Points To Remember Exam 1 Flashcards
What happens to Heat transfer when Change in entropy goes up
It goes up
What happens to Change in Entropy when Temperature goes up
It goes down because it is harder to release heat to heat
What Bonds are the most strong
Covalent
What Does A Low Pka tell us about the acidity
it is very acidic
What Amino Acids Absorb Wavelength and at What Wavelength
Tyrosine and Tryptophan absorb at 280
What does adding an acidic or basic Amino acid do to PI
Adding an Acidic Amino acid like Asp - will decrease the pI (net neutral is at a lower pH)
Adding a Basic Amino acid will increase the pI
Benzocaine Effects
ADA says that it can lead to Methemoglobin in Teething Toddler meaning it will go from ferrous to ferric and bind water instead of Oxygen
Where is myoglobin found
Red Muscle
Why does the Myoglobin not have a bohr effect or bind things allosterically
it only has two histidines and none of the Asp His interaction. it is not allosterically affect it is a hyperbollic curve
What is the prosthetic group of the hemoglobin
ferroprotoporphryin
Does Hemoglobin Act Sequentially or Concertadly
Sequentially
What Stabalizes the Hemoglobin T state
Salt Bridges
BPGs relation to Fetal Hemoglobin
Normally BPG stabalizes T state moving hemoglobin right (it is highly negative and binds to the positive hemoglobin)
Infants have serines not histidine so the BPG does not bind
Mechanism of the Bohr Effect (2 ways)
Decrease in pH protonates His146 and this will interact with the Asp 94 and thus pull F8 and the iron out of the plane thus releasing oxygen
the other way is that CO2 binds the amino end of hemoglobing making carbamino hemoglobin and stabalizing salt bridges
What Wavelengths show Oxyhemoglobin and Deoxyhemoglobin
940nm - Oxyhemoglobin
660nm- Deoxyhemoglobin
Magnetism and Oxygenated vs Deoxygenated
deoxygenated is magnetic (paramagnetic)
oxygenated is nonmagnetic (diamagnatic)
Glucose affect on hemoglobin
diabetes causes HbA1C which is glycosylated hemoglobin.
The Schiff Base happens on to hemoglobin which is reversible
but the amidori reaction is irreversible
Mutation in Sickle Cell
GTG -> GAG so Glu becomes Val
The affect Sickle cell has on pI
Sickle Cell has more net positive below pI and less negative above the pI than normal
Alpha and Beta Thalassemia
Alpha is missing Alpha only has Beta subunits of hemoglobin so it binds oxygen with no cooperative
Beta is missing Beta and only Alpha
loses oxygen binding and cooperativity
Cofactors Vs Coenzymes
Cofactors are small and inorganic and coenzymes are large organic
What Cofactors does Kinase Need
Mg to stabilize and Calcium concentration depended
Trypsin
Cleaves Basic Amino acids arginine and lysine
Chymotrypsin
Cleaves large hydrophobic aoromatic at the carboxyl side.
Like Phe Met Trp Tyr
Thrombin
cleaves at Arg-gly bonds
Elastase
cleaves small uncharged side chains. Like Valine
it is a serine protease in pancrease to remove elastin and is released in pancreas
is seen a degrader of elastin in the mouth
Is water in the active site
no
What are the Michaelis Menton Assumptions (3)
Formation and breakdown are at a steady state
Product formation is irreversible (k4 =0)
K2 is way less than K3
Km formula
Km = K2 +K3/K1
V formation Equation
K1[s][E]
VBreakdown Equation
(K2+K3)[ES]
What is the Michaelis Menton Equation
V= Vmax[S]/(Km+[S])
What is Kcat
K3
Reading the lineweaver Burke Plot
X Axis = 1/S
Y Axis 1/V
X Intercept = -1/km
Y Intercept = 1/Vmax
Malonate Succinate Inhibition Example
Malonate looks like succinate so it is competitive inhibition
DIPF/DFP
Di-isopropyl Fluorophophate - an inactivator of serine proteases by covalent interaction, and it is not reversible
Where do Allosterically affected enyzmes act in cell pathways
they usually act on the rate limiting or committed steps
Concerted Allosteric Model
When one substrate binds to the enzyme the whole thing will open up in to the R state
Sequential Allosteric model
Induces the next site only so it goes TT -> TR-> RR each substrate bound
What does ATCase Do
What Are the substrates
What is its activator and inhibitor (where do they bind)
What is the enzymes structure
It synthesizes pyrimidines like CTP and UTP
It uses Aspartate and carbamoyl phosphate
Increase in ATP will bind to regulatory site activating it
CTP will bind to the same regulatory site to inhibit it
The Catalytic site is six subunites two trimers
The Regulatory Site is 6 subunits 3 dimers
Where does Phosphorylation occur (amino acids)
Serine Threonine and Tyrosine
Cyclic AMP and Its method of activating a protein kinase
Cyclic AMP removes repressor to activate the protein kinase
Zn as a Cofactor
Polarizes Carbonyl groups causing them to be more susceptible to nucleophilic attacks
Mg action as a cofactor
Polarizes the P=O bond so it will be more stabalized when a kinase phosphorylates
Pantothenic Acid
Precurser to CoA
Reaction Type Acyl Transfer
Riboflavin
The precurse to Flavin Coenzyme (FAD)
Used in Oxidation Reduction Reactions
Niacin
Is the precurser to Nicotinamide Adenine Coenzymes (NAD)
Used in Oxidation Reduction Reactions
Pyridoxin
precurser to Pyridoxal phophate
Used in Transaminations
Coenzyme A how does it react
It uses its high energy thioester bond and transfers two c acyl group
Periostat
Inhibits Colleganase
Collegenase (how its released what it does what is its cofactor) what is another name for it
It is released by WBC and also by bacteria
aka MMP8
uses zn as a cofactor
synthesized as zymogen and works under low pH(bacteria cause)
It degrades bone
Alpha Amylase
breaks down carbohydrates
