Flashcards in Clinical Genetics And Biochemistry Deck (239):
What is a transposon and how much of the human genome is made up of transposon repeats?
A mobile genetic element. 45% of human genome
Are transposons well or poorly conserved?
What are piRNAs?
Piwi protein interacting RNAs which control transposon activity. They are an example of non-coding RNA
What is heterochromatin and how much of the human genome is made up of it?
Tightly packed repetitive DNA with little or no active gene expression. Stains darkly with giemsa stain. Makes up 6.7% of the human genome.
What is euchromatin?
Loosely packed DNA with lots of active gene expression. Pale staining with giemsa.
What is chromatin?
DNA and histones
What makes up 3 - 4% of the human genome?
Non coding mRNA genes
Is heterochromatin well or poorly conserved?
What does non coding RNA do?
It regulates the expression of protein coding mRNA genes
Give examples of non-coding RNA
PiRNA and microRNA. PiRNA regulates transposon activity. MicroRNAs can silence protein coding mRNA or stop translation
What makes up 1.2% of the human genome?
Protein coding mRNA gene
Are RNA genes well or poorly conserved?
What are the three types of mutations?
Conferring disease susceptibility (risk allele)
What is a polymorphism?
What are the 5 types of disease causing mutations in DNA and chromosomes?
SNPs (single nucleotide polymorphism aka point mutation)
Indels (small insertions or deletions)
CNV (copy number variants, large indels)
Microsatellites (dynamic) (expansion or contraction of tandemly repeated DNA)
Minisatellite (expansion or contraction of tandemly repeated DNA)
Which disease causing mutations are associated with repetitive DNA?
What is a SNP?
Single nucleotide polymorphism. It is pathogenic if it changes the open reading frame or is found in the promoter or regulatory region as this will change the amount of mRNA produced.
What is an indel?
Small insertions or deletions. SNP indel = 1 nucleotide inserted or deleted. Micro indel = more than 1 nucleotide inserted/deleted
What is a CNV?
Large indel, duplication or inversion
What are micro and mini satellites and which of them is dynamic?
Contractions or expansions of tandemly repeated DNA. Microsatellites are dynamic.
What is a Barr body?
Chromatin of an inactive X chromosome. It is seen as a blob of condensed chromatin at the edge of the nucleus of a cell in interphase.
What is a manifesting heterozygote?
A female carrier of an X linked recessive condition who shows some symptoms due to skewed X inactivation
What does hemizygous mean?
A boy with one affected X chromosome in an X linked recessive condition
What is a true homozygote?
Have inherited 2 copies of the same mutation (usually due to consanguineous mating)
What is a compound heterozygote?
Inherited 2 different mutations but has phenotype of homozygote (most homozygotes are actually compound heterozygotes, unless consanguineous mating is involved)
What is consanguineous mating?
1st cousin mating
What is a dynamic mutation?
The mutation increases in length between the parent and the child e.g. Microsatellites
What is genomic imprinting? Give an example
Where expression of an allele is dependent on its parental origin e.g. Paternal 15q12 deletion causes Prader-Willi syndrome in boys. Maternal 15q12 deletion causes angelman syndrome in girls.
7 Location of mutations in protein coding genes
Exon donor consensus
Exon acceptor consensus
Poly A tail
8 Location of mutations in protein coding genes
Intron donor consensus
Intron acceptor consensus
Within an exon
Poly A addition signal
What is the point of the untranslated region of a gene?
It is where microRNAs look for sequences to regulate gene expression
What happens if there is a mutation in the enhancer or promoter region of a gene?
There will be an increase or decrease in gene product
What happens if there is a mutation at the start codon?
No translation of abnormal translation
What happens if there is a mutation at the intron donor consensus (beginning of intron) or intron acceptor consensus (end of intron)?
What is an intron?
Non coding section of a gene
What is an exon?
Coding section of a gene
What happens if there is a mutation in the stop codon?
