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366 Cards in this Set
- Front
- Back
proteins/amino acids are linked by ______ bonds
|
peptide
|
|
Which level of protein structure participates in backbone H-bonding?
|
Secondary
|
|
Why is histidine very special?
|
It's a good buffer
|
|
1) What amino acid can form disulfide bonds?
2) And what happens if there is too much of this AA? |
1) Cystine
2) can form stones |
|
In an alpha helix, H bonds occur between backbones of SAME or DIFFERENT strands?
|
different
|
|
In a beta sheet, H bonds occur between backbones of SAME or DIFFERENT strands?
|
different
|
|
Name the FOUR types of bond/interactions that can drive tertiary and quaternary structure formation
|
H-bonds
ionic bonds disulfide bonds hydrophobic interactions |
|
Name of a protein composed of 3 different subunits
|
heterotrimer
|
|
What is the main function of glutathione (2 GSH)?
|
Reduce disulfide bonds
|
|
What molecule does glutathione (2 GSH) become during the process of reducing disulfide bonds?
|
GSSG
|
|
What kind of structure is insulin secreted as?
What kind of structure does insulin have to be in order to get absorbed? |
hexamer
monomer |
|
How does Lispro increase activity of insulin?
|
it destabilizes the hexamer formation, increasing insulin break down into monomer
|
|
Describe the overall structure of immunoglobulins?
(types of chains, bonds and regions) |
-2 light chains & 2 heavy chains
- inter and intra chain disulfide bonds - variable & constant regions |
|
What is a holoprotein?
|
a protein with ALL of its groups
|
|
What is an apoprotein?
|
a protein WITHOUT all of its group
|
|
In what state does the iron have to be in in hemoglobin for it to bind oxygen? (give name and oxidation state)
|
Ferrous
2+ oxidation state |
|
When no oxygens are attached to hemoglobin, what form is it in?
|
taut form
|
|
What is cooperative binding of oxygen to hemoglobin?
|
binding of 1st oxygen to Hb increases the affinity of the other oxygens to bind
unloading of oxygen from hemoglobin occurs in the same way |
|
Oxygen cooperative binding is also called __________ binding
|
allosteric (binding is affected by changes at a different site)
|
|
2,3-BPG is an example of ______ _____________
|
self regulation
|
|
Describe where 2,3-BPG is found in the body and its main function
|
found in RBC
stabilizes the taut Hb form to release oxygen into tissues that need it more readily |
|
What is MetHb?
|
-methomeglobin
-ferric state (Hb-Fe^3+) of hemoglobin that cannot bind oxygen |
|
What is the role of NADH methemoglobin reductase?
|
it's an enzyme which converts methemoglobin (Hb-Fe^3+) to hemoglobin (Hb-Fe^2+)
|
|
Name 3 potential cases of methemoglobinemia
|
1) drugs/toxins can oxidize Fe^2+
2) deficiencies in NADH methemoglobin 3) MetHb mutations can make it resistant to reduction by NADH methemoglobin reductase |
|
An increase in cross-links in the serum suggests what?
|
increased bone degredation
|
|
An increase in procollagen levels in the serum suggests what?
|
increased bone synthesis
|
|
High carboxyhemoglobin levels in the body indicate what?
|
CO poisoning
|
|
Where does synthesis of collegen take place?
By what means does synthesis of collegen occur? |
in the RER
hydroxylation and glycosylation |
|
Where does cleavage of procollagen occur?
|
outside of the cell
|
|
If a protein is found that cleaves 2,3-BPG is expressed in the body, would this increase, decrease or have no effect on the oxygen content of Hb?
|
increase (2,3-BPG increases oxygen unloading from Hb, so if 2,3-BPG is broken down (cleaved), there would be more oxygen still bound to Hb)
|
|
What is a polar molecule?
|
molecule in which electrons are shared UNEQUALLY between other molecules
|
|
What type of molecules can dissolve readily in water?
|
polar, hydrophilic molecules (like dissolves like)
|
|
What would happen to a cell if placed in a hypertonic environment?
Hypotonic? Isotonic? |
Shrink
Swell (can cause the cell to rupture) No change in cell shape |
|
Will bacteria rupture if placed in a hypotonic solution?
|
No (the have a cell wall)
|
|
To dissolve an acid, you must place it in (stronger/weaker) (acid/base). Why?
choose one from each parenthesis group |
stronger acid
(a stronger acid solution will have more protons to donate) |
|
To dissolve a base, you must place it in (stronger/weaker) (acid/base). Why?
choose one from each parenthesis group |
stronger base
(a stonger base solution will be looking to gain a proton) |
|
Is Hendersen-Hasselbalch equation log (unprotonated/protonated) or log (protonated/unprotonated)?
|
log (unprotonated/protonated)
|
|
Which extracellular biological buffer system (that we've learned thus far) is used to maintain acid-base balance?
|
bicarbonate buffer system
Effective pKa = 6.1 (CO2 adjusted by breathing) |
|
Which intracellular biological buffer system (that we've learned thus far) is used to maintain acid-base balance?
