Week 1 - Metabolism and Replication/ Transcription/ Translation Flashcards
Which amino acids are responsible for kinks or turns in the secondary structure of proteins?
glycine and proline
Sulphur in the R groups of amino acids affect protein structure how?
Creation of disulfide bonds. Cysteine and Methionine
How do disulfide bonds affect protein structure?
stabilize the tertiary structure
Differences between myoglobin and hemoglobin?
•Myoglobin transports O2 to mitochondria for storage
-hyperbolic curve for oxygen saturation
•Hemoglobin transports O2 from lungs to tissue
-sigmoidal curve for oxygen saturation
-easier for O2 to enter tissue
What causes proteins to unfold?
Ph
damage
temperature
organic solvents
Why do proteins aggregate when they denature?
The hydrophobic regions are exposed and can allow them to clump together in big groups
Name a few disease where aggregation of denatured proteins occurs:
Parkinson’s
Alzheimer’s
cataracts
type II diabetes
What happens in prion disease
Creation of beta sheets (alpha helixes are more normal) leads to self association and formation of amyloid fibers. Unclear as to whether it is the fibers themselves or vacuoles they produce that causes disease.
What is a mechanism of aggregation prevention?
Chaperones can prevent the aggregation of misfolded or toxic proteins by breaking up the large aggregate inclusions
Explain the method that chaperones use to break up toxic protein inclusions
chaperones often ubiquitinilate the toxic proteins. This tags them for digestion from the proteosomes
Link between cancer and chaperones?
Cancer tends have a lot of aggregation and lots of chaperones working to reverse this problem. By turning off the chaperones, these problems will not be corrected and the cancerous cells will die rather than continue to proliferate.
What causes the sigmoid curve of oxygen saturation in hemoglobin?
Cooperativity of the subunits. After one O2 attaches, it is much easier for the other ones to join as well. Changes from T state to R state
What is 2,3 bisphosphoglycerate?
It is an allosteric factor that binds and causes deoxygenated hemoglobin to have a lower affinity for oxygen. Basically promotes the T-state. Usually occurs in HIGH altitudes. ENHANCES ability to deliver oxygen to the best location.
What it the T-state
tense state in hemoglobin. It has a lower affinity for oxygen. This allows it to stay deoxygenated as it cycles through the body until hitting the high concentration of oxygen in the lungs. As soon as one oxygen binds it can quickly bind the rest.
What is the R state?
relaxed state in hemoglobin - after oxygen binds to the hemoglobin, the rest of them can easily jump on.
What mutation leads to sickle cell anemia?
A single point mutation in which glutamate is exchanged for a valine. This causes aggregation of beta chains.
Symptoms and treatment for sickle cell anemia?
Sym: swollen hands and feet, organ damage, necrosis, fever and intense pain, problems with lung function
Treatment: Hydroxyurea - basically activates fetal hemoglobin, which has a higher affinity for oxygen
When does fetal hemoglobin stop being produced and adult start?
4 months
Subunits for adult and fetal hemoglobin?
HbA = 2 aplha and 2 beta HbF = 2 alpha and 2 gamma
What does a nucleotide consist of? A Nucleoside?
Nucelotide = nitrogenous base, 5 carbon sugar, phopshate Nucleoside = nitrogenous base, and sugar
What is the base sugar in DNA? RNA?
DNA = 2'deoxyribose RNA = ribose
Purines in DNA/RNA?
Adenosine and Guanine
Pyrimidines in DNA?
Thymine and cytosine
Pyrimidines in RNA?
Cytosine and Uracil
DNA and RNA sequences are linked by what bonds at what position?
Phosphodiester bonds between the 3’ sugar of one nucleotide and the 5’ sugar of the nest
are DNA strands antiparallel or parallel?
antiparallel
rRNA’s main job?
complexed with proteins to form ribosomes, which are involved in translation of mRNA to peptides
What are the two types of Chromatin? Features?
