Week 1 Flashcards
3 main categories of genetic disorders
-single gene disorders -multigenic/multifactorial disorders (many genes+environment) -chromosomal disorders
Parts of chromosome (4)
-telomere -centromere -p leg: short -q leg: long
Mitosis -cells -splitting -daughter cells
-autosomal replication -all chromosomes line up at metaphase plate for sister chromatids to be split -only splits once -daughter cells are diploid (2n)
Meosis -cells -splitting -daughter cells
-sex chromosome replication -splits twice -homologous chromosomes will line up at metaphase plate to be split, then sister chromatids will be split in metaphase 2 -daughter cells are haploid (n)
Non-disjunction -what is it? -results in? -likelihood
-when chromosomes fail to separate -result in trisomy/monosomy -likelihood of non-disjunction increases at maternal age of 35
When and how to identify genetic errors?
-ultrasound during pregnancy -1 week newborn follow up -first and second year: monitor milestones -school/puberty: developmental disorders
Normal karyotype - short hand - description
-46, XY -all chromosomes lined up in pairs of homologous chromosomes, same length, no bands missing
Trisomy 18 -other name -short hand -prognosis -symptoms
-Edwards syndrome -47, XY, +18 -prognosis: 95% spontaneous abortion, babies don’t typically survive 1st year -finger overlap, rockerbottom feet
Cri du chat -short hand -symptoms
-46, XY, del (5p) -wide set eyes, jaw and mouth deformation, cries like a cat, weight loss due to retrognathia (tongue is further back)
Klinefelters syndrome -short hand
-47, XXY -looks normal; BOYS: have feminine characteristics, small testes, low muscle mass, usually funny/immature;
Turners syndrome -short hand -symptoms
-45, X0 -amenorrhea, broad chest, webbed neck, lack secondary sex characteristics
Trisomy 21 -other name -short hand -when to check -incidence increase
-down syndrome -47, XY, +21 -ultrasound at 12 weeks of gestation to check for extra tissue around neck -mom at 40 is 1:100; mom at 50 is 1:10
Monosomy 14 -short hand
-partial deletion of 6 -45, XX, -14, (del 6q) -not viable unless there is mosaicism
How genetics can cause disease in: -normal chromosomes -chromosomes with balanced translocation -chromosomes with unbalanced translocation
-epigenetics/ chromosomes look normal but still have mutated alleles, recessice, carrier of a disease -length of each segment is equal, phenotypically normal, BUT could have takes off regulatory gene and cause loss of function/gain of function -unequal distribution; most likely cause deletion of some genetic material
Non-classical inheritance (4)
-trinucleotide-repeat mutations -mutations on mitochondrial genes -genomic imprinting -gonadal mosaicism
trinucleotide-repeat mutations -when? -worsening -example
-repeats generated during gametogenesis -clinical features worsen with each successive generation -Huntingtons disease, Fredrick ataxia (ataxic gait), Fragile X
mutations in mitochondrial genes -inheritance -example
-maternal inheritance -Leber hereditary optic neuropathy
genomic imprinting -other name -how? -example
-epigenetics -selective inactivation of alleles by differential patterns of DNA -angelman and prader-willi syndromes
gonadal mosaicism -how? -example
-not all gametes carry the mutations or chromosomal aberrations -osteogenesis imperfecta
Normal abnormalities NOT due to genetics -club foot, how? -cone head, how?
-due to low levels of amniotic fluid, child gets squiched in the womb and achilles tendon becomes shortened; easily fixed -head is squished in birth canal
Fragile X -signs -diagnosed
-large mandible, large ears, do poorly in school -not usually diagnosed until failing school
Pierre Robin -signs
-small chin, retro tongue
Central Dogma
DNA transcribed into mRNA which is translated into a protein
Replication of leading strand
- Need 1 RNA primer made by primase (DNA dependent RNA polymerase) - 5’ to 3’ -Replicates towards the fork -Once primer is set then DNA polymerase binds to start copying DNA into mRNA
Replication of lagging strand
-Creates okazaki fragments (shorts fragments of DNA) that are discontinuous -5’ to 3’ synthesis -Replicates away from the fork -Multiple primers required -Once primer is set then DNA polymerase binds to start copying DNA into mRNA
DNA polymerase (3)
-Epsilon: Helps w/ synthesis of leading strand; Has proof reading activity -Alpha: Adds about 20 nucleotide base pairs to the 3’ end and then discontinues b/c it doesn’t have proof reading activity -Delta: Helps w/ synthesis of lagging strand; fills in gaps of okazaki fragments
DNA polymerase reads strand and makes daughter strand
3’ to 5’ and 5’ to 3’
Enzymes that uncoil duplex DNA for replication
-Helicase: breaks hydrogen bonds -Single stranded DNA binding proteins: works after helicase, prevents H bonds from re-forming -Topoisomerase: involved in unwinding
Topoisomerase
1: open up neg. coils by making single stranded breaks 2:breaks double strands, opens up positive coils, has ATPase activity; breaks phophodiester bonds
How many replication forks are there?
