CMB Week 2 Flashcards
In sickled cells, valine causes a … that polymerizes when Hb is …
In sickled cells, valine causes a hydrophobic patch that polymerizes when Hb is deoxygenated.
In HbS, when RBCs rupture, the vessels become …
In HbS, when RBCs rupture, the vessels become occluded (trapped cells).
Vaso-occlusion is a complex event involving - - - - leading to tissue damage from ….
Vaso-occlusion is a complex event involving - endothelial activation - leukocyte and red cell adhesion - hemoglobin polymerization - ischemia and infarction leading to tissue damage from necrosis.
The sickle cell trait provides a … in areas where falciparum malaria is endemic
The sickle cell trait provides a survival advantage (balanced polymorphism) in areas where falciparum malaria is endemic
Three tests used to diagnose sickle cell disease
1) Solubility test 2) Hemoglobin electrophoresis 3) DNA analyses (Restriction Fragment Length Polymorphism)
Solubility test for sickle cell disease
- blood is added to a solution with high ionic strength (2% sodium metabisulfite) - Deoxyhemoglobin S has a low solubility in this solution whereas deoxyhemoglobin A is soluble - this test cannot distinguish the trait from the disease state
Hemoglobin Electrophoresis
- agarose gel using a citrate buffer pH 6.0 - larger molecules will migrate more slowly - HbS will move more slowly than normal HbA - AS (sickle cell trait) will show as two pieces, with heavier HbS at the top - HbF - smallest, will run quickest
DNA analyses: Restriction Fragment Length Polymorphism (RFLP)
- more sensitive method that can be used to detect the DNA mutation in HbS - RFLP based on the ability of restriction endonucleases to cleave specific sites within the DNA sequences - if the cleavage site contains a mutation, the restriction endonucleases can no longer cleave at that site leaving a larger DNA fragment compared to the DNA with the normal sequence
One method for prevention of crises in sickle cell anemia is partial exchange …, although this is only used in select cases due to the complication of ….
One method for prevention of crises in sickle cell anemia is partial-exchange blood transfusion, although this is only used in select cases due to the complication of iron overload (transfusion-induced hemosiderosis)
transfusion-induced hemosiderosis
- iron overload - there is no excretory pathway in the body for eliminating excess iron and its accumulation can result in organ failure.
Besides blood transfusions, what are two other forms of treatment for sickle cell anemia?
- bone marrow transplantation to repopulate the patient’s bone marrow with normal donor cells - induction of HbF synthesis
Why would increase levels of HbF help in sickle cell disease?
- HbF has been shown to inhibit sickling - inhibits Hb polymerization - in individuals who express higher levels of HbF, the RBCs do not become as deformed and vaso-occlusive crises do not occur
What drug increases the expression of HbF
hydroxyurea
If a proline is substituted into the alpha helical region of hemoglobin, an unstable hemoglobin can arise because:
Prolines are helix breakers and the breaking of an α-helical segment can cause an unstable hemoglobin
Hemoglobinopathies of increased oxygen affinity are often characterized by … anemia and ….
Hemoglobinopathies of increased oxygen affinity are often characterized by hemolytic anemia and Heinz body formation.
Patients with higher than 10% of HbM will show …
Patients with higher than 10% of HbM will show cyanosis
Patients with higher than 35% of HbM will have clinical symptoms such as …
Patients with higher than 35% of HbM will have clinical symptoms such as headache and weakness.
A higher than 80% of HbM is not …
A higher than 80% of HbM is not compatible with life.
The deficiency of the enzyme … that can reduce the ferric iron back to the ferrous state can also result in …
The deficiency of the enzyme diaphorase that can reduce the ferric iron back to the ferrous state can also result in methemoglobinemia.
Operon
cluster of genes that code for proteins involved in a particular metabolic pathway
An operon is made up of several structural genes arranged under a … and regulated by a …
An operon is made up of several structural genes arranged under a common promoter and regulated by a common operator
The lactose operon is an example of …
inducible operon
The lactose operon contains genes that
encode enzymes responsible for lactose metabolism
What are the 3 structural genes in lac operon?
lac Z, lac Y, and lac A
lac Z
- gene that codes for the enzyme beta-galactosidase - beta-galactosidase breaks down lactose into glucose and galactose
lac Y
- gene that codes for the enzyme permease - permease transports lactose into the cell
lac A
gene that codes for the enzyme transacetylase
In addition to the structural genes, the lac operon has:
- promoter (P) - Operator (O) - CAP binding site (catabolite gene activator protein) - repressor gene (lac I)
The repressor gene in lac operon binds to:
lac I: lac repressor binds a) to DNA of the operator region, prevents RNA pol advancing along the operon, and transcription does not occur b) binds to lactose
In the absence of lactose (i.e. in the presence of glucose)
- lac I gene is transcribed and translated, producing the lac repressor protein - lac I binds to the operator and blocks RNA pol - no transcription - enzymes for lactose metabolism are not synthesized
If there is lactose in the environment and a small amount of the lactose gets into the cell:
- lac repressor is constitutively synthesized - lac I binds to the lactose, which induces conformation change in lac I and is now unable to bind to the operator region - RNA pol can transcribe the genes of the operon
When both glucose and lactose are available in the cell:
-transcription of the operon is negligible - adenylate cyclase is deactivated - no cAMP produced
… is active in the absence of glucose, producing … that binds to CAP. This further promotes …
Adenylate cyclase is active in the absence of glucose, producing cAMP that binds to CAP. This further promotes transcription of structural genes.