uses catalytic triad
and chloride and calcium as cofactors
Lysozyme
Breaks down bacteria cell wells
Lingual Lipase
Breaks down lipids and has a catylitic triad
Chymotrypsinogen
the zymogen of chymotrypsin that is activated in the intestine
NucleoSide vs Nucleotide
Any sugar and its base. The Nucleotide contains the phosphate group
what is the bond between sugar and base called
B glycosidic link
what is the bond of sugar to phosphate called
phosphodiester
Hydrogen bonds between AT and CG
A=T and CG has three
The major and Minor Grooves
Can be seen as the minor groove being on the side of the two glyosidic bonds and the major groove being on the other side of the bases
The three types of DNA
B DNA - is the common normal one
A DNA - is both DNA and RNA it is wider
Z DNA - is very narrow and turns opposite direction and is not stable
Histones Assembly
Histones are Basic to attach to negative phospho parts of DNA
H2B H2A H3 and H4 four a tetramer and then two of these peices get together to form an octomer. Around 140BP
Then the linker DNA is pressed in by a H1 histone type adding like 20 - 100BP
H1 histone property
It is positive at both ends to bind the DNA
It is what pushes the linker DNA tightly on the histone
What stain is used for a karyotype
Giemsa
What Factors promote denaturing and what oppose it
Promote - Negative phosphates oppose. Entropy wants disorder
Oppose - Hydrogen bonding
and van der waals of bases in the center
hypochroism
DNA absorbs at 260 nm. And the denatured absorbs more and the natured absorbs less
DNA polym III
main DNA polymerase that goes fast and has its own nucleotide proofread mechanism
DNA polym I
Goes Slow for repair, and also replaces the primer strand that was removed
RNA hybridase
removes the primer of okazaki fragments and the one for the leader strand
DNA ligase
puts together the new polym I piece of DNA that filled in the primer locations on to the rest of the regular DNA
Uses ATP in Eukaryotes and NADPH in bactera
Telomerase
Uses a template on itself to add RNA to the end of the DNA strand that gets coded on the other side by polymerase in order so it does not shorten
Single Strand Binding Proteins
Bind single stranded DNA so it does not reanneal
Go - Senescet Cells
Senescent cells are out of the cell cycle and cannot be induced to go back in to the cycle
but some G0 cells can be reversed and go back to the cell cycle
senescent aka post mitotic
Retinoblastoma
When phosphorylated will increase E2F thus inducing S phase proteins and transition to S phase
When dephosphorylated it will sequester E2F and not allow its action
G1 and G1/S Cdks
They will phosphorylate Rb thus increasing E2F and going to S phase
What happens to cyclin after cell cycle
ubiquitin ligase will ubiquinate it and it will get degraded
p27
will block G1/S CDK thus stopping cell cycle due to less E2F
This is removed by myc
p53 Path
Break dna which releases protein kinase. This will phosphorylate p53 which will no longer bind mdm2 and thus will go and transcribe p21 which will inhibit G1/S Cdks so it cant activate Rb so it wont go to S phase
myc Pathway and affects
mitogen reaches receptor gets to myc
myc wil
degrade p27 thus allowing G1/S to phosphorylate Rb
will increase G1 CDK
Will directly increase E2F allowing s phase entry
myostatin
inhibits proliferation of myoblasts
Tautomerization
Amino - Imino
Keto - Enol
A-T Adenine Tautomerizes to bind with A-C so the next generation is G-C
Transition and Transversions
Transition is purine to purine or pyrimidine to pyrimidine
A-T to G-C
transversions is A-T to T-A
Deamination
Deamination examples
C - U so then it binds A in next generation
A goes to Hyooxanthine which binds C
G goes to Xanthine
Depurination
Lose a base, but the backbone keeps it together this will halt replication
Oxidation
will icnrease with age, deaminatin is an example but also addinga methyl group (usually bad) but you can demethlylate
UV radiation
Can covalently link adjacent pyrimdines creating like a thymine dimer
Ionization Radiation
Direct - can break the backbone
Indirect - will go through creating free radicals for damage
5 Bromo Uracil
Is a thymine analog so if it replaces it is more likely to be a tautomerize so then it will bind to G and not A
thus results in a switch to G-C
Acridine
Intercalate that gets in to DNa to cause a framshift, EtBr is an example
Aflatoxin
Mold like thing that gets converted to a mutagen in the body
3 Repair Mechanisms
Mismatch Repair - exonucleas repair done by DNa polym itself
Nucleotide excision repair - catalyzed by exinulease removes several upstream and downstream problem nucleotides and is used for things like pyrimidine dimers or framshift. uses old more methylated strand for template
Base Excision - replaced one base that is a problem
The gap is filled by Dna polymerase and ligase
DNA glycosylase
removes base in base excision repair
AP endonuclease
Breaks phosphodiester bond at the five prime site in base excition repair
AP lyase
Cuts the 3 prime site in order to remove the other side of the nucleotide for nucleotide excision repair
Uracil Repair
Deaminated C that has become U is removed and made back by this uracil repair
Uracil DNA glycosylase (is the type of glycosylase that does this)
Ames Test
Test for potential carcinogen by placing mutagen with a colonie on a selctive plate
compare how many colonies live without required nutrients with and without the mutagen to see if it is a mutagen
Xeroderma Pigmentosa
a disease of the skin caused by mutation ins the nucleotide excision repair pathway
