown or urea buildup (uremic fetor which is an ammonia or urine like smell from the mouth), common in starvation(when there’s extreme starvation, the body breaks down protein after it has already broken down glycogen stores and fat) or kidney disease.
Ammonia and liver: The liver converts toxic ammonia (from protein breakdown) into urea for excretion. In liver disease, this conversion is impaired, so ammonia builds up in the blood, which can lead to confusion or coma (hepatic encephalopathy) or In liver failure, the breath may have a musty, sweet, or ammonia-like odor due to ammonia and other nitrogenous waste products building up in the blood and diffusing into the lungs.
This smell is sometimes referred to as “fetor hepaticus” — a musty, pungent, or ammonia-like breath odor specific to liver failure,
Explain the biochemical mindset behind this presentation or explain briefly the biochemical pathways that cause this clinical presentation
: Why do we feel sleepy after eating a heavy meal
General answer: Why do we feel sleepy after eating a heavy meal
oIt takes a great deal of energy to digest a large meal. When your stomach is full, blood and energy are directed into the gut and away from other non vital organ systems in order to break down and absorb the food.
oWith so much blood and energy usage, less energy is available for anything else so you feel like relaxing.
Or After a heavy meal, the body redirects more blood and energy to the digestive system to aid digestion. This reduces stimulation to other parts of the body, including the brain or which makes the brain slightly less active , leading to drowsiness. Additionally, the parasympathetic nervous system becomes more active (rest-and-digest mode), slowing down body functions and making you feel relaxed and sleepy.
Macromolecule specific answers:
Carbs and tryptophan
1.A meal rich in carbohydrates is digested to glucose which stimulates the pancreas to release large amounts of insulin.
2.Insulin also induces the synthesis of serotonin from an essential amino acid in your brain called tryptophan.
3.Serotonin plays a large role in reducing appetite and creating a feeling of well-being and relaxation and simply tells your brain to go to sleep!
4.Seratonin can also be converted into melatonin, a brain chemical that regulates sleep cycle
In summary, plenty carbs means more insulin meaning more glucose into cells. More insulin means more amino acids are pushed into the muscles but it doesn’t push tryptophan into the muscles because tryptophan is highly protein bound so it doesn’t easily move into the muscles like that. Because the other amino acids are pushed into the muscles, the competition is reduced for tryptophan so it can easily enter the blood brain barrier to be converted to serotonin (causes relaxation) which converts to melatonin (tells body it’s time to sleep) in the pineal gland which is in the brain. This leads to you feeling sleepy.
Fats: Fats slow down the digestive system. Fats also take a lot of energy and time to digest and absorb, so the body will redirect blood flow to your digestive system, leading to less blood flow elsewhere, and you will feel less energetic after eating a meal rich in fats.
2.Fatty foods slow therefore down the brain and impair mental function. A high-fat meal in the digestive system significantly reduces alertness and affects speed and accuracy in tasks requiring sustained attention.
In summary, fats take longer and use more energy to digest because Fatty foods delay gastric emptying by releasing cholecystokinin (CCK). CCK slows stomach contractions, keeping food in the stomach longer. This slows digestion and absorption, making you feel sluggish or sleepy because the redistribution of blood to your gut is taking longer than in a high carb diet but more because of the cck release causing slow gut motility. Or
Slow gut = prolonged blood diversion + sedative hormone effect (CCK) → sleepiness.
CCK has a calming/sedating effect, which can enhance post-meal drowsiness.
Proteins:
A rich protein diet will have lots of tryptophan and will induce the same effect as carbohydrates and tryptophan above
A high-protein diet can cause drowsiness because it contains tryptophan, the precursor of serotonin and melatonin. Although tryptophan competes with other amino acids to enter the brain, some still crosses, leading to sleep-regulating neurotransmitter production. Additionally, protein digestion uses more energy, which may contribute to post-meal sluggishness.
However:
• In high-carb meals, the drowsiness is mainly due to insulin and tryptophan-serotonin-melatonin pathway.
• In high-fat meals, it’s more about delayed gastric emptying and CCK’s effects, which keep food in the gut longer and prolong blood flow to the gut.
• In high-protein meals, there is blood redistribution, but it’s usually not as pronounced as with fats (because proteins don’t delay gastric emptying like fats do), and the drowsiness is more due to the tryptophan-serotonin-melatonin pathway and the high energy cost of digesting proteins (thermic effect).
Note:
Use the biochemical knowledge to explain human behaviour and simple events that happen all the time around you
How do you assess the biochem pathways involved after taking history and physical exam ?
There are six things to ask yourself
After taking a history and performing the physical examination,
1. which biochemical reaction/marker may be responsible for the disease and why or what biochem principles are at play here?
2.Once you are dealing with reactions, then are enzymes playing any role in the patient’s condition, and how does it in turn affect the patient’s symptoms?