Repressible operon
- transcription of the operon normally takes place (operon is ON) - activated repressor protein binds to operator and prevents transcription
The tryptophan (trp) operon is an example of a …
repressible operon
If there is plenty of trp around, and no more is needed, the operon is …. If there is no trp around, it needs to be synthesized, and the operon is …, allowing the production of the enzymes for trp synthesis
If there is plenty of trp around, and no more is needed, the operon is repressed. If there is no trp around, it needs to be synthesized, and the operon is transcribed, allowing the production of the enzymes for trp synthesis
Regulation of transcription in response to lack of amino acids (prokaryotes)
- Uncharged tRNA binds to the A site of the large ribosome subunit, activating stringent factor ReIA - ReIA synthesizes polyphosphorylated guanosine (ppGpp) - Results in selective inhibition of transcription (protein synthesis is inhibited), until AAs are available
Hereditary persistence of fetal hemoglobin (HPFH)
a benign condition in which significant fetal hemoglobin production continues well into adulthood, disregarding the normal shutoff point after which only adult-type hemoglobin should be produced
As HbF switches to HbA, the activation of β chain acts to …
As HbF switches to HbA, the activation of β chain acts to down regulate the production of gamma and delta goblins
In HbSC, the individual is … and …
In HbSC, the individual is heterozygous for the sickle cell trait and heterozygous for the HbC disease.
Common motifs in proteins that bind DNA and regulate transcription
- helix-turn-helix - leucine zipper - zinc finger
Cis-acting regulatory elements (CREs)
specific regulatory DNA sequence that binds trans-acting protein factors
Nuclear receptors mostly sense small hydrophobic molecules such as ….
Nuclear receptors mostly sense small hydrophobic molecules such as steroid and thyroid hormones.
Apolipoprotein B is a protein that carries fat molecules around in the body. The ApoB mRNA is made in the ….
Liver
In the intestine, on ApoB-100 protein, the C residues in the codon CAA (glutamine) is deaminated to U, making a nonsense codon; creating a shorter protein Apo B-48. This is an example of
mRNA editing
Chylomicrons
- a large plasma lipoprotein particle - transports neutral lipids from the intestine to the tissues by way of the lymph.
RNA interference (RNAi)
mechanism of gene silencing through decreased expression of mRNA, either by repression or by increased degradation
RNA interference (RNAi) is mediated by
microRNA (miRNA), a short 22 bp non-coding RNA
endonuclease DICER cleaves double-stranded RNA creating
endonuclease DICER cleaves double-stranded RNA creating short double-stranded RNA fragments called small interfering RNA (siRNA) and microRNA
RISC – RNA-induced silencing complex
a multiprotein complex, specifically a ribonucleoprotein, regulates mRNA expression
RISC associates with …, which acts as a …
RISC associates with one strand of siRNA or miRNA, which acts as a template for RISC to recognize the complementary sequence on mRNA
Once RISC has recognized the target mRNA, RISC can …
Once RISC has recognized the target mRNA, RISC can repress the translation of the target mRNA
Slicer/Argonaute/Ago are proteins found in RISC that can …
Slicer/Argonaute/Ago are proteins found in RISC that can cleave the target mRNA leading to degradation.
Phosphorylation of Eukaryotic Initiation Factor 2 (eIF2)
inhibits its function and inhibits translation at the initiation step.
On DNA, histone proteins are covalently modified at their … terminal end by … or …. to influence …
On DNA, histone proteins are covalently modified at their NH2 terminal end by acetylation or phosphorylation to influence gene expression.
Methylation modifies the … of the DNA, typically acting to …
Methylation modifies the function of the DNA, typically acting to suppress gene transcription.
Which two DNA nucleotides can be methylated?
adenine and cytosine
Adenine DNA mythelation only occurs in …
prokaryotes
CpG islands
unmethylated CpGs are often grouped in clusters called CpG islands
In many disease processes, such as cancer, gene promoter CpG islands acquire …, which results in …
In many disease processes, such as cancer, gene promoter CpG islands acquire abnormal hypermethylation, which results in transcriptional silencing.
Chromatin remodeling:
Chromatin remodeling is the modification of chromatin architecture to allow access to the condensed genomic DNA, influencing gene expression.
Chromatin remodeling relaxes the …
the nucleosome
Transposons
mobile segments of DNA that move in random manner from one site to another, on the same or different chromosome
Direct transposon movement, …
Direct transposon movement, cuts out and then inserts the transposons at a new site.
In replicative transposon movement, the transposon is … elsewhere while the original …
In replicative transposon movement, the transposon is copied and the copy is inserted elsewhere while the original remains in place.
Transcriptional factors are of clinical significance for at least two reasons:
1) mutations can be associated with specific diseases 2) they can be targets of medications
Oncogene
a gene that has potential to cause cancer
Many transcription factors are either … or … so mutations or aberrant regulation of them is associated with …
Many transcription factors are either tumor suppressors or oncogenes, so mutations or aberrant regulation of them is associated with cancer.
Three groups of transcription factors important in human cancer
1) the NF-kappaB and AP-1 families (2) the STAT family (3) the steroid receptors
Mutations in the … transcription factor are associated with Rett syndrome, a …
Mutations in the MECP2 transcription factor are associated with Rett syndrome, a neurodevelopmental disorder
A rare form of diabetes called MODY (Maturity onset of diabetes of the young), can be caused by mutations in … or …
A rare form of diabetes called MODY (Maturity onset of diabetes of the young), can be caused by mutations in hepatocyte nuclear factors (HNFs) or insulin promoter factor 1 (IPF1)
Mutations in the … transcription factor are associated with …, a disease in which individuals are unable to produce the finely coordinated movements required for speech
Mutations in the FOXP2 transcription factor are associated with developmental verbal dyspraxia, a disease in which individuals are unable to produce the finely coordinated movements required for speech
Mutations in the … transcription factor cause the autoimmune disease called IPEX, which leads to a …
Mutations in the FOXP3 transcription factor cause autoimmune disease called IPEX, which leads to a dysfunction in regulatory T-cells
Li-Fraumeni syndrome is a rare hereditary disorder, leading to …, caused by mutations in the … gene
Li-Fraumeni syndrome is a rare hereditary disorder, leading to cancer predisposition, caused by mutations in the tumor suppressor p53 gene.
