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USMLE Step 1 Kaplan Biochem


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What drug block DNA Topoisomerase II? Prok? Eukar?
Prok: nalidixic acid/quinolones

Eukaryotes: etoposide
and teniposide
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?
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
early death

The krabbe got your eyes!
What accumlulates in Gaucher's Dz?
- brain
- liver
- spleen
- bone marrow

G is for Glucocerebrosidase

What are the findings in Gaucher's Dz?
Characteristic Crinkled paper enlarge cytoplasm
gaucher's cells
- 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:
- brain
- kidney
- liver
- 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
mucopolysaccharidoses: Hunter'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
Cloudy corneas
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
Cerebral degeneration
What collagen is affected in Osteogenesis Imperfect?
Type I for bONE
What do you see in patients with Osteogenesis Imperfecta?
skeletal deformities
blue sclera
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
2) CRE
3) PPREs
Which response element is induced with the new tx for insulin resistance?
- thiazolidinediones
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
congenital deafness
limb 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
- Hypotonia
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
- introns
- promoters
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
* Phenylketonuria
* 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?

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.
X-linked recessive
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
O-linked glycosylation

What a.a. is associated w/ endoplasmic reticulum and export of proteins?
N-linked glycosylation
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?
S-adenosaylmethionine (SAM)
What does tyrosine make?
Thyroid T3/T4
What is the smallest a.a.?
What a.a. makes tyrosine?
What is made with tyrosine?
thyroid T3T4
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-
glutamic acid
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?
Private tim hall
What does PVT TIM HALL stand for?



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