Translation will not be stopped and the protein will get bigger
What happens if there is a mutation in the poly A addition signal?
mRNA will not be polyadenylated resulting in less stable mRNA and hence less protein
What is the poly A tail added to?
It is added to mRNA to increase its stability
What effects can a mutation have on a protein?
Loss of function (little/no protein produced or faulty protein produced)
Gain of function (harmful product or enhanced function or new function)
Dominant negative (mutant protein interferes with function of wild type protein e.g. Mutation in one collage oligomer will disrupt the whole collagen structure)
What is snRNA?
Small nuclear RNA. It is involved in splicing.
What can mutations in miRNA cause?
EDICT (eye disease)
What can mutations in snRNA cause?
MOPD type 1 which is a type of primordial dwarfism
What is long ncRNA?
Long non coding RNA (>200 bp)
What do mutations in long ncRNA cause?
What is a SNP RFLP?
Restriction fragment length polymorphism. Gain/loss of a restriction site.
What is a transition?
SNP which results in a purine to purine change (A to G) or a pyrimidine to pyrimidine change (T to C)
What is a purine
Adenine and guanine
What is a pyrimidine
Cytosine and thymine
Which bases bind together?
A binds T
G binds C
What is a transversion
Where a SNP results in a purine (A or G) being swapped for a pyrimidine (C or T) or vice versa
What is a synonymous SNP?
Silent mutation (amino acid remains the same)
What is a non-synonymous SNP?
Results in a different amino acid with very different properties from the original one
What is a Missense mutation?
Changes in the coding sequence result in one amino acid being swapped for another. Can be conservative or non-conservative.
What is a conservative Missense mutation?
Changes in the coding sequence result in an amino acid change. The new amino acid has similar properties to the old one.
What is a non-conservative Missense mutation?
Changes in the coding sequence result in a change in amino acid, the new amino acid does not have similar properties to the old one
What does a SNP indel cause?
A frameshift mutation, since it inserts/deletes 1 nucleotide (ie not a multiple of 3).
What causes a frameshift mutation?
Inserting/deleting a number of nucleotides which is not a multiple of 3
What is a nonsense mutation?
It causes insertion of a premature stop codon
What are the 3 methods of detecting SNPs?
Restriction digest followed by gel electrophoresis (SNP RFLP only)
Glycogen formation from glucose
Glycogen breakdown to form glucose and glucose-6-phosphate
Production of glucose from other metabolic pathways (especially glucose from pyruvate)
What is glycolysis?
Anaerobic conversion of glucose to pyruvate
What are the products of glycolysis?
Net 2 ATP
What are the 3 stages of glycolysis?
Glucose to fructose-1-6-bisphosphate
DHAP to glutaraldehyde
Glutaraldehyde to pyruvate (occurs twice)
How many carbon atoms in pyruvate?
Where and how is glycolysis controlled?
At the formation of glucose-6-phosphate
At the formation of fructose-1,6-bisphosphate. Phosphofructokinase is regulated by fructose-2,6-bisphosphate. Lots of glucose = lots of fructose-2,6-bisphosphate which activates phosphofructokinase. Vice versa for low glucose.
What are the only tissues that have an absolute requirement for blood glucose for metabolism?
What energy source can the brain use in starvation?
Ketones from fatty acid breakdown
When does most gluconeogenesis occur?
Where is most glycogen stored?
Mainly in muscle but some in liver
Where is glycogen made?
Where is most glycogen stored?
Mainly in muscle but some in liver
When does most gluconeogenesis occur?
What energy source can the brain use in starvation?
Ketones from fatty acid breakdown
What are the three steps of glycolysis which have a large negative delta G and are essentially irreversible?
What is hexokinase inhibited by?
What is phosphofructokinase inhibited by?
Citrate and ATP
What is phosphofructokinase activated by?
What is pyruvate kinase inhibited by?
Alanine and ATP
What is pyruvate kinase activated by?