The STAT family of transcription factors are associated with …
The STAT family of transcription factors are associated with breast cancer.
A variety of cancers are associated with the … of transcription factors.
HOX family
Most Osteogenesis Imperfecta (OI) cases are caused by
type I collagen mutations
Severity of OI disorders from most severe to mildest
Most severe: OI type II ➡️ type III ️ ➡️ type IV ➡️ type I (mildest)
OI type I is the most …. It is an autosomal … Features include:
OI type I is the most mild and most common. It is an autosomal dominant inherited disorder. Features include: - blue sclerae, mild to moderate bone fragility before puberty. - hearing loss, which progresses to severe as adults - mitral valve prolapse - easy bruising - large joints are hyperextensible
OI type IA has no …, while type IB does.
dentinogenesis imperfecta
Dentinogenesis imperfecta (DI) is a
genetic disorder of tooth development.
OI type II is the … form of the disease, and leads to … due to … The disease is caused by new … Characteristics:
OI type II is the most severe form of the disease, and leads to death in utero or in the perinatal period due to respiratory failure. The disease is caused by new dominant mutations. Characteristics: - multiple utero fractures - triangular face flat mid face - small beaked nose - bluish-gray sclerae
OI type III is a progressively … and is the most … Most are caused by .. mutations, but … mutations have been reported. Many die in childhood or adulthood due to …. Characteristics include:
OI type III is a progressively deforming OI and is the most severe form compatible with life beyond infancy. Most are caused by dominant mutations, but recessive mutations have been reported. Many die in childhood or adulthood due to respiratory, cardiac or neurological complications. Characteristics include: - macrocephaly (increased head circumference) - triangular flat mid face - bluish sclerae which lighten with age - long bone and spine deformities
OI type IV includes a variety of … forms of …. inherited disorders, with mild to moderate … Characteristics include:
OI type IV includes a variety of moderately severe forms of dominantly inherited disorders with mild to moderate bone fragility. Characteristics include: - prenatal fractures - osteoporosis - macrocephaly - scloliosis -short stature
OI type IVA has no …, while type IVB does.
dentinogenesis imperfecta
When recombinant DNA encoding a protein is introduced into a host organism, the recombinant protein will …. Expression of foreign proteins requires the use of …
When recombinant DNA encoding a protein is introduced into a host organism, the recombinant protein will not necessarily be produced. Expression of foreign proteins requires the use of specialized expression vectors.
Recombinant DNA (rDNA) are:
Recombinant DNA (rDNA) are formed by laboratory methods, and are sequences generated from multiple sources, creating DNA that would not otherwise be found in biological organisms.
Vector (DNA)
Any molecule that has the ability to replicated inside the host
Vectors are generally derived from ….
plasmids and viruses
Plasmid:
Plasmid is a small DNA molecule within a cell that is physically separated from a chromosomal DNA and can replicate independently. They are most commonly found in bacteria as small, double stranded molecules.
Bacterial protein expression systems, such as … and …. are commonly used in molecular cloning because they are …, …., and ….
Bacterial protein expression systems, such as E. coli and plasmids, molecular cloning because they are easy to culture, grow fast, and produce high yields of recombinant proteins.
What type of vectors are used if the DNA segment being cloned is exceptionally large?
- bacteriophages - retroviruses - bacterial or yeast artificial chromosomes
Recombinant DNA: Explain cloning (using plasmids)
After the vector (plasmid) is inserted inside the bacteria (host), the plasmid replicates as the host replicates. The plasmid contains a selectable marker, often an antibiotic. After replication, there are multiple products, some with the gene of interest, some without. Next, antibiotics are added to this mixture, and only the bacteria with the antibiotic resistant plasmids will survive.
Eukaryotic multi-domain proteins expressed in bacteria are often …, because bacteria are prokaryotes, and they are not equipped to …
Eukaryotic multi-domain proteins expressed in bacteria are often non-functional, because bacteria are prokaryotes, and they are not equipped to perform post-translational modification or molecular folding.
Eukaryotic Recombinant Protein production: mammalian in vivo expression systems usually produce …., but …
Eukaryotic Recombinant Protein production: mammalian in vivo expression systems usually produce functional proteins, but yield is low, it’s time consuming, and costly.
Explain gene therapy
In gene therapy, a viral vector containing DNA encoding the functional gene is inserted into the target cells. Virus unloads its genetic info, the functional gene is translated to functional proteins that restores the target cells into their normal state.
Examples of virus types that are used as gene therapy vectors
- retroviruses - adenoviruses - adeno-associated viruses - herpes simplex viruses
Retrovirus
a single-stranded RNA, invades the host cell, and uses reverse transcriptase to transcript its RNA into DNA. The viral DNA is integrated into the host cell’s DNA
Adenovirus
- has double stranded DNA - can cause respiratory problems (common cold)
Adeno-associated virus
small, single-stranded DNA virus that can insert its genetic material at a specific site on chromosome 19
Herpes simplex virus
double-stranded DNA virus that infect neurons
Two nonviral options for delivery in gene therapy
- Direct introduction of the therapeutic DNA into the target cells. Can only be used with certain tissues and requires a large amount of DNA 2. Creation of an artificial lipid sphere (liposome) with an aqueous core, which can carry the therapeutic DNA trough target cell’s membrane
What factors have kept gene therapy from becoming an effective treatment for genetic disease?
- short-lived nature of gene therapy - immune response (attack of foreign invader) - problems with viral vectors (toxicity, virus regaining its function, inflammatory responses) - multigene disorders - most diseases arise from mutations in more than a single gene.
Gene knockdown
experimental technique where expression of one or more of an organism’s genes are reduced.