|
phosphate buffer system
Effective pKa = 7.2 |
|
Something that's oxidized is also called the _______ agent
|
reducing
|
|
Something that's reduced is also called the _______ agent
|
oxidizing
|
|
Name of carbohydrates that differ only at ONE asymmetric carbon
|
epimers
|
|
molecules that have the same molecular formula and sequence of bonded atoms, but differ ONLY in the three-dimensional orientation of their atoms in space
|
stereoisomers
|
|
The structure of monosaccharides in SOLUTION
|
cyclic
(their stereochemistry at the anomeric carbon can also change) |
|
What compounds can form glycosidic bonds?
bonds are formed between what? |
sugars
bonds between anomeric carbon and the O or N group of another molecule |
|
N-glycosidic bonds are found where?
|
nucleosides & glycoproteins
|
|
O-glycosidic bonds are found where?
|
disaccharides, oligosaccharides, polysaccharides & glycoproteins
|
|
Name the 3 monosaccharides
|
glucose
galactose fructose |
|
Name the 3 disaccharides
|
sucrose
lactose maltose |
|
What is sucrose composed of?
|
glucose-fructose
|
|
What is lactose composed of?
|
glucose-galactose
|
|
What is maltose composed of?
|
glucose-glucose
|
|
What is the only sugar that will give a negative reducing sugar test?
|
sucrose
|
|
How many double bonds do saturated fatty acids have?
Is the melting point higher or lower compared to unsaturated fatty acids? |
none (each carbon has a maximum amount of single bonds)
melting point is HIGHER than unsaturated. (introducing impurities such as double bonds will lower the melting point) |
|
Name the 2 types of unsaturated fatty acids
How many double bonds do they have? |
monounsaturated (1 double bond)
polyunsaturated (>1 double bonds) |
|
Can cis-structured fatty acids stack?
Is their melting point higher or lower than trans fatty acids? |
No.
Less stacking mean lower melting point. (that's why trans fatty acids are so bad for you --> higher melting point) |
|
Instead of glycerol, sphingolipids have what common core component?
|
ceramide
|
|
What common core component do steroids have?
|
cholesterol
|
|
Proteins fold into correct stuctures due to their __________ sequence of AA
|
primary
|
|
Heat shock proteins use energy from ATP hydrolysis to overcome _________
|
kinetic barriers
|
|
The role of isomerases in protein folding
|
helper proteins that help overcome kinetic barriers
|
|
What are chaperons/chaperonins?
|
heat shock proteins that assist in protein folding
|
|
Proteases are enzymes that break the ______ ________
|
amide backbone (& separates the protein into its individual AA)
|
|
Proteases work best in basic or acidic environments?
|
acidic
|
|
What is ubiquination?
|
proteins being tagged with ubiquitin for degradation
|
|
What is the role of ubiquitin after it has been tagged to a protein?
|
brings it to a proteasome, where the protein will be degraded into individual AA's
|
|
What is a proteasome?
|
protein chopping factory within a cell
(protein must have ubiquitin added to be degraded by proteasome) |
|
What attaches the ubiquitin to a protein?
|
ligases
|
|
PEST sequences are associated with proteins that have a ______ ____________ _________
|
short intracellular half-life
|
|
PEST sequences are found in proteins with high or low turnover rates?
|
high (thus acting as signal peptides for protein degradation)
|
|
Explain what happens when there is too much glucose in the body. (in terms of protein modification and glycosylation/glycation)
|
increase glucose = increase in glycosylation/glycation (bad) = increase in AGEs (aggregates) = increase in complications
|
|
Are proteins with high or low turnover rate affected more by Glycosylation/glycation
|
low turnover rate
|
|
Why is hemoglobin more affected by sugar levels than other proteins?
|
once sugar binds to Hb, oxygen cannot bind as readily
(so as glucose increases, glycosylation increases, and the amount of oxygen bound to Hb DECREASES) |
|
What does the term AGE stand for?
When are AGE levels high? |
advanced glycation end products
AGE levels are high when blood glucose is high (diabetics) |
|
What does HbA1c test measure?
|
hemoglobin glycation in RBC's, who's life span is 120 days.
can be used to ***** what glucose levels have been over a long period of time |
|
If you want to assess how well a pt has controlled their sugar levels over time, what test do you use?
|
HbA1c
|
|
Two proteins that are the same, but encoded by different genes and that function in different tissues
|
isoforms
|
|
When a variant occurs in a population; NOT a mutation, just a difference
|
polymorphism
|
|
Creatine kinase is an example of _______-_______ variation
|
tissue-specific
|
|
Creatine kinase is important in regenerating _____
|
ATP
|
|
If CK-MM is detected, where is the problem?
CK-BB? CK-MB? |
CK-MM = skeletal muscle
CK-BB = brain CK-MB - cardiac |
|
creatine kinase M and B are examples of what? (think structure)
|
isoforms (2 proteins that have same structure but encoded by different genes to work in different tissues)
|
|
A2γ2 is a structure for what type of hemoglobin
Does it have increased or reduced 2,3-BPG binding? |
HbF
Reduced, since oxygen must be transferred from maternal to fetal Hb |
|
α2δ2 is a structure for what type of hemoglobin?
|
HbA - a normal Hb variant
|
|
HbC is abnormal hemoglobin where the normal glutamic acid residue at the 6th position of the β-globin chain is subsituted by _________
|
lysine residue
|
|
HbS is abnormal hemoglobin (sickle cell) where the normal glutamic acid residue at the 6th position of the β-globin chain is subsituted by _________
|
valine residue
|
|
Polymerization occurs only when Hb is in the ______ form.