3.The interaction between hormones and their receptors and biochemical reactions should not be overlooked. Are hormones involved?
4.Medicine is now molecular and will be nano-, so for now, how relevant is the DNA sequence and most likely protein result in this setting?
5.Which selective laboratory and imaging tests should I order. Looking at the history and laboratory data, what is the most likely biochemical explanation for the results.
6.What treatment plan should I offer and what will be the result i.e. what markers will let me know that the treatment is working
Why is it important to identify biochem concepts underlying clinical presentation?
If a person presents with muscle cramps, what basic biochem concept is involved?
If a person presents with
Hypercholesterolemia and hyper-lipidemia ; what basic biochem concept is involved?
If a person presents with diabetes, what basic biochem concept is involved?
If a person presents with mental retardation what basic biochem concept is involved
Identifying the basic underlying biochemical concept is key. With this progress can be made regarding diagnosis and treatment. Without this knowledge, you will see yourself practicing trial and error medicine.
Basic biochemical concept
And Health related application
Carbohydrate metabolism (Glycolysis)-
Muscle cramps, diabetes
(Muscle cramps during carbohydrate metabolism (glycolysis) occur when oxygen is low, forcing muscles to use anaerobic glycolysis, which leads to lactic acid buildup and low pH, causing fatigue and cramps. Also, ATP depletion leads to overuse of glycolysis cuz the body senses an energy shortage so it’ll overuse glycolysis cuz it’s a faster way to get energy. This affects calcium reuptake because ATP is needed to pump calcium back into the sarcoplasmic reticulum. This leads to prolonged muscle contraction and cramping.
Lipid metabolism (Cholesterol/fatty acids absorption, degradation and biosynthesis)-
Hypercholesterolemia and hyper-lipidemia
In summary: Perfect. Here’s a short but comprehensive explanation:
Lipid metabolism issues—like poor absorption, excessive synthesis, or impaired breakdown—can lead to:
→ Hypercholesterolemia (high cholesterol levels)
→ Hyperlipidemia (high levels of lipids/fats in the blood)
This happens because:
• Cholesterol biosynthesis or dietary intake exceeds the body’s need, so it accumulates in blood.
• Impaired degradation or clearance of fats/lipoproteins (like LDL) also causes buildup.
Summary:
Disrupted lipid metabolism → excess fat/cholesterol in blood → hyperlipidemia & hypercholesterolemia.
Urea cycle, amino acid metabolism-
Hyperammonemia, mental retardation due to uremic encephalopathy or hepatic encephalopathy
Here’s a brief but comprehensive list of hyperammonemia manifestations:
• Confusion
• Irritability or behavioral changes
• Lethargy or drowsiness
• Vomiting
• Slurred speech
• Tremors
• Seizures
• Coma (in severe cases)
• Cerebral edema (brain swelling)
Why?
Ammonia is toxic to the brain. When it builds up (due to liver dysfunction or urea cycle disorders), it disrupts brain metabolism and neurotransmission.
Explain the biochemical mindset behind this presentation or explain briefly the biochemical pathways that cause this clinical presentation - Sickle cell
At position 6 of the β-chain of haemoglobin, valine a hydrophobic uncharged amino acid replaces glutamate, a hydrophillic charged amino acid.
2.The absence of the polar amino acid promotes the non-covalent polymerisation (aggregation) of haemoglobin, which distorts red blood cells into elongated fibres and assumes the abnormal sickle shape.
3.Naturally, the elasticity and solubility of haemoglobin will decrease.
4.The sickling shape in addition to not being able to carry the maximum amount of oxygen, also causes blockage in small capillaries, leading to poor oxygen delivery, ischemia and pain.
5.Malaria becomes more pronounced because sickling reduces the number of RBCs and a little attack by the parasites can have a profound effect. Or less parasites cause profound problems in SCD patients or SCD patients need just little parasites to cause problems
Great question.
The substitution of glutamic acid (polar and hydrophilic) with valine (nonpolar and hydrophobic) in hemoglobin causes a problem:
• Valine doesn’t like water, so it tries to hide from the watery environment that is inside the red blood cell.
So, valine tries to avoid water by sticking to other hydrophobic parts nearby—like other hemoglobin molecules that also have this abnormal valine.
• These valines on different hemoglobins attract each other like magnets, forming chains or clumps (polymers).
• These long chains make the red blood cell stiff and change its shape into a sickle.
or • This hydrophobic patch on one hemoglobin molecule sticks to a complementary hydrophobic region on another hemoglobin. • This leads to abnormal interactions and clustering or clumping(polymerization) of hemoglobin molecules when there is low oxygen • These clusters form long stiff fibers, which deform the red blood cell into a sickle shape.