Euchromatin - diffuse and easy to transcribe
Heterochromatin - compacted and difficult to access and trasncribe
What is the charge of DNA
It is overall negatively charged because the sugar phosphate backbone of DNA is very negatively charged around the outside
Does DNA have grooves?
Yes alternating minor and major grooves. Major is much more commonly able to interact with other proteins because it is larger
What are the major conformations of DNA and their features
B -Common - right handed
A - Compact - DNA hybrids - also right handed
Z - Strange - left-handed - formed transiently
of human genes
20,000
what % of human genome is exons
1%
what % of the human genome is intron/exons?
20%
HIstones contain large amount of which elements?
arginine and lysine
histones come together in groups of:
octomers
What is a nucelosome?
An octomer and histomes along with the string of DNA that is wrapped around it
What is a solenoid?
Groups of nucelosomes wound into helical, tubular coils in order to further compact the DNA very tightly
What is a HAT?
Histone acetyltrasnferase - They add acetyl groups to histone tails (arginine/lysine)
How does acetylation of histones affect transcription of DNA
- Increases it
- histone acetylation plays a most crucial role in destabilizing chromatin structure in part because the presence of the acetyl group removes the overall positive charge from the lysine, making it more difficult to neutralize the negative charge of DNA as it is compacted
What is HDAC?
Histone Deacetyltrasnferase
-acetyl groups removed by this enzyme
What is a SIR protein
implicated in longevity
How are HATs and HDACs important in cancer therapeutics?
HDACs are often upregulated in cancer cells, leading to silencing of expression of tumor suppressor genes (such as p53)
HDAC inhibitors are used as anticancer drugs
mRNA structure
5’ cap - leader - start codon - coding region - stop codon - trailer with polyA tail
Main job of tRNA
carry amino acids to ribosomes and ensure they are incorporated into the correct positions of the polypeptide chain
accuracy occurs because pairing of 3 bases in the tRNA anticodon with the corresponding 3 bases in the codon of the mRNA
structure of tRNA
is in a cloverleaf shape
Major enzyme involved in DNA replication?
DNA polymerase
Which direction is DNA replicated?
DNA polymerase moves on the parental strand in the 3’- 5’ direction producing a new strand in the 5’ to 3’ direction
What does DNA polymerase require to begin sythesis
a free 3’ hydroxyl group of a nucleotide primer - which is synthesized by primase
What synthesized the leftover ends of the chromosome
telomerase synthesizes these ends
What does semi-conservative replication mean?
It means when its’ replicated the two parental strands are still there but they are no longer together. Thats why its not completely conservative.
What supplies the energy for continued replication from 5’ to 3’ ?
The energy required to move forward in the 5’ to 3’ direction is provided by the breaking of phosphate bonds
Method for prokaryotic replication?
-SIngle beginning point of replication - OriC
- Can begin another round before the first one ends
Goes bidirectionally
helicase - unwinds the DNA
ssBP - stabilizes the strands and keeps them from reassociating or being cleaved
topoisomerase - relieves the coiling tension causes by opening up the double-stranded DNA
Why can’t stuff replicate 3’ to 5’ ?
This NEVER happens in any organism because it is energetically unfavorable
What happens to the leading and lagging strands at the replication fork?
Leading strand - continuous replication toward the fork 5’ to 3’
Lagging strand- noncontinuous replication toward the fork. must make mulltiple 5’ to 3’ pieces away from the fork and then sort of patch these okasaki fragments together
How prevalent is sickle cell anemia?
- Most common inherited blood disorder in the U.S.
- affects 70-80,000 americans
- especially affects African and Hispanic Americans
- More common where Malaria is BIG (tropical/subtropical)
Tests used to diagnose?
Universal newborn screening hematocrit blood smear HGB electrophoresis GEnetic testing
How does electrophoresis detect SCD?
The sickle blood cells have irregular folding and cuase the charge to be different. Therfore speed through the gel differs from the normal.
What is a gyrase for?
Prokaryotic DNA replication. The gyrase’s function is to relieve the tension put on the DNA by unwinding the strands.
