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Biochemistry - Victor > Steele Proteins 2/3 > Flashcards

Steele Proteins 2/3 Flashcards

0
Q

Proteins are broken up into two class shapes: globular and structural (elongated, fibrous). Which class do enzymes fall under? Collagen?

A

enzymes are globular, collagen is structural.

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1
Q

Approximately how heavy is a 400 amino acid protein?

A

40,000 daltons (1 amino acid is approximately 100 daltons)

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2
Q

What kind of charge does phosphorylation add to a protein?

A

negative.

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3
Q

What is a zwitterion?

A

A molecule with two ionizable groups.

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4
Q

If both the carboxy and amine group are both protonated, is the amino acid more acidic or basic?

A

acidic.

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5
Q

What is pKa?

A

pKa is the pH of an aqueous solution of that amino acid at which the group is half protonated and half unprotonated (half acid, half base).

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6
Q

T or F. The higher the pKa, the more strongly the proton is held by the group that contains it.

A

True. (in general, if pH is more “acidic” than the pKa, then the aa is more in acid form. if the pH is more “basic” than the pKa, then the aa is more in basic form.)

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7
Q

What does buffering do?

A

Helps a molecule resist change in pH of a solution at 1 pH unit above and below the pKa.

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8
Q

What buffers blood?

A

carbonic acid and bicarbonate.

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9
Q

T or F. Proteins are good buffers.

A

False. Only histidine and alpha amino groups have pKas in range, but they are too sparse in serum.

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10
Q

T or F. Some membrane proteins have lipid anchors instead of embedding directly into the membrane.

A

True.

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11
Q

T or F. Glycosylation and disulfide bonds occur on the external domain.

A

True. Internal domain have reduced sulfhydrul groups, phosphorylation, and no complex carbs.

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12
Q

Where do the two major types of glycosylation occur? Hint, one involves asparagine, one involves serine/threonine.

A

Sugar is linked to side chain N of asparagine. Sugar is linked to OH of serine/threonine.

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13
Q

T or F. Some diseases result from proteins that are perfectly functional but improperly localized.

A

True.

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14
Q

What is NLS an example of?

A

Nuclear localization signal, example of targeting sequence. Importin protein recognizes NLS.

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15
Q

What are 4 methods of protein isolation?

A
  1. Ion exchange chromatography (based on charge)
  2. Gel filtration chromatography (based on size)
  3. Affinity chromatography (based on ligands/substrates/binding proteins/ab)
  4. absorption chromatography (based on hydrophobicity)
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16
Q

T or F. Proteins of same function in difference species have related sequences.

A

True.

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17
Q

T or F. Tertiary structure may be more conserved than primary sequence.

A

True.

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18
Q

Bovine ribonuclease and human ribonuclease are examples of ______? (what word defines the relationship these two enzymes have)

A

Orthologs

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19
Q

Human ribonuclease and angiogenin are ________.

A

Paralogs. different functions.

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20
Q

What mutation causes sickle cell disease?

A

Glutamic acid at position 6 of Beta chain is changed to Valine. V is hydrophobic, Glu is charged).

21
Q

T or F. Electrophoresis can separate proteins based on size, charge or both.

A

True.

22
Q

What is an allozyme?

A

forms of a protein encoded by different alleles of a gene (eg maternal and paternal alleles). “Allo-Allele”

23
Q

What is an isozyme?

A

forms of a protein encoded by different genes but catalyzing the same reaction. “isolated genie”

24
Q

MB creatine kinase 2 (CK2) in the blood stream is a sign of ______. CK3 and no CK2 is a sign of ______.

A

Myocardial infarction. Skeletal muscle damage.

25
Q

Cardiac troponin is now used to detect MI. What makes it better than CK2?

A

Peak goes higher (more sensitive), stays up longer (persists for clinical discovery).

26
Q

What is exo N terminal proteolysis?

A

removal of n terminal amino acid (eg initiator methionine excision).

27
Q

What is endo N terminal proteolysis?

A

removal of peptide. (eg signal peptide removal).

28
Q

What does acetylation of the N terminus do?

A

Provides stability against degradation by random aminopeptidases. Protects amino terminus from non enzymatic glycation by reducing sugars. 80% of human cytosolic protein are acetylated.

29
Q

How is protein glycation a diabetes diagnostic?

A

Hb is not N acetylated, rendering it susceptible to N terminal glycation. Diabetics have lots of sugar in blood, higher levels of glycation.

30
Q

Which amino acids have an OH available for phosphorylation?

A

Serine, threonine, tyrosine

31
Q

What processes is protein phosphoryation involved in?

A 
1 signal transduction
2. cell cycle transduction
3. cytoskeletal rearrangements
4. molecular transport
5 transcription translation
6 many others.
32
Q

pSer:pThr:pTyr?

A

1800:200:1. Due to stability. Tyrosine often phosphorylated but its very transient.

33
Q

T or F. 2% of the human genome encodes protein kinases and phosphatases.

A

True.

34
Q

Describe the NFkB process of activation?

A

Inflammation leads to phosphorylate IkB-NFkB, leading to degradation of IkB, revealing the NLS on NFkB. NFkB translocates to nucleus, activates transx.

35
Q

Binding of 4 _____ molecules activates PKA by dissociating the holoenzyme (r2c2) into 2 regulatory subunits and 2 catalytic subunits.

A

cAMP

36
Q

Ubiquitin is a tag involved in ________.

A

Proteolytic destruction.

37
Q

T or F. Ubiquinated protein gets digested by proteosomes and release peptide fragments and releases ubiquitin.

A

True.

38
Q

How does velcade treat multiple myeloma (overproduction of plasma cells leading to elevated Igs)?

A

Velcade inhibits protease activity in proteasome, blocking degradation of proteins. Myeloma cells are more sensitive to the blockage, dies.

39
Q

Describe the structure of hemoglobin.

A

Heterotetramer, 2 alpha, 2 beta, (2 gamma in fetus). One heme per chain, (4 hemes per hemoglobin).

40
Q

What happens structurally when oxygen binds to the iron molecule in heme?

A

It pulls the histidine residue up, resulting in conformational change.

41
Q

The deoxy form of hemoglobin is also known as the ____ form. Oxy is the ____ form.

A 
deoxy= T (taut)
oxy= R (relaxed)
42
Q

Decrease in pH ______ affinity for oxygen in hemoglobin, facilitating its release.

A

lowers.

43
Q

How does 2,3 BPG affect hemoglobin?

A

Only binds hemoglobin in T form. binding stabilizes form, decreases affinity for oxygen. Hemoglobin can release more oxygen to tissues.

44
Q

T or F. Fetal hemoglobin has lower affinity for oxygen than adults.

A

Heavens no!

45
Q

T or F. Enzymes have a large effect on Keq of a reaction.

A

No, it does not affect Keq.

46
Q

A reaction can occur spontaneously if delta G is ______.

A

negative (exergonic).

47
Q

The initial reaction velocity can vary with varying substrate concentrations.

A

True.

48
Q

What is Km?

A

Kilometers.

Also, the concentration of substrate at which the rate of a reaction is half of the maximum possible rate.

49
Q

What is the michaelis menten equation?

A

Vo=Vmax [S]/([S] + Km). An enzyme with high Km achieves high catalysis only when the substrate concentration is high.

50
Q

What does the x intercept and y intercept of the lineweaver burk plot show?

A

x intercept: -1/Km

y intercept: 1/Vmax

Biochemistry - Victor (17 decks)

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