So simply put:
Hydrophobic valine makes hemoglobin molecules stick together in water, forming fibers that distort the cell.
Glutamate is hydrophilic (loves water):
• It’s negatively charged and mixes well with water.
• So, it doesn’t try to hide or stick to other hemoglobins.
• It just stays happily exposed to the watery environment inside the red blood cell.
2. No abnormal sticking:
• Since glutamate doesn’t form sticky patches, hemoglobin molecules stay separate.
Exactly — you’ve got it!
On a regular day with normal oxygen levels, some polymerization may still happen, but it’s minimal and less harmful because the oxygenated hemoglobin S structure hides the hydrophobic valine better.
But when oxygen levels drop, polymerization increases sharply — the hemoglobin S shape changes, valine is more exposed, and HbS clumps together more aggressively, leading to sickling of red cells.
So yes — it’s not all-or-none. Polymerization can happen mildly at normal oxygen levels but becomes much worse in hypoxia.
Explain the role of enzymes as part of the biochem part after taking hx and physical exam in clinical practice
The role of enzymes in clinical practice
1.Biochemical reactions involve enzymes and identification of those that catalyze rate determining steps. This knowledge is necessary since the enzymatic control step may be used as a therapeutic target.
2.For example atherosclerosis patients with high cholesterol are treated with statins, (lovastatin, simvastatin) a drug that inhibits HMG CoA reductase(HMG-CoA stands for 3-Hydroxy-3-Methylglutaryl-Coenzyme A. Reductase), the enzyme catalyzing the committed step in cholesterol synthesis.
HMG-CoA is a metabolic branching point — it can go toward cholesterol synthesis (cytoplasm) or ketone body production (mitochondria), depending on the body’s energy state.
3.Enzymes levels in blood can be used as an indication to ascertain the state of a particular tissue. Alanine transferase (ALT) is within the liver cells so high amounts of this enzyme in the blood is indicative of liver damage. The cocktail given to HIV patients is composed of protease inhibitors that work on three crucial enzymes the virus uses to increase infection .
4.Absence of certain enzymes will cause certain substrates to accumulate with disastrous consequences e.g. absence of phenylalanine hydroxylase(absence can cause mental issues but confirm) leads to phenylketouria (PKU) or absence of adenosine deaminase leads to severe combined immunodeficiency (SCID) disease. The presence of these enzymes are tested prenatal i.e. in the womb so treatment can start right after birth.
Phenylketonuria (PKU):
• Problem: The body lacks phenylalanine hydroxylase, an enzyme that breaks down phenylalanine, an amino acid found in food.
• Effect: Phenylalanine builds up in the blood and brain.
• Consequence: This can cause brain damage, mental retardation, and developmental problems if not treated early.
• Solution: A low-phenylalanine diet started early in life prevents these problems.
2. Severe Combined Immunodeficiency (SCID):
• Problem: The body lacks adenosine deaminase (ADA), an enzyme important in breaking down certain waste products in white blood cells.
• Effect: Without ADA, toxic substances build up and destroy immune cells.
• Consequence: The child has a very weak immune system, making them extremely vulnerable to infections.
• Solution: Treatments include enzyme replacement, gene therapy, or bone marrow transplant.
What hormone checks are you to ask as part of the biochem part after taking hx and physical exam in clinical practice
Summary of checks
1.synthesized in the right origin?
2. Binding to receptor? Is it available to work?
3. Downstream signaling
4. Is the target responding
Is there a likely hormone-receptor interaction
1.Hormones are produced by one tissue and often conveyed by blood to another part of the body to effect physiological activity. The hormone binds to a receptor, which mediates the physiological response.
Right origin?
Tumors producing hormones in the wrong place (Ectopic hormone production)
• Some tumors can wrongly produce hormones in places they shouldn’t.
• Example: A lung tumor producing ACTH (normally from pituitary), causing Cushing’s syndrome.
Simple summary:
Even if the gland is supposed to make the hormone, problems like genetic defects, gland damage, enzyme issues, or nutrient deficiency can stop proper hormone synthesis — or cause abnormal hormone synthesis elsewhere.
2.Hormonal effect is vital because many diseases occur as a result of abnormal hormone production. This could be under- or over-production of the hormone. For example TSH is used to screen patients for thyroid disease – High TSH suggests hypothyroidism – low levels of thyroid hormone and vice versa – low ATP, weakness, fatigue, low BMR, cold intolerance, decreased sweating etc.
3.Furthermore the hormone-receptor interaction could also be the cause of the disease. In cholera, the receptor is permanently locked to a channel that allows free flow of water, sodium and chloride ions into the intestinal lumen for constant excretion.
4.Sometimes the hormone-receptor complex could be alright but the downward cellular response may not be as expected.
What does it mean?