What do topoisomerase 1 and 2 do?
Topoisomerase 1: Enzyme nicks a single strand of the double stranded DNA allowing the strands to rotate. Afterwards fixes it.
Topoisomerase 2: Does a magic trick where it takes two double stranded pieces of DNA and passes one through the other by putting a double-stranded break into one of the strands. This is very important to relieve strain.
Hayflick limit
limit to number of times a normal cell will divide because of telomeres
Give an example of an endogenous and exogenous process that utilizes reverse transcirption
Endogenous - Telomerase
Exogenous - Retroviral integration
Phases of the cell cycle?
G1 - Normal growth
S - Synthesis - DNA is replicated
G2 - Cells prepare to divide
M - Mitosis - BAM
What does Telomerase do?
Attaches to DNA overhangs left over from replication and acts as a template for more nucleotides as well as a reverse transcriptase. It adds to the 3’ end and allows DNA polymerase to have enough space to add nucleotides on the 5’ end
Why is Telomerase a target for anti-cancer drugs
cancer cells many times up regulate telomerase in order to be immortal
What does Thalassemia
result from an altered ratio of alpha:beta globulin. In its severe forms can have similar patholgy to Sickle cell anemia when the inidvidual has one sickle cell allele as well.
What is HbC
Almost the same as sickle cell, only it is the type that swaps out a glutamte for a lysine (not valine like HbS)
What is the relationship between the DNA coding strand, the DNA template strand and mRNA?
basically the coding strand is going to match up with the corresponding opposite nucleotides on the template strand. Just keep in mind that the coding strand is going to be 5’ to 3’ rather than 3
to 5’. If these are switched you have to count backwards. The mRNA is the EXACT SAME as the coding strand, except that the T’s are changed to U’s.
A single mRNA can make how many proteins in Prok vs Euk ?
Prok = many proteins Euk = just one protein
transcription vs replication - source of energy?
hydrolysis of high-energy bonds provides the required energy for both!
RNA polymerase for prokaryotes?
One RNA polymerase, sigma bindis to core enzyme and directs bidning to promoters
RNA polymerase for Eukaryotes?
Pol 1 - produces rRNA
Pol 2 - produces mRNA, miRNA, and lincRNA
Pol 3 - produces tRNA and small rRNA
Do Euk and Prok have introns?
nope, just Euk. Only Euk have splicing
Temporal evens of mRNA
add 5’ cap, poly-A tail added, splicing occurs
Euk/Prok initiation of transcription:
Euk - requires over 100 cofactors
Prok - Polymerase gets going without anything but sigma and some other small stuff
Role of alternative splicing?
Ability to produce a lot of variance with the same amount of genes. Basically you just splice the mRNA’s differently and you’ve got different proteins! BAM!
What are the important nucelttode sequences for splicing?
GU at start and AG at end of splice
Basic mechanism for splicing
forms a lariat out of the intron and it gets dumped off as the two ends connect
lincRNA
long non-coding RNA - used to regulate silencing of genes and stuff - new thing
HIV uses what proteins
Nef, rev, and Taf are used to get around cell’s requirements for RNA leaving the nucleus with cap and tail and stuff
How is sickle cell protective for malaria?
When parasite, plasmodium falciparum invades blood cells, altered shape of sickle cells are preferentially removed by phagocytic cells in the spleen. this limits infection
What is a transcranial doppler used for?
To screen for stroke. Especially effective in young, good for sickle cell. Looks for high velcities of blood indicating blockages.
Effects of splenic damage for patient?
Immunocompromised because cannot remove antibody-coated bacteria. Increased susceptibilty to streptococcus pnemonia. Need antibiotics.
What is the effect of the BCL11A gene mutation
BCL11A was found to inhibit gamma expression after birth. Possible target for genetic therapy in SCD.
what is deltaG^o ?
Free energy change when starting with equimolar substrates and products
what is deltaG^o’ ?