-multiple are occurring at once
Egophony
-inc. resonance of the voice with inspiration and expiration; voice sound muffled; when asked to say “E” could sound like “A”
Community acquired pneumonia -cause? -order -plan -prescribe
-Strep. pneumonia (gram positive) -would need x-ray and UA -would use monotherapy drug for both CAP and UTI -would prescribe fluoroquinolones; specifically levofloxacin due to effect on gram - and gram + and higher impact on respiratory bacteria
Fluoroquinolones (-floxacins) MOA
-inhibits topoisomerase II (DNA gyrase, supercoiling) and topoisomerase IV (unique to prokaryotes; separates two circular strands to allow for replication)
Messenger RNA
-5’ Cap -3’ poly A Tail -single stranded -Has uracil instead of thymine -Makes codons (3 base pairs codes for one AA)
Enzyme required for transcription
-RNA polymerase
RNA polymerase -types -where will it bind
-I: makes rRNA -II: makes mRNA -III:makes tRNA -TAATAA box (consenses sequence of TAAT) and CAAT (increases activity of TAATAA box)
RNA polymerase vs DNA polymerase efficiency
RNA polymerase is more efficient than DNA polymerase b/c DNA polymerase requires a lot of help and RNA polymerase can just do everything by itself
Promoter -what is it -where is it located
-gene sequence that is present close to gene being transcribed and is the binding site for RNA polymerase -must be upstream from start of gene
Enhancer -what is it -binds to -location
-Enhances transcription by promoting binding of RNA polymerase to the promotor site - Binds to activation factors, can be upstream or down stream since DNA folds
Silencer -binds to
- Binds to repressor proteins which activate them and cut off transcription
Post transcriptional modifications
-poly a tail and cap help to protect ends of mRNA from degradation
Poly A tail
- Comes from ATP -Enzyme: poly A polymerase (adds it)
Methylguanine cap
- Includes a methylated guanine residue which gets added to the nucleotide in the diphosphate form
Splicing -what is it? -introns -maturation
- Removing introns from exons; Taking out garbage you don’t need -Introns - non-coding; Have them b/c they protect the exons (coding sequences) b/c these are very vulnerable to mutation - This helps in maturation of primary sequences and takes pre mRNA to mRNA
Alternate splicing -what is it? -why is it important?
○ Changing the arrangement of the exons in the mature RNA (shuffling them) ○ Increases diversity of proteins by reshuffling the coding of the exons
Beta thalecemia
-decreased amount of Hb beta chains in respect to Hb alpha chain -can be caused by mutation in TATA box which would cause reduction of binding for Hb beta chain
Non-sense mutation
-truncated mutation
Point mutation
-can cause substitution of one AA with another
How can RNA virus be incorporated into host DNA?
- Reverse transcription -Integrase enzyme: Incorporation of the virus genome into the host cell
Reverse transcription
-RNA to DNA (single stranded that’ll replicate and become double stranded) -This requires reverse transcriptase (eukaryotes don’t have this)
tRNA
-single stranded, folded -anticodon binds to codon on mRNA - 3’ end will bind to AA with ester bond -brings AA from cytoplasm to ribosome to make protein chain
Ribosome -parts
-40s: binds to mRNA -60s: houses tRNA with AA -A: acceptor site, accepts tRNA that is bound to AA -P: peptidyl site -E: binds to uncharged RNA and then falls off ribosome
Genetic code is universal
-prokaryotes and eukaryotes have same genetic code
Genetic code is degenerate -what? -importance?