Even if a hormone binds correctly to its receptor, the message it’s supposed to send inside the cell may not work properly. This means that the problem is not with the hormone or receptor, but with the cell’s internal response pathway—also called the signal transduction pathway.
Example:
Think of it like this:
• The hormone is a key, and the receptor is a lock.
• The key fits into the lock, so the door opens—but the electric wiring inside the house is faulty, so the lights don’t come on.
• In the body, this is like the hormone activating the receptor, but the internal messengers inside the cell (like second messengers, enzymes, or transcription factors) are not working well.
What causes this?
• A defect in G-proteins, second messengers (like cAMP, IP3, calcium), or other signaling molecules.
• Mutations in proteins involved in the cascade of reactions inside the cell.
• Diseases like type 2 diabetes, where insulin binds to its receptor, but the cell doesn’t respond properly (called insulin resistance).
Simple summary line:
“Sometimes the hormone binds correctly, but the internal cell machinery fails to respond, leading to poor or no effect.”
Why is the DNA,RNA or protein part of biochemistry important in clinical practice ?
What relationship if any exists between DNA, RNA or protein.
1.Some diseases are hereditary and runs through families. It is essential to know if such is responsible for the diseased state.
2.It is also essential to ascertain whether the patients daily routine exposes him/her to mutagenic agents.
3.Actually many drugs used to treat cancers are targeted to interfere mainly with the synthesis of DNA in the fastest growing cells.
4.DNA codes for proteins, which controls the integration of many cellular processes that affect physiological or pathological changes, e.g bacteria toxins are proteins, the enzymes that are affected by the toxins are proteins and the immune cells that will fight these toxins are also proteins.
5.DNA technology/genetic engineering/molecular medicine is the future of medicine for diagnosis and treatment whether you like it or not. It is thus important that students become comfortable with DNA and RNA and its role in futuristic medicine.
Bacteria uses proteins to attack
Immune system uses proteins to protect
How do you know the selective laboratory/imaging requests you should order to help me formulate a diagnosis?
What selective laboratory/imaging requests should I order to help me formulate a diagnosis?
1.Now is the time to coordinate all your knowledge and order a selective lab request. You may never know the level of knowledge of the patient so this is the most important part of your work.
2.Once the results are in, you are both a scientist and physician. You must know how to decode the data, make sense of the information using up-to-date evidence, e.g. low blood urea nitrogen (BUN) – liver problem since urea is synthesized only by the liver. High BUN – either overproduction by the liver or decreased excretion by the kidneys.
3.The biochemistry that you disliked combined with other observations can now be used as rational guidelines for explaining objectively the disease process in chemical terms.
Did the laboratory data confirm/refute/explain the biochemical concept?
Collagen is the most abundant protein in body
Phenylketonuria is related to mental health
Amino acid 29,30 were exchanged to lead to long acting insulin.
BRCA1 and BCRA2 mutation leads to high chance or 80% of ovarian and breast cancer
Good question!
Why does phenylalanine buildup cause mental retardation in PKU?
In Phenylketonuria (PKU), the enzyme phenylalanine hydroxylase is missing or deficient. This enzyme normally converts phenylalanine → tyrosine.
When it’s absent:
1. Phenylalanine accumulates in the blood and brain.
2. High levels of phenylalanine disrupt brain development and damage neurons.
3. It also blocks the transport of other essential amino acids (like tyrosine and tryptophan) into the brain, which are needed for neurotransmitters like dopamine and serotonin.
4. This leads to impaired brain function, delayed mental development, and if untreated, mental retardation or intellectual disability.
That’s why PKU is screened at birth — early dietary control (low phenylalanine diet) prevents brain damage.
Would you like a very short version to memorize?
How do you know what therapeutic plan you should initiate
Research on bubble baby
What therapeutic plan should I initiate
1.After diagnosis, therapy is initiated and patient response should be monitored to assure improvement scientifically i.e. unbiased, precise and consistent.
2.This is important because monitoring may be measured by different health personnel.
3.Basically, you must know enough about the disease process to know which biochemical marker to monitor, the expected response and the effectiveness over time.
4.In diabetic ketoacidosis, serum glucose and pH should be measured to confirm improvement with therapy.
Sure!
Bubble Baby (Severe Combined Immunodeficiency - SCID)
The term “Bubble Baby” refers to babies born with SCID (Severe Combined Immunodeficiency) — a rare genetic disorder where the immune system is almost completely absent.
Why the name “Bubble Baby”?
Because these babies are so vulnerable to infections, some were kept in completely sterile, plastic bubble environments to avoid exposure to germs — hence the nickname.
What causes SCID?
• Most commonly due to Adenosine Deaminase (ADA) deficiency.
• Without ADA, toxic metabolites build up, damaging the T cells and B cells, which are crucial for immune defense.
• So, the baby can’t fight even minor infections — which can become fatal.