Free energy change when starting with equimolar substrates and products at 25 C and pH 7
How do enzymes decrease the activation energy and increase the reaction rate of reactions?
Provide proximity and orientation of reactants
Ensure specificity of substrates and prodcuts
Stabilize the transition complex
How do enzymes affect deltaG?
They don’t, just reaction rates.
Km = ?
substrate concentration at 1/2 Vmax.
Vmax =
the maximum rate achieved by the system, at maximum (saturating) substrate concentrations.
Different forms of pyruvate kinase?
4 different isoforms
( 2 from the same gene PK-m1, PK-m2 - cancers )
PK-L - Liver
PK-R - Red blood cells
Wy does PK-M2 isoform of pyruvate kinase cause cancer?
PK-M2 in human cancers has reduced activity and ‘chokes off’ glycolysis. This allows glycolytic intermediates to be diverted to biosynthetic pathways that provide building blocks for cell proliferation.
What is a competetive enzyme inhibitor?
Molecules that bind at the substrate binding site(s) and prevent substrate binding. Substrate analogs and some transition state analogs are competitive inhibitors. Competitive inhibitors increase Km, but do not change Vmax.
What is a noncompetetive enzyme inhibitor?
Molecules which bind an enzyme and inhibit its activity without inhibiting substrate binding. Suicide inhibitors and some transition state analogs are in this class. Noncomptetive inhibitors decrease Vmax, but do not change Km. ( they are irreversible and never unbind) permanently disable enzyme function
What is an allosteric enzyme inhibitor?
Molecules which bind an enzyme distant from the substrate binding site and cause a conformational change which alters the substrate binding site and prevents substrate binding. Allosteric inhibitors function primarily on oligomeric enzymes, and can not be described by Michaelis-Menten kinetics.
How do competitive inhibitors affect Km and Vmax?
Increase Km
Don’t change Vmax
How do non-competitive inhibitors affect Vmax and Km?
Decrease Vmax
Don’t change Km
Do allosteric inhibitors change Km or Vmax?
Yes, possibly both.
What do you call an enzyme that requires a cofactor before and after it get the cofactor?
before - apoenzyme
after - holoenzyme
What do you call a cofactor that becomes permanently attached to an enzyme?
prosthetic group
Why is NAD a better indicator of the cell metabolism status of a cell than FAD?
NAD is soluble inthe cell and can therfore act to regulate other proteins or metabolism itself. FAD becomes a permanent prosthetic of the enzyme so it doesn’t work for any sort of ratio indicator.
3 Function of redox reactions:
1) Fuel oxidation (ex. FADH2)
2) Detoxification (ex. NADPH)
3) Biosynthesis (ex. NADPH)
DeltaE0’ is?
the change in redox potential under standard conditions.
Purpose of a detoxification reaction?
Make toxins more soluble to pee out by adding oxygen!
Dietary precursor of NADH and NADPH?
Niacin (found in meat, whole grain, cereals)
What happens if you don’t get enough niacin?
Niacin deficiency causes Pellagra
Patients get diarrhea, dermatitis, demetia, and glossitis (a bright red, smooth tongue)
Dietary precursor to FNM and FAD is?
Riboflavin (Vitamin B2) Found in milk, eggs, organ meats, legumes, and mushrooms
What happens if you don’t eat enough milk, eggs, legumes, organ meats, and mushrooms?
You will get riboflavin deficiency!
Symptoms: glossitis, cheilosis (scabs at corners of mouths), keratitis, seborrheic dermatitis, normochromic anemia (Lack of blood cells, that are functionally normal)
How do you test for riboflavin deficiency?
Measuring the activity of an FAD dependent enzyme present in blood: The erythrocyte glutathione reductase assay. Add more FAD and see if that creates more activity!
Which cofactor is important for collagen synthesis, neurotrans syntesis, and oxygen sensing?
Ascorbic Acid ( Vitamin C )
What happens if you don’t eat your citrus and vegetables?
You will get ascorbic acid deficiency!
