Study Guide Questions Section 1 Flashcards
non-polar amino acids?
glycine, valine, leucine, isoleucine, alanine, proline
hydrophobic amino acids?
leucine, isoleucine, proline, methionine, tryptophan, phenylalanine, tyrosine
hydrophilic amino acids?
serine, threonine, asparagine, glutamine, cysteine
very hydrophilic amino acids?
glutamate, aspartate, histidine, arginine, lysine
pKa of lysine, arginine, aspartate, and glutamate?
lysine: 10.5
arginine: 12
asp: 4
glu: 4
henderson-hasselbach?
pH = pKa +log[base]/[acid]
definition of pKa?
the pH when the concentration of acid and its conjugate base are the same
what is pI?
the pH when the positive and negative charges are balanced
what is the pKa of bicarbonate?
6.1
six differences between DNA and RNA?
DNA: double-stranded, has thymine instead of uracil
RNA: has an OH at 2’ of ribose, has no repair mechanism, more fragile, has more errors
what is the direction of activity of DNA polymerase’s exonuclease?
3’–5’ usually and 5’–3’ for primer removal
why is codon preference useful?
it helps to conserve energy for microorganisms
what is a synonymous SNP?
a point mutation that leads to the codon for the same amino acid (silent mutation)
what is a non-synonymous SNP?
a point mutation in which the codon leads to a different amino acid being selected (missense mutation)
what is read-through SNP?
a point mutation that changes a stop codon into a codon that codes for an amino acid
what type of process is peptide formation?
dehydration
how many genes and polyproteins does HIV have? how does it carry out its function with this number of genes?
it has three genes and two polyproteins
protease cleaves the polyproteins into smaller proteins that have different functions
what is the structure of collagen?
rope-like helix
what is the structure of a peptide bond?
planar like a double bond
what stabilizes secondary structures?
hydrogen bonds
what stabilizes tertiary and quaternary structures?
hydrogen bonds, ionic interactions, hydrophobic interactions, van der waals, and sometimes disulfide linkages
name three compounds that have disulfide bonds:
insulin, immunoglobulins, ribonuclease
what is protein folding driven by?
entropy
another name for chaperones and what do they do?
heat shock protein
they prevent collection of newly-synthesized proteins to facilitate in the formation of secondary structure
name two processes that proteases are important for:
food digestion and blood clotting
which amino acids form salt bridges?
aspartate, glutamate, arginine, lysine, histidine
what is the charge of a protein above its pI?
negative
what is the charge of a protein below its pI?
positive
how does vCJD get to the brain of its new host?
it gets through intestinal epithelium via transcytosis and gets transmitted to the brain through macrophages or dendrites
what is different in the structure of normal and abnormal PrP?
normal PrP are helical
abnormal are beta sheets
amino acid sequence is the same
how did people get Kuru?
from eating brains of humans in a traditional ceremony
what does vCJD look like under a microscope?
like a sponge around the plaque
what is proteopathy?
disease from protein misfolding
what are the two prospective causes of Alzheimer’s?
amyloid plaques from ABeta proteins and neurofibrillary tangles
what do reticulocytes makes?
hemoglobin and red blood cells
neutrophils last how long and have what degradative enzymes?
one to two days contain proteases (elastase) nd myeloperoxidase
what are foam cells?
when macrophages engulf LDL with cholesterol
what do eosinophils do?
defend against parasitic infection
what is plasma and what is serum?
plasma = liquid portion of blood that contains salts, vitamins, amino acids, proteins, fats serum = plasma that is spin down to remove the coagulation factors
what does albumin do?
consists of up to 50% of the plasma proteins
stabilizes osmotic pressure, aids in the transport of water-insoluble compounds such as bilirubin
negatively charged to bind to positively charged compounds
what do the alpha1, alpha2, beta, and gamma peaks signify?
alpha1: alpha 1 antitrypsin = SERPIN that inhibits elastase; defects in this protease will cause emphysema; tobacco smoke oxidizes the methionine and inhibits the function of this enzyme
alpha2: haptoglobulin = binds hemoglobin; GC globulin = transports Vit D; ceruloplasmin = transports copper; prothrombin = precursor to thrombin; antithrombin III = a SERPIN that inhibits the formation of thrombin in the presence of heparin
beta: transferrin = transports 2 Fe 3+; hemopexin = binds heme
gamma: immunoglobulins (majority A, M, and G)
why is CRP called acute phase protein?
inflammatory response due to infection, cancer, and inflammation
can increase 50,000 times when triggered
what does fibrinogen do and how?