Knockout mutation
replacement of a gene segment by homologous recombination that results in a nonfunctional or null allele
Knock-in mutation
point mutation that results in a partially functional or nonfunctional allele
Northern Blot
- Isolate the RNA of interest 2. Gel electrophesis - RNA fragments are separated by size on the gel 3. Blotting - the RNA fragments are transferred to a membrane (something more stable than gel) 4. Hybridization - A probe is used to identify the RNA of interest. Probe is usually fluorescent, complimentary DNA (cDNA) 5. Wash off excess probe 6. Visualization (radiography)
Southern Blot
- DNA is cleaved into several smaller fragments. 2. Gel electrophesis - DNA fragments are separated by size on the gel 3. Blotting - the DNA fragments are transferred to a membrane (something more stable than gel) 4. Hybridization - A probe is used to identify the DNA of interest. Probe is usually radioactive, complimentary DNA (cDNA) 5. Visualization (radiography)
What are two main difference between Northern Blot and Southern Blot?
Southern Blot uses DNA fragments, while Northern Blot uses RNA. In Southern Blot, before analysis, the DNA has to be cleaved by enzymes, in Northern Blot, the RNA is not cleaved.
In Southern Blot, before analysis, the DNA has to be cleaved by enzymes, in Northern Blot, the RNA is not cleaved. Why?
RNA not cleaved because it is already short.
Polymerase Chain Reaction (definition)
technique used to amplify a DNA sequence - creating thousands to millions of copies of the sequence
What are the main components required for PCR:
- template (DNA sample) - DNA polymerase (a thermally stable enzyme for replication of DNA) - primers (small single-stranded DNA sequences complimentary to either end of the region being amplified) - buffer - mixture of nucleotides (G, A, C, T) - thermocycler (automated heating/cooling device)
Steps of PCR
- DNA is denatured - temp. increased to 95 degrees C. The two strands separate 2. Cool down mixture to allow primers to anneal to each DNA strand. 3. Temp brought to 72 degrees C, add nucleotides and DNA pol can now replicate the DNA 4. Repeat steps 1-3 to amplify the DNA
Potential yield from PCR calculated by
Yield = (2^n)x, n = number of cycles, x = original copies of DNA
In situ hybridization (ISH) is a ….
In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ)
DNA microarray analysis
- method for simultaneous evaluation of multiple genes - can only be used for known genes and their products
Differential expression analysis by differential display
Purpose of these techniques is to compare two different RNA populations (normal vs diseased, one tissue type vs another, control vs treated)
Body Mass Index (BMI)
determines the relative weight for stature of an individual
BMI is calculated by
(weight kg)/(height meters)^2 (703) X (weight lb)/(height inches)^2
Range of BMI for healthy individual
19.5 - 25
Range of BMI for overweight individual
25.1 - 29.9
Range of BMI for individuals w/ morbid obesity
>40
Range of BMI for obese individual
>30
Macronutrients are …
Macronutrients are required in the diet in large amounts and are responsible for providing energy.
What are the types of macronutrients?
carbohydrates, lipids, and proteins.
Micronutrients are the …
Micronutrients are the vitamins and minerals necessary for the cells’ proper metabolism.
What are the types of microminerals?
sodium, potassium, calcium, phosphate, and magnesium
Types of trace elements (micronutrients)
iodine, iron, selenium, molybdenum
What are the four principal factors that influence energy need?
- body surface area (related to weight and height) 2. age and hormonal status 3. gender 4. activity level
What is Basal Metabolic Rate (BMR) or Resting Metabolic Rate (RMR)?
the amount of energy that keeps an individual alive without physical activity
Basal Metabolic Rate (BMR) is determined by which factors?
- body surface 2. age and hormonal status 3. gender
What are the water soluble vitamins? Water soluble vitamins are readily ….
Vitamin B family and vitamin C; Water soluble vitamins are readily excreted from the body.
What are the fat soluble vitamins? Fat soluble vitamins are … in the body for …, and pose a greater risk for … when consumed ….
DEKA; Fat soluble vitamins are stored in the body for long periods of time, and pose a greater risk for toxicity when consumed in excess.
Body surface area is proportional to
heat loss
Infants and children use … for rapid growth, and therefore have … BMR.
Infants and children use more energy for rapid growth, and therefore have higher BMR.
In adults muscle tissue is gradually replaced by fat and water (…), causing a … of … BMR per …
In adults muscle tissue is gradually replaced by fat and water (requiring less energy), causing a decrease of 2% BMR per decade of life.
What is the effect of hormones on BMR?
Hormones like thyroxin, sex hormone, growth hormone, increases BMR.
Women have a … BMR than men due to … and effects of …
Women have a lower BMR than men due to lower lean muscle mass and effects of female hormones on BMR.
The caloric value of food is measured in … and equals the ….
The caloric value of food is measured in kcal/g and equals the heat that is released by combustion of the food in the body.
caloric value for protein
4 kcal/g
caloric value for carbohydrate
4 kcal/g
caloric value for fat
9 kcal/g
caloric value for alcohol
7 kcal/g
Carbohydrates are taken up by the body in the form of …
Carbohydrates are taken up by the body in the form of mono-, di-, and polysaccharides and fibers.
Insufficient carbohydrates in diet can lead to
ketosis and dehyhydration
Excess carbohydrates in diet is converted to
glycogen and triacylglycerol (fat) for long term storage
Fats taken up in diet are …. They also supply essential …, such as … and …, and …
Fats taken up in diet are used for energy. They also supply essential fatty acids, such as linoleum and linolenic acid, and cholesterol.
Excess fat in diet is stored as
triacylglycerol
Excess dietary fat causes elevated … and increased risk of …. High fat intake is also associated with increased risks of …., …., and …. cancers.
Excess dietary causes elevated serum lipids and increased risk of heart disease. High fat intake is also associated with increased risks of colon, breast, and prostate cancer.
Mono-unsaturated fatty acids lower
plasma cholesterol levels
Sources of mono-unsaturated fatty acids include
olive oil, safflower, canola, peanut oils
poly-unsaturated fatty acids contain
essential fatty acids
Symptoms of essential fatty acid deficiency
scaly dermatitis, hair loss, and poor wound healing
Excess proteins are converted to … or …. Both are eventually converted to … in … tissue.