Symtpoms: scurvy - slow wound healing, irritabilty, anemia, gingival lesions, enlargment of costochondral junctions, petechiae (small circle rashes)
How does ascorbic acid affect a cell’s oxygen-sensing function
Generally enhances the activity of HPH, which causes HIF to be ubiquitinilated and degraded under normal oxygen conditions. Under low oxygen conditions HPH is inhibited by fumarate and HIF is allowed to be transcibed. This causes increased growth, angiogenesis, and glucose transport to the area.
What is pyruvate dehydrogenase?
Pyruvate dehydrogenase is a gatekeeper that regulates glycolytic substrates complete oxidation in the mitochondria.
Start codon for translation?
AUG
Codons read?
5’ to 3’ (5’ on left)
2 critical regions on tRNA?
1 - The anticodon (3 bases that pair with the mRNA’s codon) reads opposite of codon
2 - single stranded region at 3’ end that binds to amino acid corresponding to codon
what is wobble base-pairing?
The genetic code is redundant. Several differnt codons can specify a particular amino acid. More than one tRNA for each amino acid. The wobble position is the 3’ end of the codon. The first two spots have more stringent bases, but this spot can often have multiple bases attach to it.
Where does the energy for bonds in the polypeptide come from?
BReaking the high-energy bond between the tRNA and the amino acid being added to the chain. Each amino acid carries with it the activation energy for the addition of the next amino acid in the chain.
What are the robosomal subunits? What do they do?
Small subunit will find the translation initiation site. (AUG)
Large subunit catalyzes the formation of the peptide bonds - does work!
What is a ribozyme?
Part RNA, part protein. Catalytic. Probably first catalysts of living cells.
What are the three sites in the ribosome?
A site: Where the incoming tRNA is coming in
P site: the action site!
E site: the exiting tRNA
Usually only two sites occupied at once.
Start codon for bacterial translation?
Shine Delgarmo sequence. Can be in the center of an mRNA, thus mRNAs often can code for multiple proteins
3 steps in peptide elongation
1 - tRNA carrying amino acid binds to A site
2 - tRNA at the P site is released from the peptide chain by breaking the high energy bond and reattching it to the next amino acid at the A-site
3 - mRNA moves through the ribosome and prepares to receive next tRNA
Stop codons?
UAA, UAG, UGA
polyribosome
multiple ribosomes on the same mRNA molecule getting some translation done in eukaryotes!
What does tetracycline do?
blocks binding of aminoacyl-tRNA to A-site of ribosome.
Streptomycin
Prevents transition from translation initiation to chain elongation and causes miscoding. Affects ONLY bacteria.
Chloramphenicol
Blocks the peptidyl transferase reaction on ribosomes. Affects ONLY bacteria
Erythromycin
binds in the exit channel of the ribosomes and thereby inhibits elongation of the peptide chain. Affects ONLY bacteria.
Rifamycin
blocks initiation of RNA chain by binding to RNA polymerase. Affects ONLY bacteria
Puromycin
Causes premature release of nascent polypeptide chains by its addition to the growing chain end. Affects bacteria and eukaryotes.
Actinomycin D
binds to DNA and blocks the movement of RNA polymerase. Affects bacteria and eukaryotes.
Cycloheximide
Blocks translocation reaction on ribosomes. Affects ONLY eukaryotes.
Anisomcin
Blocks the peptidyl transferase reaction on ribosomes. Affects ONLY eukaryotes.
a-Amanitin
blocks mRNA synthesis by binding preferentially to RNA polymerase II. Affects ONLY eukaryotes.
What makes us more advanced than other animals if we don’t have that many more genes?
More complex regulation of our genome!
-spliceosome, etc..
6 steps at whcih eukaryotic gene expression could be regulated?
1 - DNA structure 2 - When, where, and how often a gene is transcribed 3 - How transcript is spliced 4 - Which mRNAs are translated 5 - Rate of mRNA degradation 6 - Regulation of protein
Referring to gene regulation, what is cis and what is trans?
