Glossary of USMLE Step 1 Kaplan Biochem
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- What drug block DNA Topoisomerase II? Prok? Eukar?
- Prok: nalidixic acid/quinolones
- Which cells contain telomerase? What are they linked with?
- embryonic, germ cells, stem cells except somatic cells
- cancer/malignant cells have a high level of telomerase
They are linked with apoptosis
- What is another name for topoisomerase II in PROK?
- DNA gyrase
- What nucleic acid has the most methyl groups?
- What happens when you take a methyl out of Cytosine?
- It becomes demethylated to Uracil
- During what cell cycle does DNA repair occur?
- G1 Phase
- When does mismatch repair occur? (phase)
- G2 phase
- What does p53 gene encode for?
- Protein that prevents a cell w/ damaged DNA from entering the S phase
- What disease is associated with p53 gene?
- Li Fraumeni Syndrome and many solid tumors
- What is ATM gene?
- ATM encodes for a kinase needed for p53 to work
- What is ATM gene associated with?
- ataxia telangiectasia
- What is ataxia telangiectasia?
- hypersensitivity to X-rays
predisposition to lymphomas
- What is BRCA1 associated with?
- Breast, Prostate and Ovarian Cancer
- What is BRCA 2 associated with?
- Breast cancer
- What are BRCA1 and 2 associated with?
- required for p53 activity
- What happens when UV light damages DNA? What disease is prone to this damage? Why?
- it crease thyamine dimers
- patients with Xeroderma Pigementosa
- they lack excision endonuclease
- What does Xeroderma Pig. consists of?
- - Extreme UV sensitivity
- excessive freckling
- multiple skin cancers
- corneal ulcerations
- What are two diseases that are associated with DNA repair?
- Xeroderma and Hereditary Nonpolyposis Colorectal Cancer (HNCC)
- What drug inhibits DNA dependent RNA polymerase?
- What drug binds to DNA preventing its transcription?
- Actinomycin D
- What drug inhibits RNA polymerase II?
- amanitin (from mushrooms)
- Which RNA do RNA Pol 1,2 and 3 code for?
- 1 2 and 3 rhyme with R M T
1 rRNA 2 mRNA 3 tRNA
- What is similar to sigma factor in Eukaryotes?
- TFIID, transcription factors II
they bind before RNA Pol, just like Sigma factors
- How does RNA pol know where to start?
- - sigma factor needs to find promoter region
- two consensus sequences are recognized as TATA BOX
- How long does sigma stay bound to DNA?
- As soon as transcription begins, sigma is released
- How does mRNA know when to stop trasncription?
- Rho-independent termination occurs when newly formed RNA folds on itself to form GC-rich hairpin loop
- How does Rho-dependet termination work?
- Rho displaces RNA pol from the 3' end of the RNA once it has paused at the termination site
- What binds to Shine-Dalgarno sequence?
- Where are Shine-Dalgarno sequences located?
- 5' end
- What is unique about prokaryotic transcription and translation?
- They can both start at the same time with the help of Shine-Dalgarno sequences which allow ribosomes to hook on and start the translation before transcription is done
- What is Shine-Dalgarno?
- Shine-Dalgarno sequences lets prokaryotes shine! They can do 2 things at the same time! Transcribe and TRANSLATE!
- What are the three STOP codons?
U Are Gone
U Are Away
U Go Away
- What is the poly-A tail added for?
- 1) protect from rapid degradation
2) transport to cytoplasm
- What is added at the 5' end of the transcribed mRNA?
- It is actually hnRNA and a methylguanosine cap Me-Gppp is added to the 5' end
- What is the function of the methyl guanosine cap?
- It helps protect the mRNA chain from degradation
- Where is the poly A tail added?
- 3' end
- What can you say about the length of the poly A tail?
- The longer the more stable the mRNA (hnRNA)
- What is another name for spliceosome?
- snRNP, SNURP
- What is the function of spliceosomes?
- They excise introns and leave only exons to be expressed
- What disease has a problem in spliceosomes/snRNP?
