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BMSC week 1: genetics and proteins


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What is the start codon? What are the stop codons?
Start: AUG (methionine)
What are the possible post-transcriptional modifications made to RNA? What are they for?
-5' cap is essential for ribosome recognition, stabilizes mRNA, and is required for export
-3' poly A tail stabilizes mRNA and binds poly A binding protein which directs nuclear export
-splicing gets rid of introns
What is a spliceosome made of? How does it work?
It is an assembly of RNA and proteins which recognizes splice sites. It helps the 3' end of the intron attack the 5' end of the intron, forming a loop and separating the intron from exon 1. Then the 3' end of exon 1 attacks the 5' end of exon 2.
What is a silent point mutation? How are silent mutations possible?
Silent mutations make no difference in the amino acid sequence. They are possible because the triplet code is degenerate. Changing the third base of a codon is usually a silent mutation.
What is a missense point mutation?
The amino acid sequence of the protein is altered because one base is changed.
What is a nonsense point mutation?
The protein is truncated because a base pair substitution caused a premature stop codon.
What is a read-through point mutation?
A mutation in a stop codon which causes translation to continue through it. The protein ends up longer than normal.
What is a frame-shift mutation? What is the manifestation of this type of mutation?
Caused by insertion or deletion of one or more base pairs. Usually no protein is produced, or a truncated protein may be produced.
Aside from silent, missense, nonsense, read-through, and frameshift mutations, what other types of mutations are there?
-splicing: a mutation in an intron or exon causes incorrect splicing
-promoter regions: a mutation in a promoter causes transcription factors to bind differently
What happens if mRNA is incorrectly packaged?
It is not recognized by nuclear pore complex, so it is not exported into the cytoplasm and translated.
What are ribosomes made out of and what does each component do?
rRNA: catalyzes formation of peptide bonds
protein: stabilize and aid in conformational changes
Where are ribosomal subunits assembled? Where are ribosomes assembled?
Ribosomal subunits are assembled in the nucleoli, then transported to the cytosol where they are assembled into ribosomes when translation is initiated.
What are the four RNA binding sites on ribosomes? What do they do?
-A site (amino acyl tRNA) binds incoming tRNAs
-P site (peptidyl) binds the nascent polypeptide chain
-E site (exit)
-mRNA binding site
What are the four regions of unpaired bases on tRNAs?
-anticodon loop recognizes mRNA
-T loop
-D loop
-3' end binds the amino acid
What functions do the eukaryotic initiaton factors (eIFs) have?
-mediate mRNA binding to ribosome
-kinase activity: phosphorylate other eIFs
-ATPases that facilitate ribosomal scanning for stop codon
-GTPases that provide energy for protein synthesis or facilitate GTP binding
What functions do the elongation factors (EFs) have?
-EF-Tu is a GTPase that delivers amino acyl tRNA to A site
-EF-G is a GTPase that binds near the A site
-EF-Ts reactivates EF-Tu by facilitating GDP/GTP exchange
What is involved in the preinitiation phase of translation?
-ternary complex: GTP-eIF-2 binds to Met-tRNA
-preinitiation complex: mRNA binds to IFs, 40S binds 5' cap, more IFs associate with Met-tRNA/40S
What is involved in the initiation phase of translation?
-40S searches for AUG on mRNA, using ATP
-eIF-2 dissociates, using GTP
-60S large subunit binds
-tRNA is in P site
What is involved in the elongation phase of translation?
-new tRNA sits in A site
-bond breaks between P-site tRNA and polypeptide chain
-new bond formed between A-site tRNA and polypeptide chain
-60S subunit moves downstream, followed by 40S
What is involved in the termination phase of translation?
-stop codon is reached
-release factors bind A site
-polypeptide is hydrolyzed from tRNA
-mRNA dissociates from ribosome, 40S and 60S dissociate (needs GTP binding to eRF3 and GTP hydrolysis)
Which drugs poison both human and bacterial translation? What is their mechanism of action?
-actinomycin D: blocks rRNA synthesis
-puromycin: inhibits protein synthesis by blocking A-site
Which drugs poison bacterial translation only? What is their mechanism of action?
