Exam 2

Question 1

Amino Acid residues that are O-linked glycosylation sites

Answer 1

Ser, Thr, Hydroxy-Lys, Hydroxy-Pro

Question 2

N-linked Glycosylation sites

Answer 2

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

Question 3

what is glycosylation

Answer 3

common post-translational modification

Question 4

functions of glycosylation

Answer 4

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)

Question 5

effects on absorbance

Answer 5

solvents, ions, h-bonding

Question 6

Difference effects on absorbance

Answer 6

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

Question 7

red max wavelength shift

Answer 7

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

Question 8

Blue max wavelength shift

Answer 8

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

Question 9

x-ray

Answer 9

-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

Question 10

Mass Spectrometry

Answer 10

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

Question 11

MALDI

Answer 11

observe singly charged ions (polymers and proteins)

Question 12

Tandem Mass Spectrometry

Answer 12

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

Question 13

omics

Answer 13

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

Question 14

hydrodynamic methods

Answer 14

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

Question 15

sedimentation

Answer 15

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

Question 16

Dynamic Light Scattering

Answer 16

-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

Question 17

electrophoresis and chromatography (general)

Answer 17

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

Question 18

Electrophoresis

Answer 18

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

Question 19

Agarose gel electrophoresis

Answer 19

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

Question 20

DNA gel

Answer 20

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

Question 21

staining with ethidium bromide

Answer 21

visualize DNA band

Question 22

DNA/RNA Autoradiography

Answer 22

-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

Question 23

SDS PAGE gels

Answer 23

-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

Question 24

Chromatography

Answer 24

-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

Question 25

GST

Answer 25

affinity tag with linker that can be cleaved by protease

Question 26

2D gel

Answer 26

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

Question 27

proteases

Answer 27

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

Question 28

centrifuge findings

Answer 28

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

Question 29

Mass analyzers

Answer 29

quadrupole, magnetic sector, time of flight

Question 30

How to find the number of charges in ESI-MS

Answer 30

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

Question 31

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

Answer 31

when charges increase, m/z decreases

Question 32

Electrospray ionization (ESI)

Answer 32

removal of solvent =less sample damage

Question 33

exact mass

Answer 33

(mono isotopic mass)sum of most abundant masses

Question 34

1D NMR

Answer 34

peaks assigned to amino acid types

Question 35

2D NMR

Answer 35

peak heights indicate strength of nuclear overhauser interactions (NOE)

Question 36

NOE

Answer 36

Nuclear Overhauser used to identify atoms in space

Question 37

Multi-dimensional NMR

Answer 37

used to determine the structure of proteins in solution

Question 38

x-ray crystallography

Answer 38

used to obtain near atomic resolution structures of proteins

Question 39

molecular mechanics

Answer 39

uses energy terms describing both covalent and non covalent interactions

Question 40

CD Spectroscopy

Answer 40

-(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

Question 41

GFP Chromophore

Answer 41

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

Question 42

time dependent FRET

Answer 42

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

Question 43

quantum yield (Q)

Answer 43

of protons emitted / # of protons absorbed

Question 44

Kasha's rule

Answer 44

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

Question 45

what side chains hav pi to pi* transitions

Answer 45

H R E Q N D

Question 46

uv/vis spectroscopy

Answer 46

observes electronic transitions between energy levels