- B-thatlassemia since mutations interfere with the splicing of Beta-Globin mRNA
- How are the introns degraded?
- They are degraded in a lariat structure and excised by spliceosomes
- How can you calculate how many introns you have?
If you have 4 exons
Then you have I=4-1
I=3, 3 introns
- Where is the activated amino acid in a tRNA?
- at the 3' end
- How does tRNA accomplish its lariat shape (loop/cloverleaf)?
- it has weird bases like:
- Where is the anticodon found in the tRNA?
- in the middle of the loop
center loop in between 5' and 3' ends
- How do you know a protein is marked for destruction?
- It has been ubiquiniated by ubiquitin
Usually because of misfolding
- Who translates proteins for cytoplasm and mitochondria?
- free cytoplasmic ribosomes
- Who transtalates proteins for secreted proteins, membrane proteins, and lysosomas enzymes?
- Rough E.R.
- How can you make a protein to be delivered to the R.E.R.?
- N-terminal hydrophobic signal sequence has to be added to be secreted or placed in the membranes
- How do you direct a prtoein to go inside a lysosome?
- It is phosphorylated with a mannose residue in the R.E.R.
- usually this protein is an enzyme to be delivered to the lysosome
- What happens to misfolded proteins?
- They are mark with ubiquitin to be destroyed by proteosomes
you will be liquidated!!!
- What are proteosomes?
- They are large cytoplasmic complexes that digest damaged proteins
- What enzyme is deficient in Fabry's Dz?
- alpha-galactosidase A
- What enzyme is deficient in Krabbe's Dz?
- BB for beta-galactosidase
- What enzyme is deficient in Gaucher's Dz?
(It is in the center of the reactions)
- What enzyme is deficient in Niemann-Pick's Dz?
- What enzyme is deficient in Metachromic Leukodystrophy?
- Arylsulfatase A
- What enzyme is deficient in Tay Sachs Dz?
- Hexosaminidase A
- What accumulates from Fabry's Dz?
- ceramide trihexoside
- What is the finding in Fabry's Dz?
- renal failure
- What accumlulates in Krabbe's Dz?
- galactocerebroside in the brain
- What is the finding in Krabbe's Dz?
- Optic atrophy
The krabbe got your eyes!
- What accumlulates in Gaucher's Dz?
- bone marrow
G is for Glucocerebrosidase
What are the findings in Gaucher's Dz?
- Characteristic Crinkled paper enlarge cytoplasm
- progessive hepatosplenomegaly
- flaring of distal femur
- What accumlulates in Neimann Pick's Dz?
- sphingomyelin and cholesterol
No man Picks his nose with hiSPHINGER
- Wnat are the findings in Neimann Pick Dz?
- increase cholesterol and sphyhingomyelin in reticuloendothelial and parenchymal cells
- Patients die by age 3
- What accumlulates in Tay Sachs Dz?
- GM2 ganglioside 2
- What are the findings in Tay Sachs Dz?
- Cherry-red spot on macula
1:30 carrier in European Jews
Death by age 3
Got a Sach of Cherries in your Macula
- What accumlulates in Metachromatic Leukodystrophy?
- sulfatide in:
- peripheral nerves
- Which lysosomal storage diseases (of the sphingolipidoses) are autonomal recessive?
- All except Fabry's!!!
- What lysosomal storage disease are x-linked?
- sphingolipidosis: Fabry's
Hunter's hit the X
- What mucopolysacharidose Dz has no corneal clouding?
They need to see what they hunt!
- What enzyme is deficient in Hurler's Dz?
- What enzyme is deficient in Hunter's Dz?
- iDURONate sulfatase
- What increases in Hurler's Sx?
- heparan and dermatan sulphate
- What are the signs of Hurler's Sx?
- Halted growth
Progressive mental retardation
Thick, coarse facial features with low nasal bridge
Joint disease, including stiffness
Heart value problems
Abnormal bones of spine and claw hand
- How do we screen for Hurler's Sx?
- Urine Heparan and Dermatan sulfate
- What is a term associated with Hurler's Sx?
- Gargoylism since there are facial deformities
- What signs and symtoms are associated with Hunter's Sx?