Thus, it is more common in the ________ tissues. |
taut (or deoxyginated)
peripheral |
|
What are proteinaceous infectious particles? (AKA infectious proteins)
|
PRIONS = non-living structures (proteins) that are involved in protein misfolding (ex. turning normal PrPc into PrPsc, which form aggregates/clumps in the brain)
|
|
What is mutant CJD?
|
when your own proteins mutate, forming prions
|
|
What is variant CJD?
|
when you ingest a prion (ex. PrPsc)
|
|
inheritance of alleles at one locus does not influence inheritance at other loci
|
independent assortment
|
|
test to see if two mutants with the same phenotype are produced by mutations of the same gene, or by mutations of separate genes
|
complementation
|
|
In complementation, mutations in different genes are _______________
mutations in same genes are _______________ |
complementary
non-complementary |
|
genetic interactions other than the autosomal recessive pattern
|
non-mendilian genetics
|
|
when different alleles have equal effects and heterozygotes have intermediate phenotypes
|
semidominance
|
|
different alleles have equal effects, but there is no blending of phenotypes
|
codominance
|
|
multiple alleles for the same gene/locus
|
polymorphism
|
|
multiple alleles for the same trait
|
polygenic inheritance
|
|
Explain epistasis
|
when one separate GENE masks the phenotypes of a totally separate gene
|
|
Define autosomes
|
all CHROMOSOMES besides X and Y
|
|
define autosomal
|
a GENE not located on X or Y
|
|
What is sex influenced inheritance?
|
AUTOSOMAL GENES which are expressed differently in males and females
|
|
Do exergonic reactions have a positive or negative ΔG?
|
negative
|
|
What do cells do to move unfavorable reactions forward?
|
couple them with more favorable reactions, so the overall ΔG is negative
|
|
What is an important carrier of chemical energy in muscle cells?
|
creatine phosphate
|
|
If [substrate] is raised, would ΔG become more favorable or unfavorable?
|
favorable
|
|
ATP/ADP ratios are maintained through _______ _________
|
aerobic respirations
|
|
Name the 3 steps in aerobic respiration
|
1) oxidize fuels (turn everything into acetyl CoA, oxidize acetyl CoA in the TCA cycle to make CO2m FADH2 and NADH)
2) Make ATP (oxidative phosphorylation) 3) Use ATP (will make ADP) |
|
Do enzymes change the ΔG of a reaction?
|
NO (they decrease activation energy AND increase reaction rate)
|
|
What is a coenzyme, and what happens to it during a reaction?
|
Coenzyme/cofactors are derived from VITAMINS
They get MODIFIED during a rxn |
|
inactive or less active enzymes that do not have its cofactors
|
apoenzyme
|
|
active enzyme (apoenzyme + cofactor)
|
holoenzyme
|
|
What does the mnemonic NVYC (envy c) stand for?
|
non-competative
vmax involved y-intercept changed catalytic rate affected |
|
what is Vmax in a reaction?
|
maximum velocity at which enzyme can catalyze the reaction
(adding more substrate will no increase the reaction since all enzymes are saturated) |
|
what is Km in a reaction?
|
substrate affinity
high affinity = low kM |
|
How is Km different from Kd?
|
Km is related to substrate AFFINITY
Kd is related to substrate BINDING |
|
A ligand or drug that does NOT activate signaling upon binding
|
receptor antagonist
|
|
A ligand or drug that activate signaling upon binding
|
receptor agonist
(a competative binder with the natural ligand at the same site) |
|
Do competative inhibitors affect the Km or Vmax?
|
Km
|
|
Do noncompetative inhibitors affect Km or Vmax?
|
Vmax
|
|
Define product inhibition
|
where the product of the reaction goes ack to the enzyme and binds to the allosteric site and inhibits the reaction from producing more product
|
|
name for inhibitors that bind to enzymes with non-covalent bonds such as H-bonds, hydrophobic bonds or ionic bonds
|
reversible inhibitors
add more substrate so inhibitor can be overwhelmed |
|
name for inhibitors that bind to enzymes with covalent bonds
|
irreversible inhibitors. (can't remove them).
Only way to make rxn proceed is to add more enzyme |
|
Name for an inactive enzyme precursor
|
zymogen
|
|
What do zymogens require in order to become active?
|
require biological change, such as CLEAVAGE
|
|
How does the activation of chymotrypsin differ to that of pepsin?
|
chymotrypsin requires outside source to be cleaved (trypsin)
pepsin cleaves itself (when in the stomach) |
|
What are futile cycles?
|
where 2 pathways run simultaneously in opposite directions and have no overall positive effect
|
|
metabolic products of one enzyme are passed directly to another enzyme w/o having to diffuse through the solution
|
substrate channeling
|
|
What forms the primary clot plug?
|
platelets
|
|
What things activate platelets?
|
Collagen
Thrombin ADP Epinephrin Immune complexes & stress |
|
The 3 roles of platelets
|
activation (Change shape)
aggregation adhesion to vessel wall |
|
Platelets are derived from
|
megakaryocytes
|
|
life span of a platelet
|
10 days
|
|
Do platelets contain a nucleus?