-erythromycin: inhibits mRNA translocation through large subunit
-tetracycline: inhibits tRNA binding to small subunit
-chloramphenicol: inhibits peptidyl transferase
Which drugs poison human translation only? What is their mechanism of action?
-ricin: cleaves large subunit rRNA
-cycloheximide: blocks tRNA movement between ribosome sites
What is the difference between the signal sequence of a secretory protein and that of a transmembrane protein?
Secretory protein: the signal sequence is usually on the N-terminus and is cleaved by signal peptidase
Transmembrane protein: the signal sequence is internal and doubles as the membrane sequence
What is the SRP? What is the basic structure and what does it do?
The Signal Recognition Particle is in the cytosol; it is made of 6 polypeptide chains bound to an RNA molecule. It has a hydrophobic pocket that binds signal sequences as they emerge. SRP helps nascent protein/ribosome complexes get to the ER; it halts synthesis until the peptide is translocated.
What is the SRP receptor? Where is it and what does it do?
The SRP receptor binds the SRP/ribosome complex; it is in dynamic equilibrium with the ER membrane. It is a GTPase that hydrolyzes GTP to free SRP from the complex.
What is the translocon? Why is it not constantly open?
The translocon, or Sec61 complex, is made of 3-4 multiprotein complexes in the ER which act as an aqueous pore. When the ribosome dissociates, the translocon dissociates as well so that Ca2+ does not leak out.
Will regions of the protein which are in the ER lumen during processing end up on the cytoplasmic or extracellular face of the cell?
Through which organelles do secretory and transmembrane proteins pass during processing?
-Golgi apparatus
-secretory vesicles,
in that order.
What modifications are made to proteins in the ER?
-formation of disulfide bonds
-lipid and N-linked glycosylation
-glycolipid anchors
What modifications are made to proteins in the Golgi apparatus?
-trimming and modifications of carbohydrates added in the ER
-packaging and sorting
What modifications are made to proteins in the secretory vesicles?
proteolytic processing:
-cleavage of pro-peptides
-cleavage to yield multiple copies of proteins from one chain
-cleavage to yield many different proteins from one chain
Where in the cell does disulfide bond formation occur and why? What is it for?
Disulfide bond formation (between two Cys residues) occurs in the ER lumen because it provides an oxidative environment. It assists with proper protein folding.
What is PDI? What happens if it doesn't work?
Protein disulfide isomerase; it catalyzes oxidation of Cys and corrects wrong Cys-Cys bridges. If it is broken or interfered with (by free radicals for example) then protein misfolding occurs, sometimes causing neurodegenerative disease.
What are some differences between N-linked glycosylation and O-linked glycosylation?
-in ER
-in eukaryotes only
-Asn-X-Ser/Thr consensus (added to Asn)
-sugar added as one unit
-in Golgi/cytosol
-no consensus (added to OH of Ser/Thr)
-sugars added sequentially
What sugars are added to the protein in N-linked glycosylation?
The preformed oligosaccharide contains 14 sugars including N-acetylglucosamine, mannose, and glucose.
Describe glycoprotein processing as the molecule passes through the cis, medial, and trans faces of the Golgi.
-mannoses are trimmed
-N-acetylglucosamine is added
-fucose may be added to core
-mannoses are trimmed again
-galactose is added
-sialic (neuraminic) acids are added to galactose
What are the purposes of glycosylation?
-protect protein from proteases
-can facilitate proper folding
-can participate in cell adhesion/ligand recognition
-affect protein function
What is the difference between A, B, AB, and O blood-group antigens?
-lipid, glucose, galactose, N-acetylglucosamine, galactose, fucose
-O + N-acetylglucosamine
-O + galactose
-O + N-acetylglucosamine + galactose
What are the two main categories of congenital defects in glycosylation and what are some common symptoms?
-defect in oligosaccharide addition in ER (lack of precursor or transferase activity)
-defects in sugar processing in the Golgi
-psychomotor retardation
How can glycosylation be used in the detection of tumors?
Many cancer cells produce abnormal glycoproteins (which may make them resistant to signal termination, for example).
What is palmitoylation? What is it for?
Palmitate is reversibly added to an internal sulfate of an internal Cys residue in the cytosol or ER.
-facilitates membrane and protein/protein interactions
-may increase rate of degradation
How is palmitoylation related to Huntington's disease?