- protuberant abdomen, claw hands, excessive hair growth, coarsening of the face with grotesque facial features; retarded growth, and behaviour problems.
- Which syndrom is severe? Hurler or Hunter?
- Hurler's Syndrome
It is termed MPS I
Hunter is MPS II
- What amino acid is unique to collagen?
- Where does glycosylation occur?
- E.R. and Golgi apparatus
- Which enzymes are requiered to make collagen?
- proline and lysine hydroxylases
- What vitamin is needed to make collagen?
- Vitamin C
- Hydroxylates Proline and Lysine in the RER
- What are some co-factors of lysyl oxidase?
- O2 and Copper (Cu)
- What Dz results from deficiency of Lysyl Oxidase and why?
- Deficient Copper (Cu2+)
Menke's Dz is a genetic deffect that decrease collagen synthesis
- What enzyme is deficient in Ehler's Danlos?
- Lysine Hydroxylase
- What are the signs and symptoms of Menke's Dz?
- Depigmented (steely) hair
Arterial tortuosity, rupture
- What collagen is affected in Osteogenesis Imperfect?
- Type I for bONE
- What do you see in patients with Osteogenesis Imperfecta?
- skeletal deformities
- What other disease is involved in Copper usage?
- Wilson's Dz but it is a Copper (Cu2+) toxicity
- What are some symptoms of Wilson's Dz?
- Liver Cirrhosis
Cu damages nerves and causes Brown Kaisser-Fleischner Rings
- What inhibits eEF-2? Elongation factor 2 in Eurkaryotes
- Diphtheria and Pseudomonas Toxins
- What inhibits protein translation in Eukaryotes?
- Diphteria and Pseudomonas
- Where do Diphtheria and Pseudomonas act?
- eEF-2 is inhibited
- How many ATPs high energy bonds are needed to translate an amino acid?
- 4 Total for each amino acid
2 ATP for charging
1 GTP for initiation
1 GTP for Elongation
- What is the antibiotic of choice for pertussis?
- Erythromycin; blocks transLOcation
- What results in Menkes Dz?
- - Fragile bones
- Fragile blood vessels
from poorly crosslinked connective tissue
- What blocks ADP ribosylation of EF-2?
- Diphtheria and Pseudomonas
- Genetic Regulation
- Chp. 5
- What is an operon?
- group of proteins required for a particular metabolic function
- Where is the regulatory region in Prokaryotes?
- Upstream on the 5' end
- What kind of mRNA does the operon produce?
- Polycistronic mRNA
- What two ways of transcriptional control exist in prokaryotes?
- regulation of activator and repressor proteins
- Where do we find Attenuation?
- Histidine Operon
- What model do we use for activator and repressor proteins?
- Lac Operon
- What two regulatory proteins exist in the Lac Operon Control?
- lac repressor protein
c-AMP-dependent activator protien (CAP)
- What does the lac operon sense?
- glucose is preferred but in the absence lactose is taken as energy
- What regulates the CAP?
- cAMP levels
if glucose is low, cAMP increases and activates it
- What happens to the lactose operon if glucose is present?
- it is shutdown
glucose decreases cAMP
so CAP doesn't bind to CAP site
- When does CAP bind to CAP site?
- when glucose is low since cAMP is high
- When is the repressor protein made?
- Always since it is embedded in the mRNA sequence
- What does lactose do to the lac operon?
- lactose induces gene expression since it prevents the repressor protein from binding to the operator sequence
- If lactose is high and glucose is low what happens?
- 1) lactose binds to repressor and stimulates gene expresssion
2) cAMP is high so it binds to CAP protein and
- When does the lactose operon stop sequence?
- when the repressor protein is bound to the operator
- When is high expression of the lac operon found?
- High lactose and no glucose
- When glucose is present does cAMP go up or down?
- they are inversely proportional
Glucose high cAMP low
glucose low cAMP high
- When glucose is high, what happens to the repressor?
- it remains active since CAP can't block it (cAMP is low)
- What compounds are formed when lactose is broken down?