|
No
|
|
vWF is responsible for anchoring
|
Platelets to the subendothelial collagen
|
|
Phospholipase A2
|
is responsible for cleaving a phospholipid and releasing arachidonic acid in platelets
|
|
Arachidonic acid
|
is used to make thrombaxane (TXA2)
|
|
Is TXA2 a vasoconstrictor or vasodialator?
|
vasoconstrictor
|
|
What are the six sites of inhibiting platelet activation?
|
1. Cyclooxygenase activity (aspirin)
2. Thromboxane synthetase 3. Thromboxane receptor 4. GPII antagonists 5. ADP inhibitors 6. ADP receptor inhibitor |
|
What's the cause of von Willebrand disease?
|
A deficiency of vWF (can't fold a scaffold to which platelets can bind)
|
|
Cause of Bernard Soulier syndrome?
|
A deficiency of GP1b-IX
|
|
What is thrombocytopenia?
|
Low Platelet count
|
|
Activation of factor VII requires
|
factor III (Tissue factor)
|
|
Activation of factor XI requires
|
factor XII
|
|
Activation of factor IX requires
|
factor XI
|
|
Activation of factor II requires
|
factor X and factor V
|
|
What's so special about Factor XIII?
|
Factor XIII is the only non-serine protease enzyme. This enzyme is a transglutaminase that forms cross-links in fibrin by removing NH3
|
|
Breakdown of fibrin requires which protien?
|
plasmin
|
|
Protein C (APC)
|
inhibits coagulation through the protein degradation of coagulation factor VIII and factor V
|
|
Cause of Hemophilia A
|
Deficiency in factor VIII
|
|
Cause of Hemophilia B
|
Deficiency in factor IX
|
|
The most common bleeding disorder
|
vWF disease
|
|
What are PGI2 and NO made by, what are they activated by and what are their functions?
|
Produced by the endothelial cells. Activated by APC (activated protein C) and is used to vasodialate.
|
|
Vitamin K Requiring Coagulation factors
|
Factor II, X, IX, and VII as well as protien C/S.
|
|
Warfarin
|
Inhibits Vitamin K Epoxide Reductase thus reducing the activation of coagulation factor II, X, IX, and VII.
|
|
Antithrombin III
|
Inhibits the activity of factor II or thrombin
|
|
Heparin
|
Induces antithrombin III's activity which inhibits thrombin's activity.
|
|
Prothrombin time (PT) measures
|
the extrinsic pathway & the common pathway
|
|
Activated partial thromboplastin time (PTT) measures
|
the intrinsic pathway and the common pathway
|
|
Endothelial cells inhibit coagulation by
|
producing PGI2, nitric oxide and inducing APC
|
|
Endothelial cells block platelet binding by being
|
negatively charged
|
|
The D-dimer test will measure the
|
breakdown of fibrin
|
|
Glanzmann's thromboasthenia affects what?
|
GPIIb
|
|
How does fibrinogen deficiency affects platelets?
|
fibrinogen is used to aggregate platelets TOGETHER, so a deficiency would decrease aggregation
|
|
What factors does Thrombin activate?
|
Factors V, VIII, XI, XIII(when calcium is present)
|
|
What makes a soft clot?
|
Fibrin (Factor I)
|
|
How is the secondary clot plug made?
|
when fibrin (factor I) hooks up with factor XIII
|
|
How does thrombin indirectly inhibit coagulation?
|
thrombin binds to the thrombomodulin receptor in the endothelial cells to activate protein C
|
|
Heme is a component of what 3 things?
|
hemoglobin
myoglobin cytochromes |
|
Glutathione (reduces/oxidizes) oxidizing agents
-pick the correct choice |
reduces
|
|
In the process of reducing oxidizing agents, glutathione becomes (reduced/oxidized)
-pick the correct one |
oxidized to become GSSG
|
|
What re-reduces oxidized GSSG back to glutathione?
|
NADPH
|
|
What happens to NADPH when it re-reduces GSSG to glutathione?
|
it becomes oxidized to NADP+
|
|
What pathway re-reduces NADP+ back to NADPH?
|
pentose phosphate pathway
|
|
When methoglobin reductase reduces Fe^3+ to Fe^2+, what molecule is oxidized in the process?
|
NADH
|
|
What pathway re-reduces oxidized NAD+ back to NADH?
|
glycolysis pathway
|
|
Is the porphyrin ring recycled?
|
No, it's degraded into bilirubin
|
|
Where does heme synthesis take place?
|
reticulocytes, hepatocytes and other heme synthesizing proteins
|
|
What 3 things are needed for heme to be synthesized?
|
Succinyl CoA
Glycine Fe^2+ |
|
What is the rate-limiting step in heme synthesis?
|
Aminolevulinic Acid (ALA)
|
|
What is the cofactor of Aminolevulinic Acid (ALA)?
|
Vitamin B6
|
|
Question: The pKa of hydroxybutyric acid is about 4.7. At what pH (2 or 12) would almost all of the hydroxybutyric acid be protonated?
|
at pH of 2. (weaks acids need to be in stronger acids to get protonated)
|
|
Which amino acid enables intramolecular covalent bonding?
|
Cysteine. Disulfide bonds are covalent bonds
|
|
Purpuric spots suggest what?
|
thrombocytopenia
|
|
Name some things that cause or can cause defects in heme synthesis.