Failure to palmitoylate Huntingtin protein accelerates inclusion formation and neuronal toxicity.
What is sulfation? Where in the cell does it occur? What is it for?
SO3 group is added to tyrosines and some carbohydrates in the trans-Golgi. It is important for extracellular matrix and mucous function.
What types of lipid modifications are made to cytosolic proteins?
-N-myristoylation: initiating Met is removed and myristic acid is added to N-terminal Gly; cotranslational, irreversible
-prenylation: farnesylation or geranylation at C-terminus via thioester, irreversible
-S-acetylation: palmitoylation, or similar fatty acid addition
How does prenylation relate to Ras and cancer?
Ras is farnesylated on C-terminus; this is required for its function. Overactivation of Ras can lead to cancer. Inhibitors of farnesylation or mutation of farnesylation site prevents action of Ras.
What are characteristics of molecular chaperones? How do they work?
They are ATPases that refold proteins. Chaperones bind to exposed hydrophobic regions, which are abnormal. Hsp70s, hsp40s, and accessory proteins work together.
How are misfolded proteins recognized and repaired in the ER?
-Misfolded proteins have glucose readded after it is trimmed off. ER-specific lectins recognize the new glucose. Chaperones are recruited.
-Misfolded protein activates a receptor kinase in ER membrane, the kinase dimerizes and endoribonuclease domain splices GRP mRNA. GRP translocates to nucleus and activates transcription of chaperones and degradative enzymes.
What happens to proteins which cannot be refolded?
-transport back to the cytosol
-deglycosylation by N-glycanase
-ubiquitinylation (marks for degradation)
-degradation in proteosomes
What problems are caused by aggregations of misfolded proteins?
-protein aggregates can absorb important macromolecules
-protein aggregates can accumulate in extracellular matrix
In the brain:
-prion diseases
What is the glycocalyx? What are its functions?
A polysaccharide network found on the surface of cells.
-adhesion (bacteria, epithelial cells, platelets)
-immune system recognition (tumor cells, foreign organisms, transplants)
-guides embryonic cells during morphogenesis
What is the extracellular matrix?
A complex of fibrous proteins that mediates cell attachment.
What does the presence of large, multiple nucleoli in a cell indicate?
Active protein synthesis (because a lot of rRNA is being made in nucleoli)
What is the function of the smooth ER?
-steroid and lipid synthesis
-storage of intracellular calcium
What is the function of the rough ER?
Site of secretory and membrane protein synthesis
What color is the dye hematoxylin and what does it bind to?
Hematoxylin is blue/purple, and it binds to acidic cellular components such as DNA and RNA. (nucleus is often blue)
What color is the dye eosin and what does it bind to?
Eosin is red/pink, and it binds to basic cellular components such as sugars and some proteins. (cytoplasm is often pink)
What are some examples of retrograde transport?
-from plasma membrane to lysosomes (endocytosis and salvage pathways)
-from Golgi to ER (protein quality control)
What are the functions of lysosomes? What are the consequences of lysosomal deficiencies?
-break down thyroglobulin into thyroid hormone
-endocytosed proteins
-old organelles
-invading pathogens
Lysosomal storage diseases are classified by the accumulation of products which are normally degraded.
-Hurler syndrome
-Niemann-Pick B disease
-Tay-Sachs disease
What are the three types of filaments that make up the cytoskeleton?
-actin filaments
-intermediate filaments
What is the purpose of actin filaments?
In non-muscle cells, they are dynamic and rearrange in response to extracellular signals.
What is the purpose of intermediate filaments?
Give cells mechanical strength and anchor junctional complexes.
What is the structure and purpose of microvilli?
Parallel bundles of actin cross-linked by villin and anchored at the plasma membrane by network of actin and keratin, called a terminal bar. The purpose of microvilli is to increase surface area.
How do spermatogonia develop into sperm?
-At puberty, diploid spermatogonia undergo mitosis to produce diploid primary spermatocytes.
-These then undergo meiosis I to produce haploid secondary spermatocytes.
-These undergo meiosis II to produce haploid spermatids. -These differentiate into sperm.
How do oogonia develop into ova?
-Before birth, all oogonia (diploid) undergo mitosis to produce primary oocytes arrested in prophase I.