- galactose and glucose
- What enzyme degrades lactose?
- Where does RNA polymerase work on?
- Lactose goes with
- Repressor attaches to?
- Attenuation??? Which operon?
- Histidine Operon
- What happens when histidine is absent?
- enzymes are produced
- What other a.a. work similar to the Histidine Operon?
- What is attenuation?
- premature termination of transcription
- What does attenuation in prokaryotes depdend on?
- The fact that transcription and translation occur simultaneously in prokaryotes
- What happens if histidine is present?
- Transcription is terminated before RNA pol reaches operon
- Can attenuation occur in Eukaryotes?
- No! Transcription and translation are two separate, independent events
- What starts translation after leader peptide is made?
- Shine-Dalgarno sequence
- What happens when histidine is low?
- the ribosomes will stall and not form the stem and loop + poly U that stops the ribosomes and they will continue to transcribe the genes of the operon
- What are activator proteins called in Eukaryotes?
- Response Elements
- Where are response elements located?
- Some upstream in promoter region
Most in an enhancer region outside of promoter even more upstream
- Where are upstream promoter elements located?
- Just upstream of -25 sequence TATA Box
- What does the upstream promoter elements include?
- CCAAT Box (-75) NF-1
GC-rich SP-1 (in between -25 and -75)
- What are the characteristics of enhancers?
- Contain activator proteins
- may be 1000 bp away from gene
- upstream, downstream, within an intron
-they are tissue specific
- What are repressor proteins in Eukaryotes called?
- What are cis regulators?
- DNA regulatory base sequences/binding sites for proteins
- What are trans regulators?
- transcription factors
- What are the properties of a trans regulatory property?
- they can diffuse through the cell to their point of action.
- What protein class are steroid receptors?
- Zinc Finger
- What protein class are cAMP response element binding prtoeins? (CREBs)
- Leucine Zipper
- Homeodomain proteins are what protein class and what are they involved in?
Regulate gene expression during development
- embryonal development
- What protein class are peroxisome proliferator-activated receptors? (PPARs)
- Zinc finger proteins
- What is the response element for 1) steroid receptors?
for 2) cAMP?
for 3) peroxisome (PPARs)
- 1) HRE
- Which response element is induced with the new tx for insulin resistance?
- What is a new drug that targets Peroxisime proliferator-activated receptors? (PPARs)
-affects lipid metabolism
- What happens when glucose is low?
- Glucagon released
- What is the effect of glucagon on gene regulation?
- increases cAMP
- What happens in time of stress?
- Cortisol secreted
- What does cAMP do?
- - activates Protein Kinase A
- CREB is activated via phosphorylation
- CREB binds to what in the nucleus?
- CREB enters the nucleus and binds CRE region in the enhancer region
- What does the GRE and CRE region do?
- They enhance or activate PEPCK gene
- Who activates GRE enhancer region?
- cortisol (glucocorticoid response element)
- Who activates CRE enhancer region?
- Active CREB (cAMP response element) which is activated by cAMP
- What are two homeodomain protein regulator genes?
- HOX and PAX genes
Homeobox and Paired-Box genes
- What disease is associated with PAX (paired-box) genes?
- Klein Waardenburg syndrome (WS-III)
dystopia canthorum, pigment abnormalities
- What are some exceptions to codominat expression?
- - Barr Body (inactive X chromosome) in women
- Ig heavy and light chain loci
- T-cell receptor loci
- What happens when genes become acetylated?
- The histones are acetylated and it increases gene expression
- How do genes become silenced? Give two diseases that follows this...
- Methylation of DNA silences genes
Prader-Willi and Angelman Sx
- What chromosome is involved in defect of imprinting?
- Chromosome 15
- What is the problem in Prader-Willi Sx?
- Prader-Willi region is inherited from Paternal Origin (P for P)
so, if father has defective chromosome 15 then symptoms will occur
- What are the symptoms of Prader-Willi Sx?
- - Childhood obesity + hyperphagia
- Hypogonadotrophic hypogonadism
- Mental Retardation
- How else can you get Prader-Willi Sx?
