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Proteins and Nucleic Acids > Exam 2 > Flashcards

Exam 2 Flashcards

1
Q

Amino Acid residues that are O-linked glycosylation sites

A

Ser, Thr, Hydroxy-Lys, Hydroxy-Pro

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2
Q

N-linked Glycosylation sites

A

Asn- x-Ser, Asn-x-Cys, Asn-x-Thr
NO PRO

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3
Q

what is glycosylation

A

common post-translational modification

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4
Q

functions of glycosylation

A
  1. affects proteins structure and stability because it changes the primary structure by adding covalently adding organic materials
  2. increases protein lifetime
  3. change shape and charge (role in molecular recognition)
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5
Q

effects on absorbance

A

solvents, ions, h-bonding

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6
Q

Difference effects on absorbance

A

something that affects the electronic structure and changes the energy for excitation

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7
Q

red max wavelength shift

A

bathochromic
shifts to the right of an absorbance vs wavelength graph
lower energy -> gap deltaE smaller

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8
Q

Blue max wavelength shift

A

hypsochromic
shifts to the left of an absorbance vs wavelength graph
higher energy

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9
Q

x-ray

A

-size of unit cell
-strength or intensities of diffraction spots show electron density
-spacing of molecules in structure
-crystal structures and structure of molecules in crystal lattice

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10
Q

Mass Spectrometry

A

-identify protein structure (primary structure)
-identify post translations modifications

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11
Q

MALDI

A

observe singly charged ions (polymers and proteins)

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12
Q

Tandem Mass Spectrometry

A

-identify protein sequence
-peptide fragmentation
-peptide identification
-(B-mercatoethanol reduces proteins trypsin cleaves peptides)

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13
Q

omics

A

global profiling to identify concentration of biomolecules in a given population of cells

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14
Q

hydrodynamic methods

A

-estimate particle mass, size, shape, density, and oligomeric state
-study transport and diffusion

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15
Q

sedimentation

A

-determine molecular weight, density, approximate shape of macromolecule
-isolate certain species from a mixture

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16
Q

Dynamic Light Scattering

A

-info on particle size and distribution of macromolecules in solution
-(big particles -> slower, big disturbance, Small Particles -> faster, small disturbance)
-info on shape and how macromolecule moves through solution

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17
Q

electrophoresis and chromatography (general)

A

-separation of biomacromolecules by size, shape, charge, Polarity, or affinity for a given binding partner

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18
Q

Electrophoresis

A

-describes how charges molecules and complexes migrate in an electric field (Separate based on size, charges, and shape)
-Assess purity

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19
Q

Agarose gel electrophoresis

A

-Separates DNA fragments by mass
-Charge is more negative on larger DNA pieces and mass is larger

20
Q

DNA gel

A

-smaller particles -> fast
-larger particles -> slow

21
Q

staining with ethidium bromide

A

visualize DNA band

22
Q

DNA/RNA Autoradiography

A

-DNA blots = find presences of certain sequences
-northern blot = RNA detected by 32P
-southern blot = DNA detected by 32P
-western blot = proteins detected by antibodies

23
Q

SDS PAGE gels

A

-separates protein mixtures based on m/z
-SDS detergent used to make m/z proportional to mass
-check purity of proteins
-estimate molecular weight by comparing to standards

24
Q

Chromatography

A

-separate proteins by size (smaller proteins are slower to exit, larger proteins are faster to exit)
-separate protein by affinity (separated by how they interact with bead)
-adjust pH of solvent to get protein off

25
Q

GST

A

affinity tag with linker that can be cleaved by protease

26
Q

2D gel

A

-gel columns with pH gradients that can separate proteins by pI in an electric field
-pH=pI -> protein is neutral

27
Q

proteases

A

-used to generally fragment proteins for sequencing (trypsin)
-cleave off linkage tags like GST (Thrombin)

28
Q

centrifuge findings

A
  1. particles with larger masses move faster
  2. particles with smaller volumes (more dense) move faster
  3. the denser the solution the slower the particle will move
  4. the greater the frictional coefficient, the slower the particle
29
Q

Mass analyzers

A

quadrupole, magnetic sector, time of flight

30
Q

How to find the number of charges in ESI-MS

A

The amount of m/z between peaks
separated by 1 - single
separated by 1/2 - double
separated by 1/3- triple

31
Q

what happens to m/z when you increase charge in ESI-MS

A

when charges increase, m/z decreases

32
Q

Electrospray ionization (ESI)

A

removal of solvent =less sample damage

33
Q

exact mass

A

(mono isotopic mass)sum of most abundant masses

34
Q

1D NMR

A

peaks assigned to amino acid types

35
Q

2D NMR

A

peak heights indicate strength of nuclear overhauser interactions (NOE)

36
Q

NOE

A

Nuclear Overhauser
used to identify atoms in space

37
Q

Multi-dimensional NMR

A

used to determine the structure of proteins in solution

38
Q

x-ray crystallography

A

used to obtain near atomic resolution structures of proteins

39
Q

molecular mechanics

A

uses energy terms describing both covalent and non covalent interactions

40
Q

CD Spectroscopy

A

-(Circular Dichroism) measure the molar absorbance difference of left and right circularly polarized light
-detects the asymmetric interaction of chiral molecules with circularly polarized light

41
Q

GFP Chromophore

A

spontaneously forms from the sequences S-Y-G in the presence of oxygen

42
Q

time dependent FRET

A

used to observe structural changes on the us-ms timescale on which receptors move

43
Q

quantum yield (Q)

A

of protons emitted / # of protons absorbed

44
Q

Kasha’s rule

A

molecules rapidly relax to the ground vibrational state of the lowest lying excited singlet (internal conversion)

45
Q

what side chains hav pi to pi* transitions

A

H R E Q N D

46
Q

uv/vis spectroscopy

A

observes electronic transitions between energy levels

Proteins and Nucleic Acids (3 decks)

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