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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
Q

Thrombin

A

cleaves at Arg-gly bonds

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26
Q

Elastase

A

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

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27
Q

Is water in the active site

A

no

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28
Q

What are the Michaelis Menton Assumptions (3)

A

Formation and breakdown are at a steady state
Product formation is irreversible (k4 =0)
K2 is way less than K3

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29
Q

Km formula

A

Km = K2 +K3/K1

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30
Q

V formation Equation

A

K1[s][E]

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31
Q

VBreakdown Equation

A

(K2+K3)[ES]

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32
Q

What is the Michaelis Menton Equation

A

V= Vmax[S]/(Km+[S])

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33
Q

What is Kcat

A

K3

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34
Q

Reading the lineweaver Burke Plot

A

X Axis = 1/S
Y Axis 1/V
X Intercept = -1/km
Y Intercept = 1/Vmax

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35
Q

Malonate Succinate Inhibition Example

A

Malonate looks like succinate so it is competitive inhibition

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36
Q

DIPF/DFP

A

Di-isopropyl Fluorophophate - an inactivator of serine proteases by covalent interaction, and it is not reversible

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37
Q

Where do Allosterically affected enyzmes act in cell pathways

A

they usually act on the rate limiting or committed steps

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38
Q

Concerted Allosteric Model

A

When one substrate binds to the enzyme the whole thing will open up in to the R state

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39
Q

Sequential Allosteric model

A

Induces the next site only so it goes TT -> TR-> RR each substrate bound

40
Q

What does ATCase Do
What Are the substrates
What is its activator and inhibitor (where do they bind)
What is the enzymes structure

A

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
Q

Where does Phosphorylation occur (amino acids)

A

Serine Threonine and Tyrosine

42
Q

Cyclic AMP and Its method of activating a protein kinase

A

Cyclic AMP removes repressor to activate the protein kinase

43
Q

Zn as a Cofactor

A

Polarizes Carbonyl groups causing them to be more susceptible to nucleophilic attacks

44
Q

Mg action as a cofactor

A

Polarizes the P=O bond so it will be more stabalized when a kinase phosphorylates

45
Q

Pantothenic Acid

A

Precurser to CoA

Reaction Type Acyl Transfer

46
Q

Riboflavin

A

The precurse to Flavin Coenzyme (FAD)

Used in Oxidation Reduction Reactions

47
Q

Niacin

A

Is the precurser to Nicotinamide Adenine Coenzymes (NAD)

Used in Oxidation Reduction Reactions

48
Q

Pyridoxin

A

precurser to Pyridoxal phophate

Used in Transaminations

49
Q

Coenzyme A how does it react

A

It uses its high energy thioester bond and transfers two c acyl group

50
Q

Periostat

A

Inhibits Colleganase

51
Q

Collegenase (how its released what it does what is its cofactor) what is another name for it

A

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
Q

Alpha Amylase

A

breaks down carbohydrates
uses catalytic triad
and chloride and calcium as cofactors

53
Q

Lysozyme

A

Breaks down bacteria cell wells

54
Q

Lingual Lipase

A

Breaks down lipids and has a catylitic triad

55
Q

Chymotrypsinogen

A

the zymogen of chymotrypsin that is activated in the intestine

56
Q

NucleoSide vs Nucleotide

A

Any sugar and its base. The Nucleotide contains the phosphate group

57
Q

what is the bond between sugar and base called

A

B glycosidic link

58
Q

what is the bond of sugar to phosphate called

A

phosphodiester

59
Q

Hydrogen bonds between AT and CG

A

A=T and CG has three

60
Q

The major and Minor Grooves

A

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
Q

The three types of DNA

A

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
Q

Histones Assembly

A

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
Q

H1 histone property

A

It is positive at both ends to bind the DNA

It is what pushes the linker DNA tightly on the histone

64
Q

What stain is used for a karyotype

A

Giemsa

65
Q

What Factors promote denaturing and what oppose it

A

Promote - Negative phosphates oppose. Entropy wants disorder
Oppose - Hydrogen bonding
and van der waals of bases in the center

66
Q

hypochroism

A

DNA absorbs at 260 nm. And the denatured absorbs more and the natured absorbs less

67
Q

DNA polym III

A

main DNA polymerase that goes fast and has its own nucleotide proofread mechanism

68
Q

DNA polym I

A

Goes Slow for repair, and also replaces the primer strand that was removed

69
Q

RNA hybridase

A

removes the primer of okazaki fragments and the one for the leader strand

70
Q

DNA ligase

A

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
Q

Telomerase

A

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
Q

Single Strand Binding Proteins

A

Bind single stranded DNA so it does not reanneal

73
Q

Go - Senescet Cells

A

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
Q

Retinoblastoma

A

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
Q

G1 and G1/S Cdks

A

They will phosphorylate Rb thus increasing E2F and going to S phase

76
Q

What happens to cyclin after cell cycle

A

ubiquitin ligase will ubiquinate it and it will get degraded

77
Q

p27

A

will block G1/S CDK thus stopping cell cycle due to less E2F
This is removed by myc

78
Q

p53 Path

A

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
Q

myc Pathway and affects

A

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
Q

myostatin

A

inhibits proliferation of myoblasts

81
Q

Tautomerization

A

Amino - Imino
Keto - Enol
A-T Adenine Tautomerizes to bind with A-C so the next generation is G-C

82
Q

Transition and Transversions

A

Transition is purine to purine or pyrimidine to pyrimidine
A-T to G-C
transversions is A-T to T-A

83
Q

Deamination

A

Deamination examples
C - U so then it binds A in next generation
A goes to Hyooxanthine which binds C
G goes to Xanthine

84
Q

Depurination

A

Lose a base, but the backbone keeps it together this will halt replication

85
Q

Oxidation

A

will icnrease with age, deaminatin is an example but also addinga methyl group (usually bad) but you can demethlylate

86
Q

UV radiation

A

Can covalently link adjacent pyrimdines creating like a thymine dimer

87
Q

Ionization Radiation

A

Direct - can break the backbone

Indirect - will go through creating free radicals for damage

88
Q

5 Bromo Uracil

A

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
Q

Acridine

A

Intercalate that gets in to DNa to cause a framshift, EtBr is an example

90
Q

Aflatoxin

A

Mold like thing that gets converted to a mutagen in the body

91
Q

3 Repair Mechanisms

A

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
Q

DNA glycosylase

A

removes base in base excision repair

93
Q

AP endonuclease

A

Breaks phosphodiester bond at the five prime site in base excition repair

94
Q

AP lyase

A

Cuts the 3 prime site in order to remove the other side of the nucleotide for nucleotide excision repair

95
Q

Uracil Repair

A

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
Q

Ames Test

A

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
Q

Xeroderma Pigmentosa

A

a disease of the skin caused by mutation ins the nucleotide excision repair pathway

Biochemistry (3 decks)

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