-At puberty, a follicle matures and meiosis I is completed; a polar body is ejected and a haploid secondary oocyte is formed, arrested in metaphase II.
-At ovulation and then fertilization, meiosis II is completed and a second polar body is ejected, leaving the egg.
What is haploinsufficiency? What mode of inheritance does it cause?
Having 50% of the gene product is not adequate for normal phenotype. This leads to dominant inheritance.
What is a dominant negative mutation?
Gene product is part of a multisubunit complex, having one bad subunit destroys complex function.
What mode of inheritance is caused by gain of function mutation?
Dominant inheritance
What is the mode of inheritance for familial hypercholesterolemia?
Autosomal dominant
What is the mode of inheritance for woolly hair?
Autosomal dominant
What is the mode of inheritance for brachydactyly?
Autosomal dominant
What is the mode of inheritance for achondroplasia?
Autosomal dominant (high frequency of gain-of-function mutation in FGF receptor 3, homozygous lethal)
What is the mode of inheritance for neurofibromatosis-1?
Autosomal dominant
What is the mode of inheritance for Huntington's disease?
Autosomal dominant
By what mechanism could a person be the first case in the extended family with an autosomal dominant disorder?
Mutation in the germ cell line of one of the person's parents.
What is the difference between penetrance and expressivity?
Penetrance refers to the percentage of people with a mutant genotype that show the disorder (quantitative). Expressivity refers to the level of severity produced by a mutant genotype (qualitative).
How is autosomal dominant inheritance distinguished from autosomal recessive inheritance on a pedigree?
Dominant inheritance usually does not skip a generation; recessive inheritance does.
What is the mode of inheritance for albinism?
Autosomal recessive
What is the mode of inheritance for phenylketonuria?
Autosomal recessive (homozygous for phenylalanine hydroxylase deficiency)
What is the mode of inheritance for galactosemia?
Autosomal recessive (homozygous for galactose-1-phosphate uridyl transferase deficiency)
What is the mode of inheritance for cystic fibrosis?
Autosomal recessive
What is the similarity between compound heterozygosity and complementation? What is the difference?
Both involve autosomal recessive inheritance.
Compound heterozygosity: two different mutations in the same gene (allelic heterogeneity) → mutant phenotype
Complementation: two mutations in different genes (locus heterogeneity) → normal phenotype
In autosomal recessive inheritance, what is the probability that the phenotypically normal sibling of an affected individual is a carrier?
What is the difference between autosomal recessive inheritance and X-linked recessive inheritance on a pedigree?
In X-linked recessive inheritance, there is no father-to-son transmission and almost no female patients with the disorder; autosomal recessive may show both.
What is the mode of inheritance for hemophilia A?
X-linked recessive (defective clotting factor VIII gene on Xq), large inversion mutation
How can X-linked dominant inheritance be distinguished from autosomal dominant inheritance on a pedigree?
X-linked: for affected fathers and unaffected mothers, no sons will be affected and all daughters will be affected
autosomal: 50% of progeny will be affected regardless of gender
What is the mode of inheritance for defective enamel of teeth?
X-linked dominant
How can mitochondrial inheritance be identified from a pedigree?
All children of affected females are also affected.
What are some diseases that exhibit locus heterogeneity?
-retinis pigmentosa
-autosomal dominant polycystic kidney disease
-autosomal recessive deafness
What are some diseases that exhibit allelic heterogeneity?
almost any disease caused by loss-of-function mutation:
-hemophilia A
-mild cystic fibrosis in males
What is polymorphism?
Having many alternative common alleles for one gene.
What is linkage analysis?
Using the rate of recombination between two genes to determine how close together they are. A double heterozygote is crossed with a homozygous recessive and the progeny are analyzed.
What are the different types of DNA sequence polymorphisms?
-minisatellites (a.k.a. VNTR)
What is an RFLP? How are they detected in linkage analysis?
An RFLP is a restriction site that is present in some alleles but not in others. Detected by:
-restriction digestion + Southern blotting
-PCR + restriction digestion
What is a minisatellite? How are they detected in linkage analysis?
A minisatellite (or VNTR) is a variation in the number of short (20-70 bp) repeats between alleles. Detected by restriction digestion + Southern blotting
What is a microsatellite? How are they detected in linkage analysis?