Excess proteins are converted to glucose or fats. Both are eventually converted to triglycerides in adipose tissue.
Non-essential amino acids can be
synthesized by the body
Essential amino acids
cannot be synthesized by the body
Nitrogen balance is the
comparison of nitrogen intake (mostly protein) and excretion of nitrogen (protein in feces and urea/ammonia in urine)
Negative nitrogen balance can result from
inadequate protein intake or lack of essential amino acids
Positive nitrogen balance reflects
increased protein intake
Dietary fiber are those components of food
that cannot be broken down by human digestive enzymes
What is the recommended daily intake of macronutrients?
Carbohydrate: 300 - 400 g Protein: 70 - 90 g Fat: 60 - 100 g 1600 - 2400 kcal
Marasmus
starvation, inadequate nutrition
Kwashiorkor (define)
Kwashiorkor results from protein poor diet - even if adequate calories. Lack of dietary amino acids results in diminished protein synthesis in all tissues.
characteristics of Kwashiorkor
- poor growth - low plasma protein levels - muscle wasting - edema - diarrhea - increased susceptibility to infection
Vitamin A Active forms: Sources:
Active forms: retinol, retinal, retinoic acid Sources: liver, egg yolk, butter, whole milk, dark green or yellow vegetables
Vitamin A functions
- β-carotene acts as an antioxidant - retinol and retinoic acid act like steroid hormones and bind to chromatin to affect cell growth and differentiation, especially of epithelial cells - cis-retinal is associated with visual protein rhodopsin which is required for vision in dim light
Vitamin A deficiency results in
- Night blindness (early symptom) - xerophthalmia (keratinization of the cornea) - anemia (vit. A needed for transferrin synthesis) - follicular hyperkeratosis (rough keratinized skin)
Vitamin D Forms: Sources:
Forms: 1-α,25-dihydroxy-cholecalciferol; D3 (cholecalciferol): produced in skin by UV irradiation; D2 (ergocalciferol): produced from yeast and used to fortify milk, butter, and other foods Sources: salt water fish, liver, egg yolk, also fortified milk and butter
Vitamin D Functions
- works with PTH to regulate calcium homeostasis - aids calcium transport by inducing calbindin in intestinal mucosa - inhibits excretion of calcium in kidneys by stimulating calcium resorption in the distal renal tubules
Vitamin D Deficiencies
- rickets (children) formation of osteoid and cartilage which are not properly mineralized - osteomalacia (softening of bone) in adults - fat malabsorption, or severe liver or kidney disease can lead to deficiency
Vitamin D toxicity
excess vit D (10 -100x recommended daily intake): hypercalcemia with widespread calcification and kidney stone formation
Vitamin E Active forms: Sources:
Vitamin E Active forms: family of molecules called the tocopherols, α-tocopherol is the most potent Sources: high concentration in seed embryos, vegetable oil, grains and leafy vegetables
Vitamin E Functions
Functions: - an important naturally occurring antioxidant in cellular membranes, lipoproteins and fat deposits - in cellular respiration, it stabilizes coenzyme Q and helps transfer electrons to this molecule - enhances heme synthesis - deficiencies have neurological symptoms
Vitamin K Forms: Sources:
Forms: K1; K2, other napthaquinones Sources: K1 in green vegetables, K2 synthesized by intestinal bacteria
Vitamin K Functions
Functions: - acts as cofactor in the post-translational synthesis of γ-carboxy glutamic acid (Gla) from glutamic acid (Glu) - Most important role in hemostasis – localizing clotting factors to the site of injury
Vitamin K deficiency
the major symptom is increased clotting time
Glycerolphospholipids have glycerol backbone to which …. esterified at the alpha carbon and … are esterified at the remaining carbons.
Glycerolphospholipids have glycerol backbone to which phosphoric acid is esterified at the alpha carbon and two long chain fatty acids are esterified at the remaining carbons.
Fatty acids can be … (contain no double bonds) or …. (contain one or more double bonds)
Fatty acids can be saturated (contain no double bonds) or unsaturated (contain one or more double bonds)
sphingosine
amino alcohol with an unsaturated hydrocarbon chain
sphingolipids
lipids containing a backbone of sphingoid bases (amino alcohols)
Fatty acids are
carboxylic acids with long chain hydrocarbon side groups
Saturated fatty acids are highly … because of the … of their … bonds.
Saturated fatty acids are highly flexible because of the free rotation of their single C-C bonds.
Unsaturated fatty acids usually have the … configuration
Unsaturated fatty acids usually have the cis configuration
Saturated fatty acids have a … melting point compared to unsaturated because the molecular geometry of saturated fatty acids is a relatively …, allowing the molecules to … together. This creates …. resulting in a relatively … melting point.
Saturated fatty acids have a higher melting point compared to unsaturated because the molecular geometry of saturated fatty acids is a relatively straight chain, allowing the molecules to stack and pack tightly together. This creates close intermolecular interactions resulting in a relatively higher melting point.
Unsaturated fatty acids have a …. melting point compared to saturated because in the molecular geometry of unsaturated fatty acids, the … creates a … that interferes with the …, reducing …, which results in a relatively … melting point.
Unsaturated fatty acids have a lower melting point compared to saturated because in the molecular geometry of unsaturated fatty acids, the cis configuration creates a rigid bend that interferes with the molecules packing, reducing intermolecular interactions, which results in a relatively lower melting point.
molecular geometry for unsaturated fatty acids with a trans configuration
straight chain
Saturated fatty acids and trans unsaturated fatty acids are straight chains —> …. —> … membrane fluidity and … rigidity
Saturated fatty acids and trans unsaturated fatty acids are straight chains —> higher melting point —> decreased membrane fluidity and increased rigidity
What is the relationship between melting point and lipid (membrane) fluidity?