What are all steroid hormones synthesised from?
What are 3 classes of steroid hormone?
Corticosteroids (glucocorticoids such as cortisol) (mineralocorticoids such as aldosterone)
Where does steroid synthesis occur?
Which enzymes are involved in steroid synthesis?
Members of the cytochrome P450 oxidase family
Which gene codes for enzymes involved in steroid synthesis?
What are symptoms of diabetes?
Unexplained weight loss
Slow healing of cuts
Ketone smell on breath due to ketoacidosis
What is the main difficulty in recognising diabetes symptoms?
What is the main difference in symptoms between type 1 and type 2 diabetes?
Type 1 symptoms develop quickly
Compare insulin and glucagon levels in type 1 diabetes?
Insulin levels are low
Glucagon levels are high
What is the 1st step in diagnosing diabetes?
Glucose in urine test
What conditions are associated with type 2 diabetes?
Low HDL cholesterol
High fasting glucose
High blood pressure
What is impaired glucose tolerance?
More insulin secreted as insulin receptors lose sensitivity
How do adipocytes contribute to insulin resistance?
They secrete adipokines which increase insulin resistance and they inhibit secretion of adiponectin which increases insulin sensitivity
What acute complications are associated with type 1 diabetes?
Hypoglycaemic coma (too much insulin or insufficient glucose from diet)
What are chronic complications of diabetes?
Retinopathy and cataracts
Neuropathy and nephronopathy caused by diabetic microangiopathy. For type 2 diabetes major causes of death are stroke and peripheral vascular disease.
What are the 4 mechanisms of glucose mediated damage?
Production of ROS
Protein kinase C
Non-enzymatic glycation of proteins
How are blood glucose levels measured?
Using immobilised glucose oxidase which generates hydrogen peroxide which generates a colour change
What is HbA 1c?
Haemoglobin A which has been non-enzymatically modified by glycation
How does insulin resistance lead to type 2 diabetes?
Overproduction of insulin, high glucose levels and free fatty acid levels damage beta cells. (Beta cells die with age but obesity and insulin resistance increase rate of death)
What is meant by an unsaturated fat?
Double bonds in the fatty acids
What is a triacylglyceride made up of?
3 fatty acid chains bound to a glycerol by ester linkages
Compare fat and glycogen as energy stores?
7 x more energy in 1 gram of fat compared to 1 gram of glycogen because glycogen carries water for hydration. Also triacylglycerols are more reduced so release more energy when oxidised. The body can only store less than one day's worth of glycogen whereas fat stores can meet energy requirements for months
Where is fat found in the body?
Under the skin
In the abdominal cavity
What is brown fat?
Fat found in newborns. Contains more mitochondria so appears brown
What are adipocytes?
Cells that store large amounts of triacylglycerols as fat droplets
What 4 functions does cholesterol have?
It maintains membrane fluidity
It is the precursor for steroid hormones
It is the precursor for bile acids
It is the precursor for vitamin D
Where does cholesterol come from
Half is synthesised de novo and half is from the diet
Where are the major synthesis sites for cholesterol?
What is the starting point for cholesterol synthesis?
What is the main role of vitamin D?
What is the difference between cholesterol and cholesteryl esters?
Cholesteryl esters are more hydrophobic and cannot be incorporated into membranes
What is a PEST sequence?
An amino acid sequence on cell cycle proteins that targets them for rapid degradation
Names the types of mutations associated with repetitive dna in order of size
Copy number variants
What is anticipation?
When a disease gets more severe with each generation (associated with microsatellites which are dynamic)
How big are microsatellites?
Less than 100bp
Name a disease caused by microsatellites
What techniques can be used to analyse microsatellites?
Triplet repeat primed pcr
How big are minisatellites?
1 - 400kb
Name a disease caused by minisatellites
Myoclonus epilepsy. There is a minisatellite repeat in the promoter region of the cystatin b gene
What do CNVs arise from?