A microsatellite is a variation in the number of simple (2-4 bp) repeats between alleles. Detected by PCR.
What is a SNP? How are they detected in linkage analysis?
A SNP, or single nucleotide polymorphism, is a variation in one base pair between alleles. Detected by:
-sequence analysis
-allele specific probes
What is reverse genetics (also called positional cloning)?
-Use linkage analysis to narrow down the location of the gene that causes the disease.
-Identify genes which are mutated in patients with the disease.
-Sequence the gene and determine its function.
What are the types of human post-natal hemoglobin?
HbA: 2 α subunits and 2 β subunits
HbA2: 2 α subunits and 2 δ subunits
What are the types of human fetal hemoglobin?
-2 α subunits and 2 γ subunits (alanine)
-2 α subunits and 2 γ subunits (glycine)
What subunits make up embryonic hemoglobin?
2 ζ subunits and 2 ε subunits
Why are globin genes only transcribed in erythroid cells?
Erythroid cells are the only cells in the body which express all the transcription factors necessary for globin gene transcription.
What is an α thal 2 deletion? What is an α thal 1 deletion?
There are two α globin genes. An α thal 2 deletion is in just one of the genes, an α thal 1 deletion is in both.
What is the difference between the β0 mutation, β+ mutation and the βE mutation?
β0: no β globin is made (nonsense, frameshift, deletions)
β+: 10% β globin produced because mutator splice site is preferred
βE: 60% β globin produced, and it is E because mutator splice site is preferred
How does Southern blot analysis work?
Measures the length of DNA fragments by how far they travel in the gel. This is good for detecting mutations which eliminate or create restriction sites (point or deletion).
How does allele-specific oligonucleotide hybridization work?
Use labeled synthesized probes which will bind only to either the normal or mutant sequence at a certain temperature. This is combined with Southern blot analysis; it is most useful if only one mutation causes the disease.
How is PCR used to identify Huntington's disease?
Huntington's is caused by an expanded trinucleotide repeat, so it gives a longer PCR product.
How is multiplex PCR used to identify deletions in Duchenne muscular dystrophy?
Multiplex PCR amplifies several regions of the gene simultaneously, and the products are compared with those of a normal patient to see which regions are missing.
How can allele-specific oligonucleotide hybridization be used to test for several different mutations simultaneously?
Combine ASO with multiplex PCR, using probes with normal sequence as well as with all mutant sequences being tested for.
How does undernutrition in childhood and adolescence lead to decreased height?
Expression of insulin-like growth factor is positively regulated by nutrition.
How does the sib-pair method identify a disease-causing gene?
For any polymorphic autosomal locus, siblings have a 50% chance of sharing one allele, 25% chance of sharing both, and 25% chance of sharing neither. When two sibs have the disease, loci which show more sharing than expected between the two are identified.
What is NOD2 and what disease is it implicated in?
NOD2 is a pattern-recognition receptor for bacterial LPS which may activate the NF-κB pathway. Defects in NOD2 are linked to Crohn's disease.
What is a haplotype?
A combination of alleles for different markers on the same chromosome.
What is the international HapMap project?
Identify common haplotypes for all regions of the genome in different populations to discover genes which contribute to susceptibility to common diseases.
Which enzyme transcribes genes that encode proteins?
RNA polymerase II
At what steps of gene expression can regulation occur? Which is most often used?
-transcription (most often)
-RNA processing
-RNA stability
-protein stability
-protein modification
What is two dimensional SDS-PAGE?
Separates proteins by molecular weight and pI using electrophoresis.
What do transcription factors (activators/repressors) do?
-bind DNA response elements (basic region of transcription factor, DNA-binding domain)
-recruit co-activators/co-repressors (activation/repression domain)
What do co-activators do?
-modify the chromatin
-help recruit basal transcription machinery (including Pol II)
What are some differences between activators and co-activators?
-co-activators do not bind DNA in a sequence-specific fashion, activators do
-co-activators are much larger; they are multi-subunit complexes
What is histone acetylase activity? Is this activating or repressing DNA transcription? What about histone deacetylase?