Treatment:
• Bone marrow transplant (curative in many cases).
• Enzyme replacement therapy (ADA-PEG).
• Gene therapy is also being used in modern medicine.
Would you like a super short version to memorize too?
Learn PBL
Note
Surgery – collagen and wound healing
●Cancer – the cell, regulation of cell proliferation
●Internal medicine – metabolic syndrome; atherosclerosis
●Pediatrics – inborn errors of metabolism; type 1 diabetes
●Ob/Gyn – mechanism of action of steroid/sex hormones
●Psychiatry – synthesis and degradation of neurotransmitters
●Orthopaedics – Calcium and phosphorus absorption and metabolism
●Dermatology – the integument system
● Aenesthesia – neuromusculoskeletal system
Explain biochem as a science and an art
Learn to use biochemistry in the process of clinical problem solving:
Medicine combines both the arts and sciences.
●The science which is very important is the attempt to understand the disease process, being objective in your observations and making rational treatment plans.
●You must know enough biochemistry of the normal state in order to know when something is wrong.
●Then you will know how to correct the disease process and which marker(s) to measure to determine the expected result with the therapy
●The art part is the dealing with the patient – expressing empathy and compassion, establishing a therapeutic relationship.
State seven applications of biochem in medicine
oHIV testing – Biochemical assays using body fluids to detect HIV antigens, antibodies or RNA. The nucleic acid test involves using probes to detect a specific 142-base sequence located on one of the HIV genes. This was much sensitive and reliable than detecting the presence of HIV antibodies, which could take time to develop. Blood banks use a combination of several biochemical tests to keep supplies safe.
oPre-natal testing - These are biochemical assays performed on the foetus to identify specific biomarkers that will indicate potential genetic defects e.g. Downs syndrome, phenylketonuria (PKU) and sickle cell. This happens when both parents are heterozygous for a condition. The test samples are either the amniotic fluid or blood from the umbilical cord. With this forewarning, therapies can be instituted soon after birth e.g. in PKUs, a phenylalanine free diet is essential to promote normal development of the child. Alternatively parents can undergo counseling or may decide to terminate a pregnancy.
oGenetic engineering – take the gene from one organism and place it in another so the latter will mass produced the products of the gene. An example is the production of insulin by bacteria using recombinant DNA technology. The α-chain or β-chain were prepared, inserted into plasmids and transformed into E. coli. The bacteria synthesized the preproinsulin chains which are purified and allowed to fold to produce active insulin. Changes made in the amino acid positions produces faster absorbing and faster acting insulin. Previous humans had to inject pig or cow insulin.
oPregnancy testing – Human Chorionic Gonadotrophin (hCG) is produced by the embryo after implantation into most body fluids including urine after at least 6 days. The biochemical assay is in the form of a test strip, which has anti-hCG antibody labeled with a colour producing agent at particular position. When dipped into urine, there is specific binding between the hCG and anti-hCG antibody-colour agent to form a complex. The complex upon combining with a second antibody produces the characteristic positive colour.
oCancer testing – There is the hereditary component of cancers especially in breast cancer where majority of cases revolve around mutations in breast cancer-1 (BRCA1) and BRCA2 genes. Females who inherit a mutation in either gene have an increased chance (>50%) of developing breast or cervical cancer over their lifetime. Biochemical testing of mutated genes in breast and other cancers are available so individuals can check their status. Carriers can schedule more screening to monitor their health status or can decide on radical procedures such as double mastectomy.
oGene-replacement therapy – Patients already afflicted with defective genes might be treated by replacing their defective gene with the normal gene and get these genes to work. The introduction of the healthy gene is through a virus that has been altered to carry the human DNA. The process was successful in a 4 year old with Severe Combined Immunodeficiency (SCID). A defect in adenosine deaminase (ADA) gene prevents T and B cell formation. Immune system cells can not proliferate normally and children with SCID die early or must be kept in a sterile environment (bubble baby). Treatment must be repeated every few months.
oGenetically modified goods – transferring genes from one organism to the other to create food products either resistant to disease or have high yielding nutrients. The first accepted GM food for consumption was the tomato Flavr Savr, which is resistant to rotting. Introduction of growth hormones into salmon, to produce lager salmon/tilapia that growth to adulthood within shorter periods.
Phenylketonuria (PKU) is an autosomal recessive disorder caused by a deficiency of the enzyme phenylalanine hydroxylase (PAH), leading to the accumulation of phenylalanine in the blood.
Effects of Phenylalanine Accumulation:
• Neurotoxicity → Causes intellectual disability, seizures, and developmental delay if untreated.
• Neurotransmitter Disruption → Reduces the production of:
• Dopamine and norepinephrine (from tyrosine) → Affects mood, cognition, and motor function.
• Serotonin (from tryptophan) → Leads to mood disturbances and behavioral problems.