Low copy repeats
Name 3 diseases associated with CNVs
Haemophilia A (x linked recessive)
Prader willi (imprinting deletion of 15q12)
Angelman (imprinting deletion of 15q12)
How are CNVs detected?
Why is colchicine used in karyotyping?
It stops the cell cycle in metaphase
Which dye is used in karyotyping?
What causes down syndrome?
What does it mean to be homozygous for a minisatellite or microsatellite?
Same number of repeats
What does it mean to be heterozygous for microsatellites and minisatellites?
Different numbers of repeats
What is a haplotype?
Alleles which are inherited together
Which type of screening is used to test for cystic fibrosis and sickle cell disease?
Which tests are used to screen for dystroglycanopathies
Where in a cell is glucose-6-phosphate converted to glucose?
In which cells is it possible for glucose-6-phosphate to be converted to glucose?
Kidney cortex, beta cells, liver, muscle
Why are 5 proteins required to generate glucose from glucose-6-phosphate?
3 transport proteins, 1 glucose-6-phosphatase and 1 stabilising protein
In terms of glucose homeostasis what are the anabolic hormones?
In terms of glucose homeostasis what are the catabolic hormones?
Glucagon, cortisol and catecholamines (adrenaline and noradrenaline)
Which cells secrete glucagon?
Alpha cells of the islets of langerhans in the pancreas
Which cells secrete insulin?
Beta cells of the islets of langerhans
What carries out the exocrine function of the pancreas?
What is the morphological difference between alpha and beta cells?
Alpha cells are larger and found at the periphery of the islets of langerhans
Beta cells are smaller and found at the centre of islets of langerhans
What do delta cells of the islets of langerhans secrete?
Somatostatin which inhibits growth hormone
What do pp cells of the islets of langerhans secrete?
Describe how insulin goes from preproinsulin to insulin?
It is secreted as preproinsulin in the ER where the signal peptide is cleaved to form proinsulin. Then the c peptide is cleaved in the secretory granule to form insulin (same process for glucagon, secreted from preproglucagon)
Describe the structure of insulin
Alpha and beta chain held together by 2 disulfide bonds
What are the 2 ways insulin can exist?
What are triggers for insulin secretion?
Increased blood glucose levels
Parasympathetic stimulation (ACh)
Where is insulin stored?
Granules in beta cells in islets of langerhans in the pancreas
What happens to insulin when it reaches target cells?
It binds to insulin receptors, gets internalised, dimerises, aggregates, autophosphorylates and phosphorylates effector proteins
Which tissues does insulin target?
What effects does insulin have on the liver?
Stimulates glycolysis, synthesis of glycogen, fatty acids, TAGs, VLDLs. Supresses gluconeogenesis
What effect does insulin have on adipose tissue?
Stimulates fatty acid synthesis
Upregulates glut4 for more glucose uptake
What effect does insulin have on muscle cells?
Increases glycogen synthesis
Increases amino acid uptake and protein synthesis
Upregulates GLUT4 for more glucose uptake
What is the cause of type 1 diabetes mellitus?
Autoimmune destruction of beta cells
What triggers glucagon secretion?
Low blood glucose conc
Some GI hormones
What decreases glucagon secretion?
High blood glucose
High FFA in blood
What is the half life of glucagon?
In which organs is glucagon degraded?
Liver and kidneys
Which tissues does glucagon affect?
Liver and adipose
How does glucagon affect the liver?
Stimulates breakdown of glycogen
Inhibits glycolysis (inhibiting PFK-1 with citrate and pyruvate kinase with alanine)
Inhibits production of glycogen
Inhibits lipogenesis (inhibition of acetyl coA carboxylase)
What effect does glucagon have on adipose tissue?
Stimulates lipolysis (cAMP activation of hormone lipase which converts TAGs to FFA and glycerol, FFA undergo beta oxidation to produce ATP. Glycerol is converted to glucose by gluconeogenesis).