Cis - is the regulatory DNA itself. Promoters, regulatory regions further away etc.
Trans - the proteins that bind to these regulatory regions on the DNA
Homeodomains proteins are?
Type of gene regulatory protein. (a protein that attaches to a complementary strand of DNA with numerous weak interaction bonds) Key regulator of animal development
What is the advantage of a heterodimer over a homodimer?
BY forming a hybrid between proteins that generally bind to specific sequence, you can increase the variety of DNA sequences recognized by regulatory proteins
How do gene switches work?
Just a protein binding to a piece of DNA to repress it under certain conditions
What happens to the lac operon when glucose and lactose are present?
OPERON OFF. The Cap is unbound because glucose has decreased cAMP production. Repressor is unbound because allolactose from the lactose has removed the repressor.
What happens to the lac operon when glucose is present, but lactose is NOT present?
OPERON OFF. Cap is unbound due to decreased cAMP. Repressor is bound due to lack of lactose.
What happens to the lac operon when both glucose and lactose are NOT present?
OPERON OFF. Cap us bound, BUT repressor is also bound because of lack of allolactose.
What happens to the lac operon when lactose is present, but glucose is NOT present?
OPERON ON. Cap is bound and repressor is unbound!!!!! Hooray!
DNA regulatory sites, distant from the promoter region?
enhancers
Gene regulatory proteins often have 2 functional domains… what are they?
structural motif - recognizes DNA sequences
activation domain - accelerates transcription
Name a few ways gene repressor proteins might operate:
1 - Competitive DNA binding
2 - bind to activator surface
3 - Acting on transcription factors
4 - recruiting chromatin remodeling complexes
5 - Recruting histone deacetylases or histone methy transferases
What do insulators do to affect regulatory proteins?
They are DNA sequences that prevent regulatory proteins from influencing distant genes
How is X-chromosome-inactivation determined in female mammals
randomly picks one of the Xs to condense. Stays constant in the body.
Describe how imprinting works…
Imprint created on certain genes, they are silenced and are either maternally or paternally inherited and DO NOT change. Therefor if you get a paternally inherited imprinted gene from your dad, you only pass it on if you are a male. Females can only pass on maternal. Also males will pass on both of the alleles as imprinted, not just the original they got from dad, so their kids will get an imprinted allele no matter which chromosome they get from dad.
How can extracellular signals affect DNA transcription?
peptide hormones, growth factors, or steroid hormones can enter into the cell and bind to receptors and cause them to bind and activate a certain DNA to elicit a response (Run from bear, faster)
Explain how iron levels are regulated in the cell! Quick!
Aconitase is the protein that regulates translation of ferritin and transferrin mRNA in two different locations. When there is no iron around, it remains bound. This blocks ferritin production (ferritin normally sequesters excess iron) and stabilizes the mRNA of transferrin, allowing it to be produced. (transferrin normally imports iron into the cell)
When Iron is abundant, it binds to aconitase and causes it to release. This increases production of ferritin and stops transferrin. Bam!
Pyruvate dehydrogenase complex RXN:
NAD + pyruvate + CoASH –> NADH + Acetyl CoA + CO2
Decarboxylation: 3 carbon pyruvate to 2 carbon acetate and CO2
Reduction: of pyruvate
Oxidation: of NAD+
Transfer: of 2 carbon acyl group to CoASH
Thiamine pyrophosphate (TPP) is involved in what kinds of reactions?
Decarboxylation reactions
Thiamine is found in what foods? What are the symptoms of deficiency?
Found in meat, legumes, whole grains, and fortified cereals
Symptoms: Beriberi(I can’t) Headache, malaise, peripheral neuropathy, and heart failure.
Wet Beriberi: cardiac probs
Dry Beriberi: neuropathy
Wernicke Encaphalopathy - Confusion, mental status changes, abnormal eye movements
Karsokoff Psychosis: Amnesia and confabulation. Often associated with Wernicke’s.
Megablastic Anemia
What is lipoate used for?