-one AA can be coded for by multiple codons -decreases frequency of mutations; makes DNA less vulnerable
Wobble position
-allows for tRNA to bind to multiple codons for single AA -wobble base of I,U,G on third position of anticodon -C and A are NOT wobble bases
Steps of translation
-Initiation: -Elongation: -Termination:
Post translational modifications
-acetylation -disulfide bond -glycosylation -lipidation -phosphorylation -ubiquitination
Acetylation
adds an acetyl group to the N terminus of protein to make more stable
Disulfide bond
covalently links the “S” atoms of 2 different cysteine residues
Glycosylation
attaches a sugar, usually to an “N” or “O” atom in an amino acid side chain
Lipidation
attaches a lipid to a protein chain
Phosphorylation
adds a phosphate to serine, threonine or tyrosine
Ubiquitination
adds ubiquitin to a lysine residue of a target protein marking it for destruction
Termination of translation
-Occurs when you get to the stop codon at the A site -There is not a specific tRNA assigned to stop codon, instead it is recognized by a release factor, which adds a water to the last AA and releases it from the tRNA
Initiation of translation
-tRNA carrying methionine attaches to the small ribosomal subunit. Together, they bind to the 5’ end of the mRNA by recognizing the 5’ GTP cap. The complex scans to find the start codon, and then initiator tRNA binds to start codon at P site. Large ribosomal unit then binds to finish forming the initiation complex.
Elongation of translation
-tRNA bring in second AA to A site, peptide bond formation occurs through RNA enzyme peptidyl transferase; mRNA will physically move brining tRNA with 2 AA from A site to P site, opening A site for new AA
Sepsis
-can occur with spread infection; even when being treated -look for persistent fever even after being treated with antibiotic
Clinical use of enzymes: Diagnosis -amylase and lipase -creatine kinase -lactate dehydrogenase -alkaline phosphatase
-acute pancreatitis -muscle disorders/myocardial infarction -myocardial infarction -liver disease/bone disorders
Clinical use of enzymes: Drugs -statins -HIV antivirals -ACE-inhibitors -Beta-lactam antibiotics
-inhibit HMG coenzyme A reductase; lowers lipids -inhibit HIV nucleoside analog reverse transcriptase, black replication of HIV -inhibit angiotensin-converting-enzyme; antihypertensive -inhibit glycopeptide transpeptidase; block bacterial cell wall synthesis
What provides speed of enzyme catalyzed reactions?
-acid/base environment -controls how stable it is for enzyme to transition ligand to product
What provides specificity of enzyme catalyzed reactions?
-functional groups and 3D conformations -specific AA and their arrangements located in the active site -enzyme will not bind to substrate if AA in active site are different or in wrong formation
Active site
-where substrate binds -very specific to substrate
Lock and key model
-Specific and exact way that substrate needs to fit into the enzyme in order to have a rxn -Substrate fits into enzyme perfectly; rigid pre-formed active site -ex glucokinase
Induced fit model -what is it? -what does it need? -what are the complexes made?
-enzyme will change to accommodate the substrate; active site loosely fits the substrate; more fluid- NOT rigid -includes cofactor -two forms; enzyme subtrate complex; transition state complex
Induced fit model- Transition state complex -role -stability
-cofactor helps to change shape of active site and position the substrate correctly in the enzymes active site so that bonding between the enzyme and substrate can occur and the reaction can be produced -very unstable; has negative delta G, meaning that it really wants to cause a reaction and change substrate into produce
Induced fit model- Enzyme-substrate complex
-enzyme binds to active site but is not tight fitting in active site and does not allow for reaction to occur
Activation energy
-Amount of energy that is utilize in order to get from the initial state to the transition state -lessened with use of enzyme -Functional groups and co-factors of the enzyme at the active site align every thing up to make everything more efficient -# of molecules determines the rxn rate
Transition state
-on graph, it is the highest peak on the line because it requires the most energy
Intermediate steps when using enzyme
-causes dips and smaller elevations in activation energy curve; will not be as high of elevation as the transition state
Functional groups -what is it -examples
-unique moiety that is with in a molecule that helps provide stabilization for rxn to occur -Phosphate, carboxyl, methyls
Cofactors/coenzymes -what is it? -examples? why?