• Myelin Deficiency → Impairs brain development and function.
• Amino Acid Transport Disruption → Phenylalanine competes with tyrosine and tryptophan for transport into the brain, reducing their availability and worsening neurotransmitter imbalance.
Are These Amino Acids Neutral?
Yes, phenylalanine, tyrosine, and tryptophan are all large neutral amino acids (LNAAs). They share the same transport system to enter the brain, which is why excessive phenylalanine blocks the uptake of tyrosine and tryptophan.
Heterozygous for PKU
A heterozygous individual has one normal and one mutated PAH allele. Since PKU is recessive, heterozygous individuals (carriers) do not develop the disease but can pass the mutated gene to their offspring.
Early detection and a low-phenylalanine diet can prevent brain damage and allow normal development.
The test strip uses an anti-hCG antibody instead of an “hCG antibody” because:
1. Antibodies Bind to Specific Targets (Antigens)
• hCG is an antigen, meaning the body (or a test) produces antibodies against hCG to detect it.
• The term “hCG antibody” could be misleading, as it might imply that hCG itself is acting as an antibody, which is incorrect.
2. Anti-hCG Antibody Specifically Binds to hCG
• The test strip is designed to detect hCG in urine.
• To do this, it uses an antibody that recognizes and binds specifically to hCG—hence, it is called an anti-hCG antibody.
3. Antibodies Are Named Based on What They Target
• An anti-X antibody is an antibody that binds to X.
• Since the test needs an antibody that binds to hCG, it is called an anti-hCG antibody.
Would you like a mnemonic to help remember this?
What we do not teach in Medical Biochemistry
1.Pointless, nit-picky information - If few people in the history of medicine had that disease, we skip it. Demonstrate the big picture more effectively
2.Details - Medical students DO NOT need to know all the mechanisms of biochemical processes, that is for Biochemistry students.
3.Any stage of the biochemical pathway that is not linked to a disease is not emphasized in detail.
Biochemistry has introduced many disciplines for future individualized medicine (…-omics)
➢Genomics – The genome is the complete set of genes in an organisms and genomics is the in depth study of the structure and function of genomes.
➢Glycomics – The glycome encompasses the simple and complex carbohydrates in an organism. Glycomics is therefore the study of the interactions, structures and functions of glycomes, and their roles in health and disease.
➢Lipidomics – The lipidome is the complete complement of all lipids found in the organism. Lipidomics is therefore the study of the structures, interactions and functions of lipidomes, and their roles in health and disease.
➢Metabolomics – The metalobome is the complete complement of all small molecules involved in metabolism. Metabolomics studies structures, functions and changes of the various metabolites.
Nutrigenomics – the study of how various nutrients affect the genetic expression of individuals or how genetic variations among individuals result in the handling of nutrients.
➢Pharmacogenomics – The use of genetic information and technologies to optimize the discovery and development of drug and drug targets for specific treatment options.
➢Proteomics – The proteome is the complement of all proteins in an organism. Proteomics is therefore the study of the interactions, structures and functions of proteomes and their roles in health and disease
➢Transcriptomics – The transcriptome is the complete set of RNA transcripts produced by the genome at a fixed point in time. Transcriptomics studies gene expression at the RNA level at a particular time.
Question 5: This abnormal biochemical process listed below is NOT a major cause of disease.
Options:
• A. Microbial infections
• B. Genetic disorders
• C. Immunological disorders
• D. Dietary disorders
Correct Answer: A. Microbial infections
Explanation:
The key phrase here is “abnormal biochemical process.”
• Genetic disorders: These arise from mutations or defects in DNA, leading to abnormal proteins or enzymes, which are biochemical processes gone wrong.
• Immunological disorders: These involve biochemical imbalances in the immune system, like abnormal antibody production or cytokine release.
• Dietary disorders: Nutritional deficiencies or excesses directly affect biochemical pathways — e.g., vitamin deficiencies disrupting enzyme function.
But…
• Microbial infections (e.g., bacteria, viruses) are external causes of disease. While they can disrupt biochemical processes, the infection itself is not an internal biochemical process — it’s a biological invasion, not a biochemical abnormality originating from within the body.
So, microbial infections are a biological cause, not a biochemical abnormality, making Option A the correct answer.
Question 1: Biochemistry is aimed at new omics. Which of the following is NOT geared at the individual?
Options:
• A. Metabolomics
• B. Transcriptomics
• C. Proteomics
• D. Pharmacogenomics
Of course!
Question 1: Biochemistry is aimed at new omics. Which of the following is NOT geared at the individual?
Options:
• A. Metabolomics
• B. Transcriptomics
• C. Proteomics
• D. Pharmacogenomics
Correct Answer: A. Metabolomics
Explanation:
Let’s first understand what each “-omics” means:
• Transcriptomics: Study of RNA transcripts — shows which genes are being expressed in an individual.