Uses its long arm and disulfide bond to transfer groups around.
What is Coenzyme A for?
covalently bind acyl groups through and transfer them to different substrates. (uses sulphur, thioester, bond)
Coenzyme A or Vit B5, deficiency symptoms?
NOPE, CoA is everywhere!
Describe step by step action of the pyruvate dehydrogenase complex:
TPP(Thiamine pyroposphate) on E1 grabs and decarboxylates pyruvate. Next lipoate on E2 reaches over and grabs the acetyl group from TPP with a thioester bond. CoASH comes and grabs it off the lipoate and Acetyl CoA is released. Next FAD on E3 is reduced by the hydrogens on the lipoate. Finally, FADH2 reduces NAD to NADH and the cycle can start over! :)
Biotin is involved in which type of reaction?
Carboxylase! They use energy from ATP hydrolysis for building C-C bonds.
Biotin deficiency?
Rare, but symptoms are:
Scaly dermatitis, thinning hair, and alopecia
Egg white contain a protein called avidin which can bind to and make dietary biotin undigestible. So raw egg eaters can get these symptoms! Crazy!
Pyridoxyl Phosphate (PLP) is used for what kind of reactions?
Cofactor for enzymes that metabolize amino acids. USED FOR transaminases, aminotrasnferases!
Vitamin B6? Deficiencies? Tell me about it!
Dietary precursor of pyridoxal phosphate.
Found in bananas, fortified cereals, meat, and rice.
Symptoms of deficiency:
Infants: Seizure, diarrhea, anemia, EEG abnormal
Adults: Peripheral Neuropathy
Diagnosis
Symptoms
Erythrocyte transaminase activity assay, +/- exogenous PLP
Direct measurement of PLP in blood
Resolution of symptoms with pyridoxal phosphate OR pyridoxine
Pyridoxine oxidase deficiency
vs
Antiquitin Deficiency
Pyridoxine oxidase deficiency: Lack important enzyme to convert pyridoxine. Will resolve with pyridoxal, but NOT pyridoxine
Antiquitin deficiency: PLP gets seqestered
Will resolve with added pyridoxal or pyridoxine
Vit B12 deficiency?
B12 = cobalamine!
produced by bacteria and found in meat and milk
Deficiency can occur in vegans, the old, or those with GI probs
Symptoms: pernicious anemia
macrocytic/megaloblastic anemia (giant RBCs)
weakness, fatigue, seizures, sensory problems
Diagnosis:
Symptoms
Blood Smeat
Cobalamin conc. in serum
What types of Rxns does cobalamine do?
transfers and rearrangements of methyl groups. So you can take a group on the molecule and move it to a different carbon
what are GLUT trasnporters?
passive glucose transporters
What are SGLT trasnporters?
active glucose transporters, use Na gradient to push stuff across membrane.
What are differences between GLUT transporters 1,2,3,4 ? Kd? affinity? location?
1 + 3:
in most cells
high affinity for glucose
low Kd
2:
Liver/pancreas
low affinity
High Kd
4:
Insulin dependent
medium affinity
medium Kd
Which GLUT transporters does glucose use in the fasting state?
glucose leaves hepatocytes (liver) out of GLUT 2
glucose enters other needy cells through GLUT 1 and GLUT 3.
Which GLUT transporters does glucose use in the fed state?
Glucose enters all cells through GLUT 1, 2, 3, and 4
What is 18-fluorodeoxyglucose or 18F-FdG used for?
It is injected into the blood stream in order to image cancer (which works because cancers have elevated glycolysis) its a radioactive label you can image.
WHich cells use anaerobic glycolysis exclusively, and why?
Red blood cells and retina cells
They have NO mitochrondria!
The key regulatory step in glycolysis?
Fruc 6 Phosph to fruc 1,6 bis-phosph Phosphofructokinase 1 (PFK-1)
Liver’s main job? Important?
Glucose homeostasis! Important because red blood cells are completely dependent on glucose concentration to function!