As melting point decreases, lipid fluidity increases
cis unsaturated fatty acids have kinked chains —> …. melting points —> … membrane fluidity and … rigidity
cis unsaturated fatty acids have kinked chains —> lower melting points —> increased membrane fluidity and decreased rigidity
amphipathic molecules contain both a
hydrophilic polar end (head) and a hydrophobic non polar end (tail)
The two most common glycerol-phospholipids in cell membranes
Cephalin (phosphatidylethanolamine) Lecithin (phosphatidylcholine)
Ceramide is a … with either a saturated or unsaturated fatty acid linked to the ….
Ceramide is a sphingosine with either a saturated or unsaturated fatty acid linked to the amino group of the sphingosine.
ceramide plus phosphorylcholine is
sphingomyelin
Increased levels of cholesterol in cell membrane …. membrane fluidity
Increased levels of cholesterol in cell membrane decreases membrane fluidity
cardiolipin is a lipid found nearly exclusively in the
inner mitochondrial membrane
The lipid bilayer is … to non lipid and charged (hydrophilic) molecules
The lipid bilayer is impermeable to non lipid and charged (hydrophilic) molecules
The lipid bilayer is relatively … to neutral hydrophobic molecules.
The lipid bilayer is relatively permeable to neutral hydrophobic molecules.
Integral membrane proteins contain sequences rich in …. which interact with the …. of the membrane lipids.
Integral proteins contain sequences rich in hydrophobic amino acids which interact with the hydrophobic hydrocarbons of the membrane lipids.
membrane proteins have a variety of functions:
- mediators of transmembrane movement of charged and uncharged molecules - receptors for binding hormones and growth factors - enzymes involved in transduction signals - structural element to maintain cell shape
Ca2+ …. membrane fluidity because of the interaction with …. phospholipids.
Ca2+ decreases membrane fluidity because of the interaction with negatively charged phospholipids.
Channels on cell membranes are classified as
voltage regulated, cAMP regulated, or chemically regulated
lipid rafts
micro domains within the inner and outer leaflet of the plasma membrane enriched in cholesterol and sphingolipids
Lipid rafts have thicker, … fluid environment. They also contain more … acyl chains, meaning …. melting points.
Lipid rafts have thicker, less fluid environment. They also contain more saturated acyl chains, meaning higher melting points.
Lipid raft structure is regulated by …. If depleted of …, rafts ….
Lipid raft structure is regulated by cholesterol. If depleted of cholesterol, rafts dissociate.
Signal transduction
when an extracellular signaling molecule activates a specific receptor located on the cell surface or inside the cell
Concentration of sodium (Na+) in the extracellular fluid
~ 145 mM Na+ in the extracellular fluid
Concentration of potassium (K+) in the extracellular fluid
~ 5 mM K+ in the extracellular fluid
Concentration of calcium (Ca2+) in the extracellular fluid
~ 2.5 mM Ca2+ in the extracellular fluid
Concentration of chloride (Cl-) in the extracellular fluid
~105 mM Cl- in the extracellular fluid
Concentration of sodium (Na+) in the intracellular fluid
~15 mM Na+ in the intracellular fluid
Concentration of K+ in the intracellular fluid
~ 140 mM K+ in the intracellular fluid
Concentration of Ca2+ in the intracellular fluid
~ 50 nM Ca2+ in the intracellular fluid
Concentration of Cl- in the intracellular fluid
~ 10 mM Cl- in the intracellular fluid
Which solutes are present in higher concentrations outside of the cell?
There are higher concentrations of Na+, Ca2+ and Cl- outside the cell.
Which solutes are present in higher concentrations inside of the cell?
There are higher concentrations of K+ inside the cell.
bulk flow
bulk movement of solutions by hydrostatic pressure
Diffusion moves
solutes from regions of high concentration to regions of lower concentration, until equilibrium is reached.
In diffusion, larger molecules ….. than smaller ones.
In diffusion, larger molecules diffuse more slowly than smaller ones.
In diffusion, distances should be kept … to achieve …. of solutes.
In diffusion, distances should be kept small to achieve rapid movement of solutes.
COL1A1 gene codes for the … of … collagen
COL1A1 gene codes for the α1 chain of type I collagen
COL1A2 gene codes for the … of … collagen
COL1A2 gene codes for the α2 chain of type I collagen
The majority of OI cases (over 90%) are caused by mutations in the
COL1A1 and COL1A2 genes
In a null allele of COL1A1 and COL1A2 genes:
In a null allele of COL1A1 and COL1A2 genes, there is a nucleotide deletion or insertion causing a frameshift, leading to an incorrect mRNA product and then a truncated or nonfunctional alpha chain. In these cases, only about 50% of normal type I collagen is produced.
The primary mutation involved in type I OI is:
Null allele of COL1A1 (only 50% of functional α1 chain) is the primary cause of type I OI.
A null allele of the COL1A2 gene leads to increase levels of …. This usually results in … forms of OI.
A null allele of the COL1A2 gene leads to increase levels of α1(I)-homotrimers. This usually results in rare recessive forms of OI.
Structural mutations in the COL1A1 and COL1A2 genes produce:
Structural mutations in the COL1A1 and COL1A2 genes produce abnormal type I collagen, with amino acid substitutions, insertions, and deletions.
OI types II, III, and IV are caused by what type of mutations?
OI types II, III, and IV are caused by structural mutations in COL1A1 and COL1A2 genes, producing abnormal type I collagen.
In abnormal type I collagen, the most common structural mutation is caused by a nucleotide change …
In abnormal type I collagen, the most common structural mutation is caused by a nucleotide change, replacing glycine.
The conventional clinical management of OI is to facilitate the achievement of …., including … and …, and to maximize skills for …
The conventional clinical management of OI is to facilitate the achievement of gross motor skills, including ambulation and head control, and to maximize skills for independent living.
In OI treatment, the surgical goal is to … and interrupt the …. and …. cycle.