zymogen
cleaved by thrombin to form fibrin which aids in the formation of a clot
what two things that were in the notes counteract the effects of histamine and how?
epinephrine narrows the blood vessels to increase blood pressure
antihistamines (Benadryl) block histamine surface receptors
what is humira?
a monoclonal antibody drug
what is hematocrit?
the percentage of red blood cells in the blood
what is heme made out of?
protoporphyrin IX and Fe2+
what is the difference in structure between hemoglobin and myoglobin and their curves on the chart?
hemoglobin has four subunits and myoglobin is a monomer
hemoglobin curve is sigmoidal and the myoglobin curve is hyperbolic
what is an allosteric effect?
cooperativity of hemoglobin subunits
what is the bohr effect?
curve of hemoglobin shifting to the right for increases in pCO2, acid, BPG
what is Restriction Fragment Length Polymerization (RFLP)?
southern blot that targets a specific mutation sequence
what is a southern blot?
detects specific DNA sequences by hybridizing with the sequence and is illuminated using a radioactive probe or tag
what is a northern blot?
detects for specific RNA sequences
what is a western blot?
detects for specific proteins
SDS separates proteins based on what property?
size
what is TAQ and what is it used for?
thermus aquaticus and it is used for PCRs
name the different types of enzymes?
lyase, oxidoreductase, transferase, hydrolate, isomerase, ligase
what is a holoenzyme?
enzyme plus prosthetic group
[prosthetic group = tightly bound cofactor]
what is an apoenzyme?
enzyme without prosthetic group
what is a metalloenzyme and give example:
enzyme that uses a metal as a cofactor
vitamin-derived molecules
what is the change in free energy for spontaneous reaction?
negative
what do enzymes do to the transition state of a reaction?
stabilize transition state
where does chymotrypsin cleave?
phenylalanine, tyrosine, leucine (hydrophobic AA)
where does elastase cleave?
alanine, isoleucine, methionine (small aliphatic AA)
where does thrombin cleave?
arginine residues
where does trypsin cleave?
lysine and arginine
what is Km?
substrate concentration at 1/2 the maximum velocity of the reaction
what is Kcat?
reaction rate
number of substrate reacting per second
what is Kcat/Km?
catalytic efficiency
why do some enzymes have sigmoidal curves?
binding of one substrate molecule enhances the binding of another substrate molecule
enzymes that follow MM kinetics have what type of graph?
hyperbolic
what is PLP, what is it derived from, and what does it do?
pyridoxal phosphate
derived from vitamin B6 (pyridoxine)
it is a coenzyme used with aminotransferases
give an example of metalloenzyme:
what metal is its cofactor?
carbonic anhydrase uses Zn2+
what are statins?
competitive inhibitors that reduce cholesterol by binding to HMG CoA reductase (used in cholesterol synthesis)
what is an ACE inhibitor?
Angiotensin Converting Inhibitor
competitive inhibitor of ACE and lowers blood pressure
what is the effect of competitive inhibition on Km and Vmax?
Vmax unchanged
Km increases
what is the effect of noncompetitive inhibition on Km and Vmax?
Vmax decreases
Km unchanged
give example of noncompetitive inhibitor:
ferrochelatase
irreversible inhibitors form what type of bond with enzymes?
covalent bonds in the enzyme’s active site
what is an isoenzyme and give examples:
catalyze the same reaction
COX-1
COX-2
give examples of irreversible inhibitors:
aspirin
penicillin
SERPINs
what do ibuprofen and naproxen sodium do?
reversibly inhibit COX-1 and COX-2
how do irreversible inhibitors affect Km and Vmax?
same as noncompetitive inhibitor
what is a homotropic effector and a heterotropic effector?
homotropic = the substrate heterotropic = not the substrate [as in feedback inhibition]
why are enzymes and substrates contained in organelles?
an increase in proximity increases metabolic efficiency
how is muscle glycogen activated?
covalently bonding with phosphate or allosterically by binding to AMP
which amino acid can be phosphorylated?
serine, threonine, tyrosine
what amino acid does ubiquitin attach to?
lysine
what makes cancer cells immortal with respect to proteasome?
pro-apoptotic factors that signal cell death are degraded by the proteasome
how does velcade work?
inhibits proteasome degradation of pro-apoptotic factors
what form are most proteases in?
inactive zymogen form
where is trypsinogen made, and what does its active form do?
made in the pancreas and participates in protein degradation in the duodenum
where are blood coagulation proteins made?
liver
when heart muscle is damaged, what other protein increases?
muscle troponin
how do the Vmax and Km of isoenzymes compare?
they are different depending on the demands of the cell
what does alanine amino transferase in the blood indicate?
liver damage
what are the primary, secondary, tertiary, and quaternary structures of DNA?
nucleotide sequence of one strand, helix with complementary strand, supercoiling of duplex helix, and supercoiled structure with histones or RNA
what form does DNA exist inside cells?