Net gain from anaerobic glycolysis:
2 ATP
Net gain from aerobic glycolysis:
32 ATP (heart, liver, kidneys) 30 ATP (skeletal muscle, brain)
NADH, FADH2, and AcCoA produce how much ATP each?
NADH: 2.5 ATP
FADH2: 1.5 ATP
AcCoA: 10 ATP
What is the rate-limiting step in glycolysis?
PFK1 - regulation of activity is tied to ATP consumption
What are the inhibitory binding sites of PFK1?
ATP and citrate
What are the activating binding sites of PFK1?
AMP and fructose- 2,6-phosphate
What is the most sensitive indicator of energy state in cells and why?
AMP, because the ratio changes the most between having a lot and a little energy built up.
How are the different version of pyruvate kinase regulated? PK-M1? PK-R? Pk-L? PK-M2?
PK-M1 - regulated just by substrate and product concentration
PK-L (liver) - inhibited by PKA during fasting
PK-R (red BCs)
PK-M2(embryonic) Phosphorylated tyrosines inhibit
all regulated allosterically by fruc 1,6 phosphate
What is the result and cause of the inherited syndrome: MSH2, 3, 6, MLH1, PM52?
Result: Colon Cancer
Cause: Mismatch repair problem
What is the result and cause of the inherited syndrome: Xeroderma pigmentosum?
Result: UV sensitivity, skin cancer, neuro probs
Cause: Nucleotide excision repair problem
What is the result and cause of the inherited syndrome: XP variant?
Result: UV sensitivity, skin cancer
Cause: translesion synthesis by DNA polymerase
What is the result and cause of the inherited syndrome: Ataxia telangiectasia (AT)?
Result: leukemia, lymphoma, genome instabilty, gamma ray sensitivity
Cause: Problem with ATM protein (important for fixing double-stranded breaks)
What is the result and cause of the inherited syndrome: BRCA2 ?
Result: Breast, ovarian, and prostate cancer
Cause: problems with repair by homologous recombination
What is the result and cause of the inherited syndrome: Werner Syndrome?
Result: premature aging, cancer problems
Cause: problems with DNA helicase and an accessory exonuclease
benzo[a]pyrene is from what? and causes what problems?
From cigarette smoke.
Creates G to A mutation problems. Seen in many cancers, especially lung cancers (scrotum cancers of chimney sweeps)
What genetic mutation results from UV rays?
thymine dimers. Adjacent thymines can form covalent bond together. Common cause of melanoma.
Explain how MutS and MutL work in eukaryotes and prokaryotes
MutS find the mismatched base pair. MutL scane the nearby DNA for a nick to determine which strand is the newer one.
In prokaryotes, MutH is the one that creates nicks in the unmethylated DNA (umethylated is new)
Describe:
base excision repair
nucleotide excision repair
base excision repair: fix a single base
nucleotide excision repair: longer stretch of bases is switched out
Xeroderma pigmentosum (XP) What is it? WHy is ti common in India?
AUtosomal recessive disease, common in India de to arranged marriages among close family.
Sensitive to UV rays, lots of skin cancer etc.
Nonhomologous vs homologous end-joining? what is it?
Two ways of repairing double-stranded breaks in DNA.
Nonhomologous - basically you just chop off the ends around the break and then stick the chromosomes together. Imprecise, causes mutation problems.
Homologous - Cut out the middle material, line it up with the sister chromatids and use the adjacent chromatid’s DNA as a template to repair lost genetic material. More difficult, but more precise.
What proteins play a key role in chromosome recombination in prok/euk?
Rad51 -euk
RecA - prok
ATM, Brca1, Brca2
What is p53’s function?
It is a g1 checkpoint. If it detects DNA damage it will arrest cells in either g1 or g2
50% of all cancers have a p53 mutation
How does the mitotic spindle checkpoint work?
It will arrest the cell in mitosis by using a complex to stop APC. APC will normally ubiqutinilate securin, which activates separase and causes it to clear the cohesin between sister chromatids.