- uniparental (maternal) disomy of chromosome 15
- When does upstream termination occur?
- When histidine is present
- When does downstream termination occur?
- when histidine is absent
* this is a normal termination
- What kindo of domain do HOX and PAX have?
- helix-turn-helix domain
- What is the first step in increase activity of beta-galactosidase activity?
- increase in cAMP due to glucose depletion
- Why does beta-galactosidase activity decrease?
- depletion of lactose
- dissociation of repressor protein
- binding of repressor to operator control region
- Chp. 6
- Recombinant DNA
- WHat does restriction sites provide?
- Usually defense against DNA viruses
- How do palindromes get protected in bacterial DNA?
- methylase enzyme modification
- How is infecting viral DNA recognized?
- unmethylated palindromes are recognized by restriction endonuclease
- What is a vector?
- piece of DNA that is capable of autonomous replication in a host cell
- What is recombinant DNA?
- when a fragment is placed inside a vector
- What is a genomic DNA library?
- colonies produced by plating the recombinant DNA with antibiotic resistance and sensitivity
- What can restriction site polymorphisms be used for?
- These enzymes cut DNA sequences and detect defects in longer sequences or shorter sequences.
Example: Sickle Cell Mutation which results in ONE long 1.35 kb fragment instead of a 1.15kb and a 0.2kb fragment (2 fragments is normal)
- What do cDNA lack?
- What must cDNA contain?
- complete coding sequence of a gene
- What is produced at the end of a cloning procedure?
- An expression library
- What do you do after reverse transcriptase has created the first strand of cDNA?
- Treat DNA with NaOH to remove mRNA template
- What enzyme do you use to create cDNA?
- reverse transcriptase
- How do you remove mRNA template strand in making cDNA?
- NaOH (sodium hydroxide)
- What must be inserted in order to produce proteins as the end product of cloning?
- - Bacterial Promoter
- Shine-Dalgarno Sequence
- What are 3 examples in which cDNA expression libraries are being used?
- 1) Recombinant Human Insulin
2) Recombinant Factor VIII (treating Hemophilia A)
3) Recombinant HBsAg (antigen(protein) is made and given to patients to immunize them against hepatitis B without introducing the live virus)
- Does the gene therapy cure the patient and subsequent generations?
- NO! it cures only the patient since it is only introduced into the affected organ and not into the reproductive tissues of the afected individual
- What is a transgenic animal?
- animal in which a new gene has been introduced into its germline
- How is gene therapy different from Transgenic Animals?
- transgenic animals have virtually new gene in every cell, including the gametophytes so that they get passed on to their offspring and these are no longer affected by the defect
- What are genomic libraries used for?
- studying DNA sequences that are not expressed
- response elements
Constucting restriction maps of DNA (sickle cell)
Id genetic markers (microsatellites)
- Chp. 7
- Genetic Testing
- What are the Autosomal Dominant Dz characteristics?
- - Only one mutant allele needed
- both sexes affected
- male to male transmission
- What are the Autosomal Dominant Dz?
- 1) Familian Hypercholesterolemia (LDL receptor def.)
2) Huntington Dz
3) Neurofibromatosis I
4) Marfan Sx
5) Acute Intermitent Porphyria
- What are the characteristics of autonsomal recessive?
- - two mutant alleles are requiered
- born to unaffected parents
- either sex
- male to male transmission
- What are some of the autosomal recessive dz?
- * Sickle Cell Anemia
* Cystic Fibrosis
* Tay-Sachs Dz (Hexosaminidase A def.)
- What are the traits of X-linked dominant?
- - One mutant allele
- either sex
- affected male passes on to all daughters
- affected female passes trait to both fem and males
- What are 2 X-linked Dominant Dz?
- - Hypophosphatemic Rickets
- Fragile X syndrome
- What are the traits of X-linked recessive dz?
- - usually males are affected
- no male to male transmission
- What are some of the X-linked recessive dz?
- 1) Duchene Muscular Dystrophy
2) Lesch Nyhan Sx (Hypoxanthine-guanine phosphoribosyltransferase HGPRT)self mutilation
3) Glucose-6-Phosphate Dehydrogenase def.