Right-handed helix
what is a quinolone?
a drug that inhibits bacterial DNA gyrase
what are examples of nucleotide analogs? what do they do?
AZT, araA, araC, dideoxyinosine
used as antitumors or antivirals
what is telomerase?
a reverse transcriptase mainly in germ and stem cells that copy RNA into DNA at their ends
what are DNA polymerase alpha, beta, gamma, delta, and epsilon?
initiation DNA repair mitochondrial DNA synthesis lagging strand synthesis leading strand synthesis
what are DNA polymerase I, II, and III?
removal of primers and fill in
DNA repair
leading strand synthesis
what is a transition?
a DNA polymorphism that changes a purine to a purine or a pyrimidine to a pyrimidine
what is a transversion?
a DNA polymorphism that changes a purine to a pyrimidine or a pyrimidine to a purine
name the causes of spontaneous mutation
deamination (loss of amido group of a base)
depurination (hydrolysis of the glycosidic bond)
oxidations (additions of an O group to a base)
name the causes of induced mutation and examples
alkylating agents, x-rays induces single and dsDNA breaks, dietary carcinogens, UV light, smoking
what biological processes lead to mutation
viral and transposon insertion, errors of replication, mutation in DNA repair enzymes
what decreases the effects of mutation?
only 2-3% of the DNA is coded, introns where mutations occur are removed, the code is degenerate (mutation changes the codon but codes for the same amino acid)
how can mutations be inherited?
if they are mitochondrial or in germ line cells
name the types of excision repair mechanisms and how they do it
base excision repair - uses N-glycosylase to remove the damaged base and an AP endonuclease removes the rest of the nucleotide creating an AP site
nucleotide excision repair - uses endonucleases to remove ~30 nucleotides
breast, colon, and ovarian cancer have gene mutation in what set of enzymes?
repair enzymes
what are suicidal proteins?
alkyl-transferases - removes alkyl groups and dies
what is Xeroderma pigmentosum?
disease due to mutations in repair enzymes [NER]
how does recombination repair work?
DNA from undamaged chromosome is used to repair the damage
where are the predominant sites that homologous recombination occurs?
in germ line cells to allow for diversity
what type of gene is often in transposable elements?
resistance genes
what percent of our DNA are transposable?
40%
what is a complex transposon?
associated genes that move with the element
what sign shows that transposition has occured?
direct repeat
what do RNA polymerase I, II, and III transcribe?
I - rRNA
II - mRNA
III - 5S rRNA and tRNA
where on the DNA does transcription begin?
promoter region
how is DNA polymerase II unique?
it has a site for phosphorylation to control transcription
what are basal transcription factors?
they identify the promoter region and stimulate RNA polymerase binding
name the types of termination and mechanism
factor (rho) dependent that uses ATP and forms a hairpin structure
factor independent where an AU rich region is followed by a GC rich stem loop
name the prokaryotic and eukaryotic inhibitors of RNA polymerase
rifampicin and amanitin (mushrooms)
what are dihydrouridine, pseudouridine, and ribothymine examples of?
post-transcriptional alterations commonly found in tRNA
why does mRNA need alterations and what are they?
it needs 5’ methyl guanine cap and a 3’ poly A tail in order to leave the nucleus
what do ribonucleases do?
process tRNA and rRNA that change the size of RNA’s primary structure
what is transesterification used in?
splicing out introns
what is the purpose of exon shuffling?
creating genetic diversity
what do enzyme cascades do to reactions?
amplify the reaction
what does COX-1 do?
produces thromboxane that is a vasoconstrictor and activates more platelets
what is required for platelet aggregation?
