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Biochemistry (TED) > Exam 2 Review > Flashcards

Exam 2 Review Flashcards

1
Q

Peptide bond structure

A

Polar; Resonance hybrid allows cis and trans formations

99% are trans with the exception of proline (90% trans)

Resonance allows les reactivity
- rigidity and nearly planar

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2
Q

4 levels of protein structure

A

Primary= amino acid sequence

Secondary= alpha helix, beta sheet

Tertiary= 3D structure and interactions

Quaternary= 2 or more polyp. chains.

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3
Q

Alpha helix properties

A

H bonds stabilize within same polypeptide chain

  • between carbonyl residue (Hacceptor) and amide NH (Hdonor) 4 molecules away
  • most helices are right handed
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4
Q

How many residues per alpha helix turn?

A

3.6 residues per turn

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5
Q

Distance between alpha helix turn?

A

5.4 Angstrom per turn

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6
Q

Distance from one alpha C to another alpha C in an alpha helix?

A

1.54 Angstroms

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7
Q

Stability of Alpha helix?

A

H bonds are interior.
-Only stable in absence of water

Amphipathic alpha helices found on:

  • protein surfaces (nonpolar towards interior)
  • membrane surfaces (nonpolar towards lipids)
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8
Q

Beta helix properties?

A

H bonds between different poly. P. Strands.

Can be parallel or anti parallel.
-both occur in nature but anti parallel is more common and stabler due to linearity of H bond.

Side chains are above and below the plane of sheet.

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9
Q

B turns

A

Caused by proline in position 2 or glycine in position 3.

Stabilized by a h bond from carbonyl oxygen to amide three residues down.

Cause anti-parallel

Type 1 and 2 turns

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10
Q

Type 1 Beta turn

A

4 residues, hydrogen bonds

Proline at position 2

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11
Q

Type 2 Beta turn

A

Glycine at position 3

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12
Q

Peptide bond rotation?

A

Peptide bonds can not rotate, the bonds on either side can.

Phi bond: C-N bond

Psi bond: C-CO bond

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13
Q

Protein domain?

A

Region of a polypeptide chain that folds into a 3D unit

folds and is stable independently

Structure is conserved

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14
Q

Myoglobin?

A

Myoglobin: main oxygen storage protein

  • 1 polypeptide chain
  • mostly alpha helix
  • 1 spot for binding oxygen
  • structurally similar to hemoglobin subunits
  • higher affinity for oxygen than hemoglobin
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15
Q

Kd?

A

The concentration of ligand when half of the protein is bound.

Lower Kd = higher affinity

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16
Q

Hemoglobin?

A

Has a lower affinity for oxygen, easier to release it than myoglobin.

Is cooperative: binding of one ligand changes affinity for binding or another at a different site

Tense state has lower affinity for O2

Quarternary

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17
Q

Fractional occupancy equation?

A

Theta= [L] / (Kd + [L])

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18
Q

Allostery?

A
  • When something binding to one site affects the affinity for ligand/substrate at another site
  • can be the same ligand or different
19
Q

Cooperative molecule binding curve vs non-coop?

A

Cooperative: sigmoidal curve

Non-coop: rectangular hyperbol

20
Q

Induced fit vs lock-and-key models of ligand binding?

A

Induced fit: binding site only had approximate match to substrate shape; changes to match it

Lock & key: substrate binds with negligible conformation change

Both are true

21
Q

Enzymes?

A
  • increase rxn rate by stabilizing high energy transition state
  • don’t change delta g
  • enzymes lower delta G double cross, meaning speeds up rxn
  • decrease reactant mobility for good fit
22
Q

Reaction coordinate diagram?

A

Hump is transition state,

Size of hump is activation energy

23
Q

Michaelis-menten equation

A

v=(Vmax[s])/((alpha*Km)+[s])

Higher Km means less binding

As substrate concentration is increased velocity is up to a saturation point

24
Q

Which A.A’s are good enzymes?

A
  • Hydroxyl groups
  • Sulfhydryl groups
  • Amino groups
  • Histidine
25
Q

Binding pockets?

A

Chymotrypsin: aromatic

Elastase: small

Trypsin: basic

26
Q

Competitive inhibitor?

A

Inhibitor binds to enzyme at same spot as substrate.

Increasing [S] outcompetes

Raises Km, no effect on V max

Hyperbola plot/ all intercept on Y axis on lineweaver plot

Y intercept is 1/ Vmax

Slope is alpha*Km/Vmax

X intercept is -1/alpha*Km

27
Q

Uncompetitive inhibitor?

A

Inhibitor binds to enzyme-substrate complex.

Hard to overcome

Lowers Km, lowers V max

Parallel, linear plot lineweaver plot

Y intercept is alpha’/Vmax
Slope is Km/Vmax
X intercept is -alpha’/Km

28
Q

Mixed inhibitor

A

Lowers Vmax while increasing or decreasing Km.

29
Q

Allosteric enzyme regulation?

A

Ligand binds reversibly at a site other than the active site:

  • causes conformational change and change in Km, Vmax
  • can be cooperative
30
Q

Ki?

A

Ki= [E][i]/[Ei]

31
Q

5’ end and 3’ end nucleotide?

A

5’= phosphate

3’= hydroxyl

32
Q

DNA read which way?

A

5-3

33
Q

Why is DNA more stable?

A

Lack of reactive hydroxyl group

34
Q

Which DNA form

Is most common?

A

B form

35
Q

Which bases pair in double helix?

A

DNA= G:C and A:T

RNA= G:C and A:U

36
Q

Pyrimidines vs purines

A

Purines: A and G

Pyrimidines: C, U, T

37
Q

DNA nucleoside names?

A

Deoxyguanisine

Deoxyadenosine

Deoxythymidine

Deoxycytidine

38
Q

DNA nucleotide names?

A

Deoxyguanylate

Deoxyadenylate

Deoxycytidylate

Deoxythymidylate

39
Q

RNA nucleoside names?

A

Adenosine

Guanosine

Cytidine

Uridine

40
Q

RNA nucleotide names?

A

Adenylate

Guanylate

Cytidylate

Uridylate

41
Q

Base charge?

A

Bases uncharged between pH 5-9

42
Q

Subunit definition?

A

Smallest unit of a protein with 4ry structure that can be removed without disrupting covalent interactions

43
Q

Trypsin vs chymotrypsin cleavage?

A

Trypsin cleaves on c-terminal side of basic a.a.’s

Chymotrypsin cleaves on c-term side of aromatic a.a’s

44
Q

Trypsin vs chymotrypsin cleavage?

A

Trypsin cleaves on c-terminal side of basic a.a.’s

Chymotrypsin cleaves on c-term side of aromatic a.a’s

Biochemistry (TED) (4 decks)

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