|
Lead poisoning
iron deficiency porphorias B6 deficiency Thalassemia |
|
With what method does Antithrombin III bind to thrombin?
|
irreversibly
|
|
Warfarin (increases/decreases) (PT, PTT)?
chose one answer from each parenthesis |
increases PT
|
|
If a patient has insufficent NAD in their body, what do you give them to treat the problem?
|
Niacin (B3) supplements
|
|
Long term iron storage is made by possible by binding iron to ________
|
hemosiderin
|
|
ferritin is responsible for _______ _______ _______ of iron and assists in gut absorption
|
short term storage
|
|
Name for genetic defects in ENZYMES catalyzing heme synthesis, which can lead to neurological disorders
|
porphyria's
|
|
Iron is transported in the blood by being bound to _________
|
transferrin
|
|
Where is most of the iron stored in the body?
|
liver
|
|
What is responsible for the reddish color of stool?
|
bilirubin
|
|
Where is bilirubin produced in the body?
|
reticulo-epithelial cells and spleen
|
|
What is produced by hepatic conjugation of bilirubin?
|
bilirubin diglucuronide
|
|
What 2 things are needed for bilirubin to become conjugated?
|
1) glucuronyl transferase
2) UDP-substrate |
|
What converts bilirubin to urobilinogen?
|
bacteria in the gut
|
|
Is presence of some indirect/unconjugated serum bilirubin normal?
|
yes
|
|
If indirect bilirubin is abnormally high in the serum, what 2 places could the pathology be?
|
pre-hapatic or hepatic pre-conjugated
|
|
If direct bilirubin is detected in the serum, what 2 places could the pathology be?
|
hepatic post-conjugated or
post-hepatic |
|
Is presence of some direct/conjugated serum bilirubin normal?
|
No
|
|
What is the intermediate in the process of conversion of heme to bilirubin?
|
biliverdin
(heme-->biliverdin-->bilirubin) |
|
Why does bilirubin need to be converted to bilirubin diglucuronide first before excretion?
|
bilirubin diglucuronide is more water soluable
|
|
How does heme synthesis play a role in globin synthesis?
|
heme stimulates synthesis of protein globulin by maintaining the ribosomal initiation complex for globin synthesis in an active state
|
|
How are glycolysis and the methemoglobin reductase reaction related?
|
they both reduce oxidizing agents
|
|
Are introns in both prokaryotes and eukaryotes?
|
no, only eukaryotes
|
|
The central dogma of biology
|
DNA -> RNA -> protein
|
|
HDAC
|
stands for histone deacetylase and is responsible for the deacetylation of histones (lysine residues), to make DNA INACTIVE
|
|
HAT
|
Histone acetyltransferase and is responsible for acetylating histones (the lysine residues), to make DNA ACTIVE
|
|
Define polycistronic DNA and what organisms they are found in
|
one mRNA transcribed MANY GENES
found in prokaryotes |
|
What do prokaryotic operons contain?
|
promoter + structural genes
|
|
Regulation of chromatin structures achieved by regulating what?
|
enzymatic activity of HDAC and HAT.
|
|
Transcription Factors do what?
|
control gene expression by regulating or inhibiting gene transcription.
|
|
RNA processing involves what 4 steps?
|
7mG guanicine cap, splicing, polyadenylation, and RNA editing.
|
|
What are the four elements found within an intron?
|
a 5' & 3' splice site, branch point, and a polypyrimidine tract.
|
|
Can splicing be regulated?
|
ya
|
|
How is splicing regulated?
|
Through the activity of SR proteins and hnRNP proteins.
|
|
T/F - Alternative splicing is a way to increase protein diversity.
|
True
|
|
T/F - When iron levels are low, ferritin mRNA is less stable.
|
True
|
|
T/F - When iron levels are high, Ferritin mRNA is more stable
|
True
|
|
T/F - When iron levels are low, TfR (transferrin receptor) mRNA is less stable.
|
False
|
|
T/F - When iron levels are high, TfR mRNA is less stable.
|
True
|
|
T/F - Nonsense mediated decay is a pathway for regulating RNA degradation.
|
True
|
|
Prader-Willi Syndrome is a result of what
|
paternal deletion of chromosome 15 q11-q13.
|
|
Angelman syndrome is a result of what
|
maternal deletion of chromosome 15 q11-q13.
|
|
Where does DNA methylation commonly occur?
|
GC rich regions of the promoter.
|
|
T/F - DNA methylation is a method of turning off gene expression.
|
True
|
|
T/F - Transcription and Translation in Prokaryotic organisms are coupled?
|
True
|
|
T/F - In prokaryotes, a repressor is responsible for inhibiting gene expression.
|
True
|
|
HDAC will (inactivate or activate) gene expression.
-pick one answer |
inactivate
|
|
HAT will (inactivate or activate) gene expression.
-pick one answer |
activate
|
|
Tautomeric shifts produce what type of mutations?
|
transitions (electron exchange exchanges purines to purines, and pyrimidines to pyrimidines)
|
|
If an exon has an ESE sequence attached to it, will it be included or excluded in the final mRNA product?
|
included
|
|
Is phosphorylation a type of post-transcriptional or post-translational modification?
|
post-translational
|
|
T/F - Use PCR to amplify RNA?
|
False. PCR is used to amplify DNA only
|
|
F and V class ATPases are examples of what?
|
proton pumps
|
|
Liver damage is likely to cause an decrease of what in the body?
|
albumin
|
|
Which part of snRPS actually does the splicing?
|
RNA portion
(snRPS has an RNA and protein portions) |
|
When there is low iron, IRE-BP are (bound/unbound) to transferrin IRE's.
