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Biochemistry > Points To Remember Exam 1 > Flashcards

Points To Remember Exam 1 Flashcards

1
Q

What happens to Heat transfer when Change in entropy goes up

A

It goes up

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2
Q

What happens to Change in Entropy when Temperature goes up

A

It goes down because it is harder to release heat to heat

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3
Q

What Bonds are the most strong

A

Covalent

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4
Q

What Does A Low Pka tell us about the acidity

A

it is very acidic

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5
Q

What Amino Acids Absorb Wavelength and at What Wavelength

A

Tyrosine and Tryptophan absorb at 280

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6
Q

What does adding an acidic or basic Amino acid do to PI

A

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

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7
Q

Benzocaine Effects

A

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

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8
Q

Where is myoglobin found

A

Red Muscle

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9
Q

Why does the Myoglobin not have a bohr effect or bind things allosterically

A

it only has two histidines and none of the Asp His interaction. it is not allosterically affect it is a hyperbollic curve

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10
Q

What is the prosthetic group of the hemoglobin

A

ferroprotoporphryin

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11
Q

Does Hemoglobin Act Sequentially or Concertadly

A

Sequentially

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12
Q

What Stabalizes the Hemoglobin T state

A

Salt Bridges

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13
Q

BPGs relation to Fetal Hemoglobin

A

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

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14
Q

Mechanism of the Bohr Effect (2 ways)

A

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

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15
Q

What Wavelengths show Oxyhemoglobin and Deoxyhemoglobin

A

940nm - Oxyhemoglobin

660nm- Deoxyhemoglobin

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16
Q

Magnetism and Oxygenated vs Deoxygenated

A

deoxygenated is magnetic (paramagnetic)

oxygenated is nonmagnetic (diamagnatic)

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17
Q

Glucose affect on hemoglobin

A

diabetes causes HbA1C which is glycosylated hemoglobin.
The Schiff Base happens on to hemoglobin which is reversible
but the amidori reaction is irreversible

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18
Q

Mutation in Sickle Cell

A

GTG -> GAG so Glu becomes Val

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19
Q

The affect Sickle cell has on pI

A

Sickle Cell has more net positive below pI and less negative above the pI than normal

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20
Q

Alpha and Beta Thalassemia

A

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

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21
Q

Cofactors Vs Coenzymes

A

Cofactors are small and inorganic and coenzymes are large organic

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22
Q

What Cofactors does Kinase Need

A

Mg to stabilize and Calcium concentration depended

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23
Q

Trypsin

A

Cleaves Basic Amino acids arginine and lysine

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24
Q

Chymotrypsin

A

Cleaves large hydrophobic aoromatic at the carboxyl side.