Which tissues are affected by adrenaline?
Liver and muscle
What affects on glucose homeostasis does adrenaline have?
Similar effects to glucagon. Stimulates gluconeogenesis and inhibits glycogen and fat synthesis
Which receptors does adrenaline bind to in the liver?
Which receptors does adrenaline bind to in muscle?
Where is adrenaline and noradrenaline stored?
Granules in adrenal chromaffin cells
What is non-enzymatic glycation of proteins?
Where glucose binds to valine and lysine side chains forming advanced glycation end products. Receptor for advanced glycation end products causes inflammation
What is the polyol pathway?
Where glucose is converted to sorbitol by aldose reductase. Sorbitol accumulates in cells that do not possess sorbitol dehydrogenase. Sorbitol accumulation causes cataracts and neuropathy by reducing myo-inositol uptake
What are the treatments for type 2 diabetes mellitus?
What does acarbose do?
Slows breakdown of carbohydrates in the gut by inhibiting alpha glucosidase
How does metformin work?
Affects insulin signalling and sensitivity
How do sulfonylureas work?
Increase sensitivity of beta cells to glucose to increase insulin synthesis
What are the steps in cortisol production?
Cholesterol to pregnenolone to cortisol
Which enzyme converts cholesterol to pregnenolone?
Which enzyme converts pregnenolone to cortisol?
A cytochrome p450 oxidase
Where is cortisol produced?
The zona fasciculata of the adrenal cortex
What is cortisol bound to in the blood?
Corticosteroid binding globulin or albumin
How does cortisol affect the immune system?
Decreases circulating leukocytes and impairs b cell and t cell response
What 6 things does cortisol affect?
Central nervous system
Bone and calcium metabolism
What is cortisol's affect on the central nervous system?
What effect does cortisol have on connective tissue?
Inhibits fibroblasts leading to loss of collagen, thinning of skin and easy bruising
How does cortisol affect the cardiovascular system?
Increases cardiac output
How does cortisol affect bone and calcium metabolism?
Inhibits bone formation
Decreases calcium uptake from the gut
Increases parathyroid release
What is also secreted with ACTH?
How do pyrimidine and purine de novo synthesis differ?
Pyrimidine the ring is built and added onto activated ribose. Purine the ring is built onto activated ribose
What is the starting point for pyrimidine synthesis?
How is de novo pyrimidine synthesis regulated?
ATCase is allosterically inhibited by CTP
How is oritidylate converted into UMP?
How is UTP converted to CTP?
How is dUMP converted to dTMP?
Methylation - this step is blocked by anticancer drugs
What is needed for the salvage pathway for purines?
What is lesch-nyhan syndrome?
Loss of HPRT activity so loss of salvage pathway for purines. Mental deficiencies and self destructive behaviour
What is the defect in severe combined immunodeficiency?
What are the treatments for SCID?
Bone marrow transplant
PEGylated ADA injection
How does allopurinol treat gout?
It inhibits xanthine oxidase which is an enzyme in uric acid production from purines
How is glycerol converted to glucose in gluconeogenesis?
Glycerol kinase converts it to glycerol 3 phosphate. Which is then converted to DHAP which is then converted to glucose
Why is glutamine required for nucleotide synthesis?
Provides NH4 for amidation of UTP to CTP in pyrimidine synthesis.
Provides NH4 for amidation of activated ribose in the first step of purine synthesis to form 5-phosphoribosyl-1-amine
How are ribonucleotides converted to deoxyribonucleotides?
Reduction using NADPH and catalysed by ribonucleotide reductase
Which enzyme is used in the salvage pathway for pyrimidines?
What happens to triacylglycerols in the lumen of the intestine?
They are hydrolysed by lipases to fatty acids and monoacylglycerols which diffuse into mucosal cells
In terms of dietary fat digestion what happens in mucosal cells?