ADP
what serine proteases does ATIII inhibit?
factors IXa, Xa, XIa, XIIa, VIIa, IIa
what molecule on endothelial cells prevents unnecessary clotting?
heparin-like molecules are expressed to maintain low levels of ATIII
what does nitric oxide do?
made by endothelial cells which inhibit platelet aggregation
what is tissue plasminogen activator?
made by endothelial cells that activates plasminogen to degrade fibrin
what does plasmin do?
breaks down fibrin
what is ferrochelatase and why is it significant?
it binds to lead and can be noncompetitively inhibited by lead
where on the tRNA are amino acids attached?
the 2’ or 3’ OH of the adenine with the carboxyl group of the amino acid
what enzyme adds an amino acid to a tRNA?
amino acyl tRNA synthetase
what allows for less than 61 tRNAs to be used for a cell?
wobble or non watson-crick base pairing
what step in charging a tRNA is irreversible and drives the reaction forward?
the amino acid being added to the amino acyl tRNA using ATP catalyzed by pyrophosphatase
what do all tRNAs have in common in relation to their structure?
similar secondary structures and 3D structures
where does wobble base pairing usually occur on the mRNA and the tRNA?
the 3’ nucleotide on the mRNA and the 5’ nucleotide on the tRNA
what is inosine and what is it used for?
adenosine deaminated and is often found at the 5’ position of tRNAs to allow for wobble
it binds with C, A, U eliminating the need of 2 tRNA molecules
what is the most energetically expensive process in a cell?
translation
what is the energy source used for translation
GTP and ATP in eukaryotes but just ATP in prokaryotes
what are the different sites in the ribosome for tRNA
A site - where the new tRNA enter
P site - contains the tRNA with the peptide chain
E site - where the tRNA sit before they are kicked out
what determines lifespan of an mRNA molecule
how rapidly it loses its poly A tail
what is the most important target for antibiotics
ribosomes
post translational modifications change which structures of proteins
primary and secondary
chaperones are particularly useful for folding what type of proteins
large ones
what happens to proteins that need to be secreted
they have signal recognition peptide that is recognized by a signal recognition particle and cleaved by a signal peptidase
what determines the amount of transcription of most genes
how often RNA polymerase binds and initiates synthesis
name the other types of control of gene expression that affect mRNA turnover
mRNA processing and splicing, transport from the nucleus, translational control and ribonucleases
what is the TATA box and what binds there
an AT rich region where RNA polymerase binds along with basal transcription factors
what is a repressor and what is an activator
gene specific transcription factors that bind to specific DNA sequences to increase or decrease RNA polymerase activity
what are enhancer binding proteins
they bind at enhancer region away from promoter and enhance transcriptional activity by bending the DNA to recruit RNA polymerase
what does it mean when a gene is constitutive or inducible?
constitutive is always expressed
induced is expressed when needed
where are enhancer sequences located?
either upstream or downstream several thousand sequences away from the promoter
what are mediator proteins?
the link enhancer sites with basal transcription factors
what are regulatory genes?
genes that code for proteins that control gene expression
what does hyperacetylation of histones do?
allows TF access to DNA which activates gene expression
what does acetylation do to lysine?
reduces the positive charge of lysines on histones which reduces the interaction between it and negative PO4 group of DNA
what are CpG islands
can have cytosine methylated which turns off the gene
transcriptionally active genes are here
what is imprinting
a differential degree of methylation from mom and dad that is inherited
heterochromatin vs euchromatin
hetero - inactive/supercoiled up
eu - active
what are VDRE, TRE, and RARE? what do they have in common?
they are vitamine D, thyroxine, and retinoic acid binding proteins
they bind these hormones in the nucleus and function as heterodimers with a common receptor monomer and recognize direct repeats
what are GRE and ERE
they are glucocorticoid and estrogen binding proteins and bind these hormones in the cytoplasm and function in the nucleus as homodimers after releasing heat shock proteins and recognize inverted repeats
recessive mutations affect the activity of
enzymes
dominant mutations affect the
structural proteins
what is haploinsufficiency
when the heterozygote of a recessive mutation has a phenotypic effect
what is thalassemia
autosomal recessive mutation that leads to decreased production of hemoglobin subunits
what is muscular dystrophy
affects dystrophin and causes muscle weakness
x linked
what is tay-sachs
autosomal recessive mutation that leads to a lysosomal storage disease due to a defect in enzyme processing
nucleotide triplet repeat expansion is due to what and usually leads to what type of disease
slipped mispairing during DNA replication and leads to neurological disorders
name the nucleotide repeat expansion diseases we talked about
huntington’s
fragile x
myotonic dystrophy
friedreich ataxia
what is huntington’s
autosomal dominant
binds CBP transcription factors and affects neuronal cell transcription
what is fragile x
a CpG island is in the promoter of FMR1 gene leads to down regulation of transcription by hypermethylation
no translational regulation
x linked
what is myotonic dystropy
autosomal dominant mutation that interferes with polyadenylation or mRNA splicing of protein kinase mRNA that keeps it in the nucleus
what is friedreich ataxia
autosomal recessive mutation resulting in splicing alteration of an intron in mRNA for mitochondrial frataxin protein used in iron metabolism