Like Phe Met Trp Tyr

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25
Thrombin
cleaves at Arg-gly bonds
26
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
27
Is water in the active site
no
28
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
29
Km formula
Km = K2 +K3/K1
30
V formation Equation
K1[s][E]
31
VBreakdown Equation
(K2+K3)[ES]
32
What is the Michaelis Menton Equation
V= Vmax[S]/(Km+[S])
33
What is Kcat
K3
34
Reading the lineweaver Burke Plot
X Axis = 1/S Y Axis 1/V X Intercept = -1/km Y Intercept = 1/Vmax
35
Malonate Succinate Inhibition Example
Malonate looks like succinate so it is competitive inhibition
36
DIPF/DFP
Di-isopropyl Fluorophophate - an inactivator of serine proteases by covalent interaction, and it is not reversible
37
Where do Allosterically affected enyzmes act in cell pathways
they usually act on the rate limiting or committed steps
38
Concerted Allosteric Model
When one substrate binds to the enzyme the whole thing will open up in to the R state
39
Sequential Allosteric model
Induces the next site only so it goes TT -> TR-> RR each substrate bound
40
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
41
Where does Phosphorylation occur (amino acids)
Serine Threonine and Tyrosine
42
Cyclic AMP and Its method of activating a protein kinase
Cyclic AMP removes repressor to activate the protein kinase
43
Zn as a Cofactor
Polarizes Carbonyl groups causing them to be more susceptible to nucleophilic attacks
44
Mg action as a cofactor
Polarizes the P=O bond so it will be more stabalized when a kinase phosphorylates
45
Pantothenic Acid
Precurser to CoA | Reaction Type Acyl Transfer
46
Riboflavin
The precurse to Flavin Coenzyme (FAD) | Used in Oxidation Reduction Reactions
47
Niacin
Is the precurser to Nicotinamide Adenine Coenzymes (NAD) | Used in Oxidation Reduction Reactions
48
Pyridoxin
precurser to Pyridoxal phophate | Used in Transaminations
49
Coenzyme A how does it react
It uses its high energy thioester bond and transfers two c acyl group
50
Periostat
Inhibits Colleganase
51
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
52
Alpha Amylase
breaks down carbohydrates uses catalytic triad and chloride and calcium as cofactors
53
Lysozyme
Breaks down bacteria cell wells
54
Lingual Lipase
Breaks down lipids and has a catylitic triad
55
Chymotrypsinogen
the zymogen of chymotrypsin that is activated in the intestine
56
NucleoSide vs Nucleotide
Any sugar and its base. The Nucleotide contains the phosphate group
57
what is the bond between sugar and base called
B glycosidic link
58
what is the bond of sugar to phosphate called
phosphodiester
59
Hydrogen bonds between AT and CG
A=T and CG has three
60
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
61
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
62
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
63
H1 histone property
It is positive at both ends to bind the DNA | It is what pushes the linker DNA tightly on the histone
64
What stain is used for a karyotype
Giemsa
65
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
66
hypochroism
DNA absorbs at 260 nm. And the denatured absorbs more and the natured absorbs less
67
DNA polym III
main DNA polymerase that goes fast and has its own nucleotide proofread mechanism
68
DNA polym I
Goes Slow for repair, and also replaces the primer strand that was removed
69
RNA hybridase
removes the primer of okazaki fragments and the one for the leader strand
70
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
71
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
72
Single Strand Binding Proteins
Bind single stranded DNA so it does not reanneal
73
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
74
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
75
G1 and G1/S Cdks
They will phosphorylate Rb thus increasing E2F and going to S phase
76
What happens to cyclin after cell cycle
ubiquitin ligase will ubiquinate it and it will get degraded
77
p27
will block G1/S CDK thus stopping cell cycle due to less E2F This is removed by myc
78
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
79
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
80
myostatin
inhibits proliferation of myoblasts
81
Tautomerization
Amino - Imino Keto - Enol A-T Adenine Tautomerizes to bind with A-C so the next generation is G-C
82
Transition and Transversions
Transition is purine to purine or pyrimidine to pyrimidine A-T to G-C transversions is A-T to T-A
83
Deamination
Deamination examples C - U so then it binds A in next generation A goes to Hyooxanthine which binds C G goes to Xanthine
84
Depurination
Lose a base, but the backbone keeps it together this will halt replication
85
Oxidation
will icnrease with age, deaminatin is an example but also addinga methyl group (usually bad) but you can demethlylate
86
UV radiation
Can covalently link adjacent pyrimdines creating like a thymine dimer
87
Ionization Radiation
Direct - can break the backbone | Indirect - will go through creating free radicals for damage
88
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
89
Acridine
Intercalate that gets in to DNa to cause a framshift, EtBr is an example
90
Aflatoxin
Mold like thing that gets converted to a mutagen in the body
91
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
92
DNA glycosylase
removes base in base excision repair
93
AP endonuclease
Breaks phosphodiester bond at the five prime site in base excition repair
94
AP lyase
Cuts the 3 prime site in order to remove the other side of the nucleotide for nucleotide excision repair
95
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)
96
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
97
Xeroderma Pigmentosa
a disease of the skin caused by mutation ins the nucleotide excision repair pathway

Biochemistry (3 decks)

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