Monoacylglycerols and fatty acids are converted to TAGs again and are packages into chylomicrons with cholesterol and apolipoprotein c-11. Chylomicrons then move into the lymph and blood
What happens to chylomicrons in capillaries?
Apo c-11 activates lipoprotein lipases which hydrolyse TAGs to fatty acids and glycerol. Glycerol goes to the liver for glycolysis or gluconeogenesis. Fatty acids either go to the muscle for beta oxidation or adipose tissue for storage
How are fatty acids transported in the blood?
Bound to albumin
Where does beta oxidation take place?
Mitochondria or peroxisomes
How are substances activated for fatty acid degradation/synthesis?
Attached to carrier protein
What is the carrier protein for fatty acid degradation?
What is the carrier protein for fatty acid synthesis?
What is the product of fatty acid activation?
Which enzyme carries out fatty acid activation?
Acyl coA synthetase
Where does fatty acid oxidation occur?
What is used to transport acyl coA into mitochondria?
What does carnitine acyltransferase I do?
Attaches acyl coA to carnitine
What does carnitine acyltransferase II do?
Recycles carntine out of the mitochondrial matrix
What is the end product of beta oxidation?
An acyl coA which is 2 carbons shorter and acetyl coA
How many steps in beta oxidation?
What occurs in step 1 of mitochondrial beta oxidation?
Oxidation catalysed by acyl coA dehydrogenase. FADH2 is formed
What are the 4 steps of mitochondrial beta oxidation?
What happens to acetyl CoA formed in beta oxidation?
It enters the citric acid cycle where is it converted to water and carbon dioxide. The electrons formed are used in oxidative phosphorylation to form ATP
What is MCAD deficiency
Medium chain acyl dehydrogenase deficiency. Cannot breakdown acyl coA chains of lengths C6 - C12
What are the symptoms of MCAD deficiency?
Fat accumulation in the liver
Low blood glucose levels
High blood octanic acid levels
High concs of C6 - C12 carboxylic acids in urine
When is beta oxidation in peroxisomes used?
For very long chain fatty acids
What is the inheritance of MCAD?
How is beta oxidation in peroxisomes different to beta oxidation in mitochondria?
In peroxisomes hydrogen peroxide is made in the first step rather than FADH2. Hydrogen peroxide is immediately broken down by catalase. No ATP is produced, only heat.
What is x linked adrenoleukodystrophy?
Lack of transporters for v long chain fatty acids = accumulation of v long chain fatty acids in blood and death
What is zellweger syndrome?
Lack of peroxisomes = v long chain fatty acids in blood = death
What are the fates of acetyl coA?
Citric acid cycle
Forms ketone bodies in the liver when oxaloacetate is consumed in Gluconeogenesis
Used for fatty acid and cholesterol synthesis
Where are ketone bodies formed?
Name some ketone bodies?
What is the affect of ketone body formation?
Ketoacidoisis and coma due to decrease in blood pH
Ketone smell on breath
Where does fatty acid synthesis take place?
Cytoplasm of liver cells and adipocytes
How is acetyl coA transported from the mitochondrial matrix to the cytoplasm for fatty acid synthesis?
What is the first committed step (irreversible) in fatty acid synthesis?
Acetyl coA is converted to malonyl coA. Catalysed by acetyl coA carboxylase and requires ATP
Which enzyme produces acetyl-CoA and malonyl coA?
What is the role of desatuare?
Adds double bonds to fatty acids
Which enzymes are used in cholesteryl ester synthesis?
Acyl coA cholesterol acyl transferase
What is used to treat high cholesterol?
Resins and statins
How do statins work?
They are competitive inhibitors of HMG-coA reductase, they increase the number of LDL receptors, they stabilise atherosclerotic plaques, they are anti-inflammatory, they improve endothelium
What is the enterohepatic cycle?
Bile salts are reabsorbed in the small intestine and returned to the liver by the hepatic portal vein where they returned to circulation