• Proteomics: Study of proteins produced by the body — reflects the functional output of genes in an individual.
• Pharmacogenomics: Study of how a person’s genetics affects drug response — very individualized.
• Metabolomics: Study of metabolites (small molecules) in the body — reflects overall metabolic activity.
Why A (Metabolomics) is the best answer:
While metabolomics can reflect individual metabolic profiles, it is heavily influenced by external factors like:
• Diet
• Environment
• Lifestyle
• Medication
So, it may not always give a clear picture of just the individual’s genetic or biochemical identity, unlike the other three, which are more directly linked to an individual’s genetic makeup or internal biology.
In short:
• Transcriptomics, Proteomics, Pharmacogenomics → more genetically and individually specific
• Metabolomics → reflects individual + external influences, so it’s less focused solely on the individual’s internal biology.
That’s why Metabolomics (A) is considered the least individual-specific among them in this context.
No problem — let me explain transcriptomics in very simple terms:
Transcriptomics = Study of RNA (messenger molecules)
Think of your genes (DNA) like recipes in a cookbook. But your body doesn’t use the cookbook directly — it copies the recipe (DNA) into messenger RNA (mRNA) so that your cells can make proteins from it.
That copied recipe (mRNA) is what transcriptomics studies.
So:
• DNA = recipe book (genes)
• mRNA = copied recipe (transcripts)
• Transcriptomics = studying which recipes (genes) are being copied and used at a given time.
This helps scientists understand which genes are active in a specific cell or condition (e.g., in cancer cells vs. normal cells).
So, transcriptomics tells us what the cell is planning to do, based on which genes it’s “reading” at that moment.
Which of the following microscope does not require the use of stain
A. Bright field
B. Dark field
C. Florescent
D. Phase contrast
Which of the following microscopes does not require the use of stain?
Answer: B. Dark field
• Explanation:
• Dark field microscopy allows you to see live, unstained specimens by scattering light and creating contrast.
• Bright field often requires stains.
• Fluorescent microscopy needs fluorescent stains/dyes.
• Phase contrast also helps see unstained samples, so it could also be considered, but dark field is most distinctly used without staining.
If your question intends to pick only one, Dark field (B) is the best-known answer.
Psychology
As part of the mariner’s culture, they lower standards. I am part of the mariner’s output, I have
to lower standards. If I don’t, the other members will not approve of me and will ridicule me. I
conform due to……
A. Norminal Social Influence
B. Normal
C. Normative
D. Norm Social Influence
Correct answer: C. Normative
Explanation:
• Normative social influence means conforming in order to fit in, be accepted, or avoid ridicule or rejection by a group — even if you personally disagree.
• In your example, you’re lowering standards not because you believe in it, but because you want group approval and fear being mocked.
So, “I conform due to… Normative social influence” is the correct understanding.
Let me know if you’d like a simple trick to remember normative vs. informational influence.
- Which of the following microscope use UV light
A. Confocal
B. Florescent
C. Phase contrast
D. Polarised
11)In order not to seem to be the odd one out and be wrong, you conform due to
A) Informed
B) Informational
C) Informative
D) Informal - Which of these best describes interpupillary distance.
A. Between one objective and one ocular
B. Two objective
C. Two occular
13.Following joints are of concern to MULTIAXIAL EXCEPT
A.Condyloid
B.Ellipsoid
C.Plane
D.Spheroid - Following joints are of concern to UNIAXIAL EXCEPT
A. Ellipsoid
B. Cylindrical
C. Spiral
D. Trocheal(hinge)
Here are the correct answers with clear explanations:
- Which of the following microscopes use UV light?
Answer: B. Fluorescent
• Explanation: Fluorescent microscopes use ultraviolet (UV) light to excite fluorochromes (fluorescent dyes), which then emit visible light to form an image. - In order not to seem to be the odd one out and be wrong, you conform due to:
Answer: B. Informational
• Explanation: Informational social influence happens when you conform because you believe others might be right, especially in uncertain situations. You’re seeking correctness, not just approval (which would be normative).
Correct term: Informational social influence (Not “informative”)
• It’s a standard term in psychology.
• You conform because you believe others have more accurate information, especially in uncertain situations.
- Which of these best describes interpupillary distance?
Answer: C. Two ocular
• Explanation: Interpupillary distance is the distance between the centers of the two ocular lenses (eyepieces) — it matches the distance between your pupils for comfortable viewing. - Following joints are of concern to MULTIAXIAL EXCEPT:
Answer: A. Condyloid
• Explanation:
• Multiaxial joints allow movement in multiple axes (e.g., ball-and-socket like the spheroid joint).
• Condyloid joints are biaxial (allow movement in two axes, not multiple).