- inorganic/organic chemicals that assist enzymes during the catalysis of reactions - iron, zinc, magnesium, copper, nickel (all pos. charged maening they are able to accept electrons)
Acid-base catalysis -what is it -example
-functional group on the protein either donates a proton (acid catalysis) or accepts a proton (general base catalysis) during the course of the reaction. -ex: chymotrypsin- in active site histidine 57 acts as a general base catalyst and accepts a proton from serine 195, activating the serine to act as a nucleophile; later in the reaction the protonated histidine 57 acts as a general acid catalyst and donates a proton to a product leaving the reaction.
Covalent catalysis
-substrate is covalently linked during the course of the reaction to an amino acid side chain at the active site of the enzyme -ex: chymotrypsin-the activated serine 195 attacks the carbonyl group of the peptide bond to be cleaved by the enzyme, forming a covalent bond
Metal ion catlysis
-enzymes contain required metal ions to allow catalysis to occur - ex: carbonic anhydrase- requires an enzyme-bound zinc at the active site to bind and orients water appropriately so it can participate in the reaction
Catalysis by approximation
-enzyme forces substrates to bind in a manner that places reactive groups in the appropriate orientation through the formation of hydrogen bonds and ionic interactions between the enzyme and substrate -ex: nucleoside monophosphate kinases; transfer a phosphate from a nucleoside triphosphate to a nucleoside monophosphate, producing two nucleoside diphosphates.
Cofactor catalysis
-required cofactor for an enzyme usually forms a covalent bond with the substrate during the course of the reaction -ex: Enzymes involved in amino acid metabolism use pyridoxal phosphate (derived from vitamin B6) to form a covalent bond
Mechanism-based inhibitors
-covalent inhbitor of enzyme -ex: acetylcholinesterase is inhibited by organophosphorus (nerve agent); produces increased amount of acetylcholine; will cause symptoms of increased autonomics, arrythmia, vomiting -ex: penicillin attracts glycopeptide transpeptidase and binds it inhibiting it from being able to help with bacterial cell wall synthesis
Enzyme kinetics -Vi -Vmax -Km; small vs large -first order -zero order
-initial velocity -maximum velocity: the max velocity that could ever occur between that substrate and enzyme -Km: substrate concentration at 1/2 max velocity; small=high affinity, large=low affinity - substrate [] km; velocity is constant=vmax; rate of reaction is independent of substrate []; ex aspirin
Hexokinase vs Glucokinase
hexokinase has lower Km because it has higher affinity for glucose ensuring that they get glucose even when glucose blood levels are low (acts with hypoglycemia, to convert glucose to G6P); glucokinase has higher Km and lower affinity for glucose (only acts with hyperglycemia, to store excess glucose)
Competitive inhibitor
-reversible inhibitor -inhibitor binds to substrate binding site of active site -will be structurally similar to substrate -increase inhibitor concentration vs substrate then the inhibitor will bind more to enzyme, will increase Km (decreasing affinity) but no change to vmax since increasing amount of substrate will still allow it to reach to normal vmax
Non-competitive inhibitor
-reversible inhibitor -inhibitor binds to the catalytic site of the active site and changing orientation of AA in active site -decreases vmax, no change to Km (substrate can still bind but no reaction occurs)
Allosteric regulation
-can be activator or inhibitor -separate binding site from active site (orthosteric site); will change confirmation of enzyme allowing/disallowing substrate to bind the enzyme -ex: calcium calmodulin activates glycogen phosphorylase kinase
Feedback inhibition of metabolic pathways
-A bunch of rxns that come right after the other where the product of one rxn is used for the next rxn; and the concentration of the end product can inhibit one of the upstream enzymes (directly or through gene transcription) -ex: glucose to G-6p which can go to glycolysis /glycogenosis/ pentose phosphate pathway
Lineweaver burke plot
-slope is km; if slope is more steep that means increase in km, lower affinity -vmax is y intercept
Mechanism for regulating enzyme activity
-substrate availability -product inhibition -allosteric control -covalent modification -synthesis/degradation of enzyme
substrate availability -typical effector -results -time required for change
-substrate -change in velocity -immediate
product inhibition -typical effector -results -time required for change
-product -increase in vmax/ decrease in Km -immediate
allosteric control -typical effector -results -time required for change
-end product -increase in vmax/decrease in km -immediate
covalent modification -typical effector -results -time required for change
-another enzyme -increase in vmax/ decrease in km -immediately (minutes)
synthesis/degradation of enzyme -typical effector -results -time required for change
-hormone or metabolite -enzyme [] or vmax -hrs to days