In OI treatment, the surgical goal is to correct bowing and interrupt the fracture and refracture cycle.
In OI treatment, the goal of pharmacological intervention is to ….. and promote …
In OI treatment, the goal of pharmacological intervention is to reduce the rate of bone fractures and promote longitudinal growth.
Flux of a substance (definition)
Definition: when there is a net movement of a substance from one point to another defined as Quantity of substance/Time
Fick’s Law
Describes the flux of a solute across a membrane through diffusion in terms of permeability (P), the membrane area (A), and the concentration difference (ΔC) Flux = P (A)(ΔC)
Nonpolar (hydrophobic) amino acids; mnemonic
Glycine, Alanine, Valine, Leucine, Isoleucine, Phenylalanine, Tryptophan, Methionine, Proline; Get A Vagina LIP To My Penis
Polar (hydrophilic) amino acids; mnemonic
Serine, Tyrosine, Threonine, Glutamine, Cysteine, Asparagine; SummerTime They Get Cold Agua (agua should remind you these are hydrophilic)
Acidic Amino Acids
Aspartic acid (aspartate), glutamic acid (glutamate)
Basic Amino Acids; mnemonic
Histidine, Lysine, Arginine; His Lys Arg Basic (His Lies Are Basic)
Clinical examples of substances with high lipid solubility
codeine, xylocaine, novocain, and alcohol
Ions pass across the cell membrane with the help of …
Ions pass across the cell membrane with the help of membrane proteins (channels).
Factors that effect the permeability of ions:
- number of channels present on the cell membrane 2. conductance of the open channel (how many ions the channel allows to pass per second) 3. open probability of the channels (what fraction of the channels are open)
Protein Mediated Transport
Many substances enter or leave cells by means off specific carriers, channels, or active transporters that are membrane proteins.
Three categories of protein mediated transport
Facilitated diffusion, active transport, and vesicle mediated transport
Facilitated diffusion
does not involve any use of metabolic energy
Facilitated diffusion: channels
- characterized by a pore that spans the membrane - pores can be open or closed - channels have specificity, saturation, and competition
Facilitated diffusion: Carriers
- protein molecules embedded in the membrane, and generally span the membrane - carriers binds molecules of solute, changes its conformation to allow this solute to cross the membrane - have specificity, saturation, and competition
anthracyclines
- class of drugs used to treat a wide range of cancers - usefulness limited due to side effect of cardiotoxicity
How do anthracylines lead to cardiotoxicity?
- anthracyclines open the ryanodine receptor, which is a channel found within the membrane of the sarcoplasmic reticulum (SR) of heart cells, which stores calcium - with the channel open, calcium diffuses from the high concentration within the SR to low concentration in the cytosol - the high cytosolic calcium concentration plays a role in causing arrhythmias
…., transport millions or tens of millions of molecules per second; while …. transports thousands of molecules per second.
Channels, when open, transport millions or tens of millions of molecules per second; while carriers transports thousands of molecules per second.
Active Transport
- transport that can proceed against an electrochemical gradient, from regions of low concentration to regions of high concentration - ATP (energy) is required for active transport
Primary Active Transport
- directly uses metabolic energy in the transport process - membrane proteins move solutes with the hydrolysis of ATP - often referred to as ATPases or pumps
Na+/K+ pump
- example of primary transport - hydrolysis of a single ATP molecule moves 3 NA+ ions out of the cell and move 2 K+ ions into the cell
Ca2+ pump
- maintains low concentrations of free Ca2+ in the cytosol - keeps high concentrations of Ca2+ within the endoplasmic reticulum and sarcoplasmic reticulum (membrane) - this steep electrochemical gradient allows Ca2+ to rush into the cytosol when a signal stimulus opens membrane channels - Ca2+ ATPase then pumps Ca2+ out of the cytosol to maintain resting potential
H+ pump
- found in the basolateral membrane of specialized stomach cells - H+ pump results in secretion of HCl during digestion
Secondary Active Transport
- indirectly uses hydrolysis of ATP to transport solutes against an electrochemical gradient - couples the movement of an ion (often Na+) down its electrochemical gradient to the uphill movement of an ion against the electrochemical gradient - two types: co-transporters and counter-transporters
Co-transporters
- secondary active transport that moves both solutes in the same direction
Na+/glucose co-transporter
- the high concentration of Na+ outside the cell creates a steep electrochemical gradient - the energy in this gradient is used to move a single glucose molecule into the cell with the movement of one Na+ ion into the cell - Na+ moves down its electrochemical gradient, and provides the energy to move glucose against its electrochemical gradient
NIS transporter
Na+/I- co-transporter that moves Iodine into the thyroid by using Na+ to drive I- against its concentration gradient
Counter-transporters (exchangers)
secondary active transport that moves solutes in opposite directions
Na+/Ca2+ exchanger
- found in cardiac and smooth muscle cell membranes - steep electrochemical gradient of Na+ is used for energy to couple the movement of 3 Na+ ions into the cell (downhill movement) to the uphill movement go 1 Ca2+ ion (out of the cell)
Vesicle Mediated Transport
- solutes transported across membrane through vesicles - endocytosis and exocytosis
Exocytosis
- intracellular solutes are encapsulated within membrane vesicles - vesicles fuse with the membrane and release their contents into the extracellular fluid
Endocytosis
- extracellular substances trapped within vesicles (formed by invagination of the surface membrane) - the vesicle pinches off the membrane and typically fuses with a lysosome, releasing its contents
Osmosis
- diffusion of water - occurs through lipid bilayer, ionic channels, and through water channels called aquaporins - most cell membranes are highly permeable to water
Water concentration is generally measured in terms of the concentration of …. The higher the concentration of …, the …. of water.
Water concentration is generally measured in terms of the concentration of dissolved solutes. The higher the concentration of dissolved solutes, the lower the concentration of water.