-pick one |
bound (binding prevents degredating of transferrin).
|
|
When there is high iron, IRE-BP are (bound/unbound) to transferrin IRE's.
-pick one |
unbound (unbound IRE's lead to degredation of transferrin)
|
|
Schmid metaphyseal chondrodysplasia occurs when
|
AA codon is made into a stop codon (nonsense mutation)
|
|
Prader-Willi and Angelman syndromes are examples of what?
|
DNA Imprinting - male & female methylate DNA differently
|
|
Three characteristics of facilitated diffusion.
|
1) specific
2) increases rate of diffusion 3) diffusion rates are saturable |
|
Name two differences between transport proteins and gap junctions
|
1) Gap junctions are cell-cell whereas transport proteins are cell-extracellular
2) Gap junctions are non-specific, transport proteins are |
|
Name the 3 types of transport proteins
|
1) Channels
2) Transporters 3) ATPase pumps |
|
T/F - Transporters require a conformational change in the protein to let things pass
|
true
|
|
Name the subunits used in P Type ATPase pumps and their function
|
has 2 α subunits that are used for transport & 2 β subunits used for regulation
|
|
What is the largest and most diverse class of ATPase pumps?
|
ABC class pumps (ATP Binding Cassette)
|
|
Name the ABC class pump in the liver that pumps out hydrophobic toxins out
|
MDR-1
|
|
In CFTR lungs, why does mucus become viscous?
|
Because NaCl can't go into the mucous and attract water.
|
|
What is the biggest reason people with CFTR die?
|
infection due to Pseudomonas aeruginosa (which is usually harmless in normal lungs)
|
|
Which confirmational state, E1 or E2 is the resting state?
At this state, which binding site is open (high or low affinity)? |
E1
high affinity |
|
In P Type ATPases, what chages the conformation from E1 to E2?
|
phosphorylation
|
|
In Na/K pump, how many of what are pumped into the cell, and what and how much is pumped out?
|
3 Na are pumped OUT
2 K are pumped IN (for every ATP hydrolyzed) |
|
In Na/K pump, what prevents K from building up inside the cell?
|
K channels
|
|
What is a receptor?
|
something that recognizes, binds a SPECIFIC ENZYME, and INDUCES A BIOLOGICAL RESPONSE
|
|
What are isoreceptors?
|
different receptors are bound and activated by the SAME ligand (produces different response)
|
|
Do carbohydrates act as ligands?
|
NO
|
|
T/F - Nuclear receptors are transmembrane receptors.
|
False
|
|
In nuclear receptors, hydrophobic ligand binding causes what to happen to the receptors?
|
dimmerization
|
|
What are the three parts to a transmembrane receptor?
|
1) ligand binding domain (hydrophilic)
2) transmembrane domain (hydrophobic) 3) signal transduction domain (hydrophilic) |
|
Name 4 second messangers we studied
|
cAMP, DAG, IP3, Ca
|
|
Definition of second messanger
|
effectors that can change concentration
|
|
In TGFβ signaling pathway, what are the main receptor used?
|
Serine/Threonin Kinase receptor
|
|
In TGFβ signaling pathway, describe what is upstream and what is downstream of Type II receptors
|
Upstream - TGFβ ligand
downstream - Type I receptor |
|
What is the TGFβ signaling pathway used to control?
|
Development and Cellular Differentiation (NO physiological role!)
|
|
In TGFβ signaling pathway, what needs to happen in order for Smads to associate with coSmads?
|
phosphorylation of Smads (AKA receptor regulated Smads) by Type I receptors
|
|
In the Ras pathway, what receptors are used?
|
tyrosine kinase
|
|
What does the Ras pathway control?
|
Physiologic things such as blood glucose levels. Also does development and cellular differentiation
|
|
In the Ras pathway, what happens to the TK receptors after the ligand binds?
|
The TK receptors form dimers
|
|
Transautophosphorylation occurs in what signaling pathway?
|
Ras pathway
|
|
In the Ras pathway, what happens after the TK receptors are phosphorylated?
|
they bind adaptor proteins
|
|
In the Ras pathway, adapter proteins recruit what?
|
GEF
|
|
In the Ras pathway, what happens when GEF is activated?
|
GEF recruits Ras(GDP) and plucks of the GDP
|
|
In the Ras pathway, what does RAS(GTP) phosphorylate?
|
RAF
|
|
In the Ras pathway, what does RAF do?
|
phosphorylates MEK
|
|
In the Ras pathway, what does MEK do?
|
phosphorylates MAP
|
|
In the Ras pathway, what does GAP do?
|
causes dephosphorylation of Ras(GTP) to Ras(GDP)
|
|
In the Ras pathway, what do phosphates do?
|
dephosphorylate downstream effectors such as Raf, MEK & MAP)
|
|
In the cAMP pathway, what receptor is used?
|
7-transmembrane receptor & G-proteins
|
|
What is the cAMP pathway used for?