4) Hemophilia A and B
- What is the trait of Mitochrondrial Inheritance?
- - inherited maternally
- ALL offspring of affected female are affected!
- What are the 3 diseases that arise from Mitochrondrial Inheritance?
- LHON, MELAS and MERRF
1) Leber Hereditary Optic Neurophathy
2) Mitochondrial Encephalomyopathy, lactic acidosis, stroke-like episodes
3) Myoclonic epilepsy with ragged red muscle fibers
- What form of inheritance is Cystif Fibrosis?
- autosomal recessive
- How do you inherit Hungtington Dz?
- Autosomal Dominat
- What form of inheritance is sickle cell disease?
- autosomal recessive
- What form of inheritance is Fragile X Sx?
- X-linked Dominant
- How is Phenylketonuria inherited?
- autosomal recessive
- How is Lesch-Nyhan Sx inherited?
- HGPRT def.
- How is Neurofibromatosis I inherited?
- Autosomal Dominant
- What is the mode of inheritance of Marfan Sx?
- Autosomal Dominant
- How is Leber Hereditary Optic Neuropathy inherited?
- Mitochrondrial Inheritance
- How is Duchenne Muscular Dystrophy inherited?
- x-linked recessive
- How is myoclonic epilepsy inherited?
- mitochrondrial inheritance
- How is Acute intermittent porphyria inherited?
- Autosomal DOMINANT
- How is Rickets inherited?
- X-linked Autosomal Dominant
- How is Cystic Fibrosis inherited?
- autosomal recessive
- How is Familia Hypercholesterolemia inherited?
- Autosomal Dominant
LDL receptor deficiency
- How is Tay-Sachs Disease inhertied?
- autosomal recessive
- How is Hemophilia A and B inherited?
- X-linked recessive
- How is Glucose-6-phosphatase inherited?
- X-linked recessive
- Which RNA is identical to the coding strand?
- the mRNA
- What is the template strand?
- The strand that is compelementary and antiparallel to the mRNA
- What amino acids (a.a.) are precursors of catecholamines?
- Phenylalanine and Tyrosine
- What does tryptophan form?
- Serotonin and Niacin
- What a.a. is involved in depression?
- Tryptophan--> makes Serotonin
- What a.a. are involved in maple syrup disease?
- Isoleucine, Leucine and Valine
I Love Vermont maple syrup!!!
- What a.a. is a secondary amine?
- What does Proline do to the protein structure?
- disrupts secondary structure
- What are the acidic a.a.?
- aspartic acid and glutamic acid
negatively charged coo-
- What a.a. are basic? 3
- Histidine, Arginine, Lysine
They are positively charged NH+
- What a.a. is associated with the Golgi apparatus? 2
- serine and threonine
- What a.a. is associated w/ endoplasmic reticulum and export of proteins?
- What are two a.a. that conatin sulfure?
- Cysteine and Methionine
- What does cysteine do to the protein structure?
- stabilize the shape of proteins (3ry structure)
- What two a.a. are linked with post-translational modificacion?
- serine, threonine and asparagine
- What a.a. is a methyl donor?
- What does tyrosine make?
- What is the smallest a.a.?
- What a.a. makes tyrosine?
- What is made with tyrosine?
- What a.a. is associated with Vitamin B3?
- tryptophan is asociated with B3 (niacin)
- What disease is also related to tryptophan deficiency and pellagra?
- Hartnup Dz
since decreases Niacin B3 and causes Pellagra (dermatitis, diarrhea, demetnia)
- What a.a. contributes to the negative charge of proteins?
- aspartic acid coo-
- What a.a. contributes to the positive charge of proteins?
- lysine and arginine
- What a.a. is abundant in RBC?
- histidine since it brings the pH to 7.0
- What is the only a.a. that is useful in maintaining the physiologic pH (7.2-7.4)?
- Histidine pK at 7.0
- What are the essential amino acids?
- PVT TIM HALL
Private tim hall
- What does PVT TIM HALL stand for?
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