• So Condyloid is NOT multiaxial, hence the correct answer.
condyloid joint (also called an ellipsoidal joint) is a biaxial synovial joint that allows movement in two directions/planes:
• Flexion–extension
• Abduction–adduction
• (Combined = circumduction)
Example: Wrist joint (radiocarpal joint) — between the radius and carpal bones.
So, yes, condyloid and ellipsoid are often used interchangeably — they both describe the same type of joint in many texts.
- Following joints are of concern to UNIAXIAL EXCEPT:
Answer: A. Ellipsoid
• Explanation:
• Uniaxial joints allow movement in only one axis (e.g., hinge or pivot joints).
• Ellipsoid joints are biaxial — movement in two planes, so it’s the exception here.
Great observation — let’s clarify this carefully:
Why is a hinge joint uniaxial?
• Uniaxial means movement around only one axis.
• Hinge joints (like the elbow and knee) allow:
• Flexion (bending)
• Extension (straightening)
These two actions occur in the same plane (sagittal) and around one axis — the transverse axis. So it’s still one axis of rotation, even though there are two opposite directions (flex and extend).
But what about abduction and adduction?
• Hinge joints do NOT allow abduction or adduction.
• That movement requires a second axis (usually seen in biaxial joints like condyloid/ellipsoid joints — e.g., the wrist or knuckles).
So if you try to move your elbow side to side (abduction/adduction), it won’t move — that’s why it’s uniaxial.
Quick Summary Table:
Joint Type Axes Movements Examples
Hinge (Uniaxial) 1 Flexion–Extension. Example Elbow, Knee
Ellipsoid/Condyloid (Biaxial) 2 Flexion–Extension, Abduction–Adduction. Example Wrist
Ball and Socket (Multiaxial) 3 Flex/Ext, Abd/Add, Rotation Shoulder, Hip
Let me know if you’d like a visual or mnemonic to remember them better.
Haha — great observation again! Let’s break it down simply:
Yes, you can move your elbow a bit side to side, but…
That side-to-side movement isn’t coming from the hinge joint (elbow joint) itself.
Here’s what’s really happening:
1. The elbow joint (between humerus and ulna) is a hinge joint — it strictly does flexion and extension only.
2. The slight side-to-side movement you notice is actually:
• From your shoulder joint (a ball-and-socket joint) allowing your arm to shift side-to-side.
• Or from rotation at the forearm (pronation/supination) at the proximal radioulnar joint — which is a pivot joint, not the hinge part.
Why the elbow is still uniaxial:
• The main elbow hinge (humeroulnar joint) only allows movement in one plane (flex–extend).
• It doesn’t allow true abduction/adduction like you see in wrist or shoulder joints.
So, even if you can move your whole forearm side-to-side, the actual hinge joint itself is not responsible for that movement — it’s coming from other joints nearby.
Simple analogy:
Imagine a door hinge — you might wiggle the door a bit sideways by pushing on it, but the hinge only rotates the door open and closed. That’s how your elbow hinge works too.
Would you like a simple diagram of these joints and their movements?
No, circumduction does not include rotation.
Why?
• Circumduction is a combination of flexion, abduction, extension, and adduction, creating a circular motion without twisting the limb around its long axis.
• Rotation, on the other hand, involves turning a body part around its longitudinal axis (e.g., medial and lateral rotation of the shoulder).
Example to Differentiate
• Circumduction → Moving your arm in a circular motion (like drawing a circle in the air).
• Rotation → Turning your palm up and down (supination/pronation) or twisting your head side to side.
Would you like a simple way to visualize this?
How to know where the angles are in joints so you know if there’s flexion or extension
Of course! Here’s the list in bullet form:
• Elbow joint
• Look at the inner angle between the upper arm and forearm.
• Flexion = forearm bends toward upper arm (angle decreases).
• Extension = forearm straightens away from upper arm (angle increases).
• Knee joint
• Look at the back of the knee (between thigh and leg).
• Flexion = leg bends backward (angle decreases).
• Extension = leg straightens forward (angle increases).
• Shoulder joint
• Look at the angle between the upper arm and the trunk.
• Flexion = arm moves forward or upward.
• Extension = arm moves backward or downward.
• Hip joint
• Look at the angle between the thigh and the trunk.
• Flexion = thigh moves forward or toward the chest.
• Extension = thigh moves backward.
• Wrist joint
• Look at the angle between the forearm and the hand.
• Flexion = hand bends toward the palm.
• Extension = hand bends toward the back of the hand.
• Spine/Neck
• Look at the angle between the head or torso and the spine.
• Flexion = bending forward.
• Extension = straightening up or leaning back.
• Fingers/Toes
• Look at the angle between the bones of the digits.
• Flexion = curling the fingers or toes.
• Extension = straightening them out.
Let me know if you want this as a printable summary or diagram too.