|
physiological (glucose and metabolism), inflamation and menstrual cycle
|
|
In the cAMP pathway, which sections of the 7-transmembrane receptor interact with the G-protein?
|
C-terminus; loop between helix 5 & 6
|
|
In the cAMP pathway, which structures are attached in the inactive state?
|
GαGDP is attached to the 7-transmembrane protein in the inactive state
|
|
In the cAMP pathway, what happens when the ligand first binds?
|
GαGDP becomes GαGTP
|
|
In the cAMP pathway, what does GαGTP do?
|
activates adenylate cyclase
|
|
In the cAMP pathway, what is the role of adenylate cyclase?
|
convert ATP to cAMP
|
|
In the cAMP pathway, what is the role of cAMP?
|
acts as a second messenger to activate Protein Kinase A (PKA)
|
|
In the cAMP pathway, what is the structure of Protein Kinase A?
|
Has 2 R (regulatory) subunits and two C (catalytic) subunits
|
|
In the cAMP pathway, when Protein kinase is activated, what goes on to phosphorylate other things?
What gets phosphorylated? |
the C subunit goes on to phosphorylate serine & threonine residues of specific proteins
|
|
In the cAMP pathway, what role does phosphodiesterase play?
|
Deactivates the cAMP pathway by converting cAMP to AMP
|
|
In the cAMP pathway, what role do GAP domains play?
|
GAP always changes GTP to GDP
|
|
In the cAMP pathway, what inhibits GAP domains?
|
cholera toxins (therefore, can't stop pathway)
|
|
In phosphoinositide pathway, what recetor/s are used?
|
USUALLY the 7-transmembrane receptor w the G-proteins.
BUT one class uses tyrosine kinase receptors |
|
What is the phosphoinositide signaling pathway used for?
|
physiological (hormones, metabolism), transport protein activity, cardiac & neuronal electric signal propagation & mental health
|
|
In phosphoinositide pathway, if a ligand binds a tyrosine kinase receptor, what happens next?
|
TK receptor phosphorylates PLC
|
|
In phosphoinositide pathway, if a ligand binds a the 7-transmembrane receptor, what happens next?
|
the 7-transmembrane receptor phosphorylates GαGDP to GαGTP, which then goes on to phosphorylate PLC
|
|
In phosphoinositide pathway, once PLC is activated, what does it do?
|
catalyzes cleavage of PIP2 into IP3 & DAG
|
|
In phosphoinositide pathway, which of the following factors are integral membrane and which are released into the cytosol? (PIP2, IP3, DAG)
|
-PIP2 and DAG are integral membrane factors
-IP3 is released into the cytosol |
|
In phosphoinositide pathway, what does IP3 do?
|
released into the cytosol to activate Ca channels which then go on to activate Protein Kinase C (PKC)
|
|
In phosphoinositide pathway, what does DAG do?
|
Activates Protein Kinase C (PKC) when it reaches DAG (allows it go go and activate effectors downstream)
|
|
In phosphoinositide pathway, what is the purpose of Protein Kinase C (PKC)?
|
it phosporylates various proteins such as transcription factors and enzymes to induce various cellular responses
|
|
In phosphoinositide pathway, how is the signal inactivated?
|
when IP3 & DAG rejoin to regenerate PIP2
|
|
In phosphoinositide pathway, what role does pertussis toxin play?
|
It prevents the release of the GDP from Gα, which blocks PLC activation and inhibits the pathway
|
|
In phosphoinositide pathway, what role does lithium play?
|
lithium blocks the enzyme that rejoins IP3 & DAG to reform PIP2
|
|
How is Gα similar to Ras & GAP?
|
Gα has domains that act like Ras (which binds GTP) and also has GAP-type domains, which induces hydrolysis of GTP to GDP
|
|
What is the abbreviation for phosphatidylinositol biphosphate?
|
PIP2
|
|
What is the abbreviation for diacylglycerol?
|
DAG
|
|
What is the abbreviation for inositol triphosphate?
|
IP3
|
|
How is proto-oncogene different than oncogene?
|
Proto-oncogenes are normal functioning genes that that have the ability to proliferate (can have a gain-of-function mutation)
Oncogenes are proto-oncogenes that have the gain-of-function mutation and can increase the chance of tumors |
|
In Gel electrophoresis, does DNA travel from - side to + side, or + side to - side?
|
- side to + side. DNA itself is - , so it will travel to the + side
|
|
What is Southern Blot used to identify?
|
DNA
|
|
What is Northern Blot used to identify?
|
RNA
|
|
What is Western Blot used to identify?
|
Proteins (labeled with antibodies)
|
|
What are palindromes?
And could they be a problem? |
A strand of DNA that reads the same as its complementary sequence when read backwards
CATATG GTATAC (same as above, but backwards) These are potential restriction sites! |
|
What is DNA sequencing used for?
|
Determining the sequence of nucleotides in a DNA strand
Can be used in finding genetic disorders |
|
What type of sequence/structure blocks the the translation of VEGF mRNA and also induces its degradation??
|
RNAi
|
|
What is the abbreviation for phospholipace c?