Acetylation of the N-terminal histone tails in order to open chromatin. This activates transcription. Removal of acetyl groups by an HDAC represses transcription.
What is CBP? What syndrome is caused by mutations in CBP?
CBP = CREB binding protein. It is a co-activator which regulates cAMP response. Mutation in CBP leads to Rubinstein-Taybi Syndrome (mental retardation, neonatal abnormalities in toes, thumbs, and face).
What is TFIIH? What syndrome is caused by mutations in TFIIH?
-phosphorylates C-terminal domain of Pol II, which initiates transcription
-involved in DNA repair
Mutations in a subunit of TFIIH leads to xeroderma pigmentosa (increased sensitivity to UV light and rate of skin cancer).
What type of ligands do nuclear receptors bind?
lipophilic ligands:
-fatty acids
-bile acids
How do nuclear receptors play a role in transcription?
Nuclear receptors are transcription factors for genes that control growth and differentiation. Different ligands that bind to the receptor change its conformation, causing it to recruit co-activators/co-repressors differently.
What is NF-κB? What inhibits it?
NF-κB (p65/p50) is a transcription factor that targets genes which mediate inflammatory and other immune responses.
-IκB is normally bound to NF-κB, inhibiting its translocation into the nucleus.
-Steroids also inhibit NF-κB, through glucocorticoid receptor.
What is IκB? How is its activity regulated?
IκB inhibits NFκB activity. -Cytokines stimulate the phosphorylation of IκB, causing it to be degraded.
-Aspirin inhibits phosphorylation of IκB.
What is SREBP? How is its activity regulated?
SREBP upregulates:
-LDL receptor (clears LDL from blood)
-cholesterol biosynthesis
-fatty acid biosynthesis
High cholesterol: SREBP is in the ER membrane. Low cholesterol: cleavage, freeing the C-terminal portion.
What are statins?
Drugs which decrease cholesterol, activating SREBP.
What is p53? How is its activity regulated? What region of p53 is usually mutated in cancer?
p53 activates genes that help the cell respond to genotoxic stress. DNA damage causes p53 to be phosphorylated, activating it. The DNA binding domain of p53 is most commonly mutated in cancer.
What is the main contributor to increased life expectancy? What is the second most important contributor?
social/societal factors, followed by public health
What factors contribute most to the cost of health care in the U.S.?
-high technology
-inappropriate care
-pharmaceutical spending
-administrative costs
People in which age group most often fail to receive health care due to financial problems?
How many people are uninsured at any one time in the U.S.? How many overall in the past year?
-47 million are uninsured at any given point
-60 million were uninsured at some point in the past year
What were the three major external causes of preventable death in the U.S. from 1977-1993?
What is aortic stenosis?
-narrowing or obstruction of the aortic valve
-blocks flow of blood from left ventricle to aorta
What type of pain is caused by aortic stenosis? What aggravates/alleviates it?
-under chest bone, may radiate
-crushing, squeezing, pressure
-exercise aggravates, rest alleviates
What is pericarditis? What type of pain does it cause?
-swelling and irritation of the sac-like membrane that surrounds the heart
-causes sharp pain (pericardium rubbing against the heart)
What is pleuritis? What type of symptoms does it cause?
-also called pleurisy
-inflammation of the lining of the lungs
-sharp chest pain, may radiate
-shortness of breath
-rapid breathing
What is a pulmonary embolus?
sudden blockage of a lung artery
What is pneumothorax? What are the symptoms?
sudden collection of air in the lung that makes it collapse without trauma
-sharp chest pain
-shortness of breath
-abnormal breathing
What is cholecystitis? What are the symptoms?
-inflammation of gallbladder, often caused by bile buildup, infection, trauma, diabetes
-sharp pain in upper abdomen
-worse for several hours after eating
-may go up to bottom of right shoulder blade
What is pancreatitis? What type of pain does it cause?
inflammation of pancreas caused by digestive enzymes activated too early
-pain starts in abdomen and reaches around to back
-worse with eating
What is costochondritis? What type of pain does it cause?
-inflammation of the junctions where the upper ribs join the cartilage
-localized chest pain that is reproducible by pressing on the chest
What is a dissecting aneurysm?
enlargement of the aorta caused by a tear in the aortic wall
What is hemoptysis?
coughing up blood

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