Cell volume depends directly on the …. in cell water and in the …
Cell volume depends directly on the number of dissolved particles in cell water and in the extracellular fluid.
Osmotic pressure is the
Osmotic pressure is the minimum pressure that needs to be applied to prevent the inward flow of water through a semi-permeable membrane.
Osmolarity is the
concentration of dissolved particles in the solution
Cell that is permeable to a solute and H2O Side 1: High H2O and low solute concentrations Side 2: Low H2O and high solute concentrations Describe movement of water and solute
- H2O will move down its concentration gradient from side 1 to side 2 - Solutes will move down its concentration gradient from side 2 to side 1 - Until equilibrium is reached
Cell that is permeable to H2O and impermeable to a solute Side 1: High H2O and low solute concentrations Side 2: Low H2O and high solute concentrations Describe movement of water and solute
- H2O will move down its concentration gradient from side 1 to side 2 until osmolarity is same for both sides - Solute will not move because the membrane is impermeable to the solute
Osmotic coefficient
to accurately determine osmolarity, a correction factor called osmotic coefficient is used. Generally osmotic coefficient is near one.
Iso-osmotic
osmolarity of one solution relative to another solution is the same
hypo-osmotic
lower osmolarity (lower concentration of dissolved particles) of one solution relative to another solution
hyper-osmotic
higher osmolarity (higher concentration of dissolved particles) of one solution relative to another solution
Tonicity is
the relative concentration of solutions that determine the direction and extent of flow of water.
isotonic solution
steady state cell volume remains constant
Cells placed in hypotonic solutions will … because …
Cells placed in hypotonic solutions will swell because there is a higher solute concentration inside the cell and lower solute concentration outside the cell, causing water to flow into the cell.
Tonicity is influenced only by …. solutes.
impermeable
Cells placed in hypertonic solutions will … because …
Cells placed in hypertonic solutions will shrink because there is a higher solute concentration outside the cell and lower solute concentration inside the cell, causing water to flow out of the cell.
Osmolarity is a …. property of a solution, while tonicity is a … property that depends both on … and ….
Osmolarity is a physical property of a solution, while tonicity is a biological property that depends both on osmolarity and cell membrane permeability.
promoter (P) in lac operon
site where RNA pol binds to initiate transcription
Operator (O) in lac operon
binds the repressor protein, regulating transcription
CAP binding site (catabolite gene activator protein) in lac operon
binds cAMP, also regulatory mechanism
Nuclear receptors are
Nuclear receptors are transcription factors that work with other proteins to regulate the expression of specific genes.
Equation for concentration
Concentration = Amount/Volume
Osmotic pressure in the capillaries causes H2O to …. the capillaries because there is a …. of plasma proteins inside the capillaries.
Osmotic pressure in the capillaries causes H2O to flow into the capillaries because there is a greater concentration of plasma proteins inside the capillaries.
Hydrostatic pressure in blood vessels is the ….
Hydrostatic pressure in blood vessels is the pressure of the blood against the vessel walls.
Hydrostatic pressure in the capillaries will tend to move … and … of the capillaries.
Hydrostatic pressure in the capillaries will tend to move water and permeable solutes out of the capillaries.
Hydrostatic pressure is greater at the …. of capillaries.
arterial end
At the arterial end, the hydrostatic pressure difference between the inside and the outside of a capillary is normally about
30 mm Hg
At the venous end, the hydrostatic pressure difference between the inside and the outside of a capillary is normally about
10 mm Hg
The net osmotic pressure difference across capillaries due to plasma proteins is usually about
15-20 mm Hg
The hydrostatic pressure difference (30 mm Hg) exceeds the net osmotic pressure difference (15-20 mm Hg) at the ….., therefore water … of the capillaries at the …
The hydrostatic pressure difference (30 mm Hg) exceeds the net osmotic pressure difference (15-20 mm Hg) at the arterial end, therefore water flows out of the capillaries at the arterial end.
The net osmotic pressure (15-20 mm Hg) difference exceeds the hydrostatic pressure difference (10 mm Hg) at the …, therefore water … of the capillaries at the ….
The net osmotic pressure (15-20 mm Hg) difference exceeds the hydrostatic pressure difference (10 mm Hg) at the venous end, therefore water flows into of the capillaries at the venous end.
The movement of water out of the capillaries (hydrostatic pressure) and movement of water into the capillaries (osmotic pressure) mostly …., with only a … of water …. This water eventually becomes …
The movement of water out of the capillaries (hydrostatic pressure) and movement of water into the capillaries (osmotic pressure) mostly balances each other out, with only a slight net movement of water out of the capillaries. This water eventually becomes lymph.
Edema results if there is …. of the capillaries.
too much water flowing out of the capillaries.
What is the blood volume inside the human body?
5 L
How much of the blood volume is RBCs?
about 40 - 45%; 2 L
Dot Blot
- Simplification of the northern, southern blot methods, however electrophoresis is not used - mixture applied directly to a membrane as a dot - nucleotide probes or antibodies used to detect molecule - can only confirm the presence or absence of a molecule, cannot differentiate size of molecules
Variable Number Tandem Repeats (VNTR)
- short repeated DNA sequences - found on many chromosomes - number of repeats is variable in different individuals - are inherited so that can be used for parental identification or personal identification
genomic library
made from the entire DNA of an organism; contains sequences for structural genes, introns, regulatory components, and all other noncoding sequences
cDNA library
generated from transcripts of structural genes (mRNA) that are expressed by cells. Reverse transcriptase is used to synthesize cDNA from mRNA
Glucocorticoid Receptor (GR)
- cortisol binds to GR and activates it -Cortisol-GR complex goes to nucleus and binds specific regulatory DNA sequences (Glucocorticoid Response Element) - GRE allows coordinate expression of a group of target genes
pre-mRNA molecules from some genes can be spliced in … ways producing …
pre-mRNA molecules from some genes can be spliced in alternative ways producing multiple related proteins or isoforms from a single gene