What signaling pathway is it used in? |
PLC
Used in the phospoinositide pathway |
|
What are quantitative multifactoral traits?
|
can be assigned a numerical value (IQ, height, etc)
|
|
What are qualitative multifactoral traits?
|
all or not phenomenon. Either occur or not. (heart attacks, neural tube defects)
|
|
If a genetic problem tells you the incidence of something, is it telling you the q^2, or q?
|
q^2
|
|
What is the primary assumption of the Hardy Weinberg model?
|
population is in EQUILIBRIUM
|
|
What are the secondary assumptions of Hardy Weinberg model?
|
These are mechanisms for changing gene frequency:
-Mutation -Genetic Drift (plays a big role in small population) -Migration -Selection (fitness..must pass genes to be "fit") |
|
What is a proband?
|
its the first family member identified with the inherited trait of interest
|
|
What are consanguineous individuals?
|
Any two individuals who are descended from a common ancestor
|
|
Vertical transmission in pedigrees is an characteristic of what inheritance pattern?
|
autosomal dominant
|
|
Horizontal transmission in pedigrees is an characteristic of what inheritance pattern?
|
autosomal recessive
|
|
A proto-oncogene
|
typically induces cell transformation
|
|
What is oncogenesis?
|
Oncogenesis is the development of cancer cells. Cancer cells commonly inactivate inhibitor growth signals, evade apoptosis, have a limitless replicative potential, invade tissues, a sustained mutagenesis and undergo angiogenesis.
|
|
List examples of oncogenes
|
Growth factors/receptors
Signal Transduction pathways Transcription factors, Cell cycle control proteins, DNA repair enzymes and apoptosis proteins. |
|
By what mechanisms do proto-oncogenes become oncogenes?
|
1. A point mutation
2. Chromosomal translocation 3. Multiple copies of DNA 4. A frame shift mutation |
|
Cyclin D does what?
|
regulates the G1 phase of the cell cycle.
|
|
Cyclin D binds to what in the cell cycle?
|
CDK4/6
|
|
CDI (also known as CDK-I..)
|
is inhibitors of the cell cycle. Cyclin-dependent inhibitors help to control the progression through the cell cycle.
|
|
p16 inhibits
|
the cylin D/Cdk 4/6 activation of RB.
|
|
p21 inhbits
|
most cylin/cdk complexes, thus it inhibits the cell cycle.
|
|
p53
|
monitors DNA damage and activates p21 to inhibit cell division, and initiates DNA repair.
|
|
Describe the make-up of Ras
|
is a monomeric G protein and a proto-oncogene.
|
|
pRB
|
stands for retinoblastoma and is an example of a tumor suppressor.
|
|
DNA repair is initiated by:
|
p53
|
|
Tumor suppressor genes become oncogenic:
|
by deletions, point mutations, or DNA methylation.
|
|
A loss-of-function mutation is an example of
|
tumor suppressors
|
|
A gain-of-function mutation is an example of
|
proto-oncogenes
|
|
MAPK activates
|
Fos (a transcription factor)
|
|
T/F - Ras induces cell proliferation.
|
True
|
|
T/F - Hedgehog is a protoncogene.
|
True
|
|
T/F - The EGF receptor is an example of a protooncogene.
|
True
|
|
What are the two types of mechanisms that induce apoptosis?
|
1. The mitochondrial pathway
2. The membrane receptor pathway |
|
T/F - Activation of caspase-8 induces apoptosis
|
True
|
|
T/F - Activation of the death receptor activates apoptosis through the activation of caspase-8.
|
True
|
|
T/F - The activation of the mitochondrial pathway is elicited through the activation of Apaf-1, Cyt c, ATP, and pro-caspase-9.
|
True
|
|
Bcl-2 is what type of protein?
|
anti-apoptotic
|
|
Bax is what type of protein?
|
pro-apopotic
|
|
What is the multiple hit hypothesis?
|
The multiple hit hypothesis is an idea that more than one mutation is required for a normal cell to become a tumor.
|
|
List the chemicals that can cause DNA damage:
|
Benzopyrene(Cigarettes)
Aflatoxin B reactive oxygen species DNA crosslinking agents Alkylating agents and various other chemical mutagens |
|
Xeroderma pigmentosum is caused by
|
the inability to repair thymine dimers which are caused by UV irradiation.
|
|
Telomeres
|
are multiple TTAGGG repeats found at the ends of chromosomes.
|
|
What is telomerase
|
is the enzyme responsible for creating telomeres and is often inactivated in adult cells, but activated during oncogenesis.
|
|
Define senescence
|
a limited capacity to divide before cells enter a non-proliferate state.
|
|
Burkitt Lymphoma is caused by what?
|
a translocation of the myc gene from chromosome 8 to 14.
|
|
Chronic Myelogenous Leukemia is caused by what?
|
by a translocation between chromosomes 9 to 22.
|
|
Cofillin and N-WASPS are involved in what process?
|
Invadopodia (tumors degrading the basement membrane of normal cells)
|
|
In the Hedgehog pathway, what is the proto-oncogene and what's the tumor supressor? (hedgehog or patched?)
|
Patched inhibits smoothed (the thing that starts the pathway), so it's a tumor suppressor.
Hedgehog inhibits patched, so the pathway can continue, so its a proto-oncogene. |
|
What are Beta-catenins and what's their role in cancer?
|
are subunits of cadherins, and are found to be increased in cancer
|
|
Whats the roll of topoisomerases?
|
maintain a certain level of DNA supercoiling
|
|
What are Geimsa stains?
|
Stains the chromosome banding patterns
|