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FINALS! BIOPHYSICS LECTURE > MODULE 4: BIOPHYSICAL TECHNIQUES > Flashcards

MODULE 4: BIOPHYSICAL TECHNIQUES Flashcards

1
Q

Biophysical techniques provide information about

A

electrical structure
size
shape
dynamics
polarity
modes of interaction

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2
Q

Methods used for gaining information about biological systems

A

Biophysical techniques

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3
Q

Biophysical techniques study the

A

structure
properties
dynamics
function

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4
Q

TRUE OR FALSE:

Biophysical techniques involve the development of novel techniques to investigate the structure, properties, and biological functions of biomolecules or the application of these techniques to monitor how the structure and dynamics of biomolecules enables specific biological functions

A

TRUE

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5
Q

purify or isolate biological specimens (organisms, cells, and molecules) / get them ready for use in some other process or further experimentation

A

PREPARATIVE TECHNIQUES

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6
Q

used to measure physical aspects (energy, pressure, volume, length, stress) of a biological system

A

ANALYTICAL TECHNIQUES

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7
Q

machine used to spin a sample of material around in circles

A

centrifuge

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8
Q

TRUE OR FALSE:

In ultracentrifuge, the force is similar to, but typically much smaller than, the normal force of gravity.

A

FALSE, much larger

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9
Q

A centrifuge designed to speed an extremely high rate of speed

A

Ultracentrifuge

can exert forces as much as 1 million times that of gravity

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10
Q

describes motion of particles in fluid under the application of a force

A

SEDIMENTATION

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11
Q

sedimentation rate of a particle depends on

A

force
density of the fluid
size
density of particles

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12
Q

what increases the sedimentation rate?

A

Applying force stronger than gravity

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13
Q

convenient technique for separating molecules of different sizes

A

ULTRACENTRIFUGATION

USED AS BOTH PREPARATIVE AND ANALYTICAL

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14
Q

Commonly used to isolate samples of pure DNA

A

ULTRACENTRIFUGATION

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15
Q

Exosomes isolation

A

ULTRACENTRIFUGATION

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16
Q

vesicles or cellular components that exist outside the cell

A

Exosomes

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17
Q

contains special optical devices and sensors that can track the movement of molecules as they are being centrifuges

A

ANALYTICAL CENTRIFUGE

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18
Q

used to detect conformational transitions and to determine the number of subunits making up molecular complex

A

Analytical Ultracentrifuge

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19
Q

Can calculate the size and approximate shape of molecules

A

Sedimentation

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20
Q

laboratory technique used to separate DNA, RNA, or protein molecules based on their size and electrical charge

A

ELECTROPHORESIS

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21
Q

It applies electric current to biological molecules

A

Electrophoresis

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22
Q

used to move molecules to be separated through gel

A

electric current

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23
Q

TRUE OR FALSE

Electrophoresis relies on sedimentation.

A

TRUE

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24
Q

TRUE OR FALSE

In electrophoresis, the force results from an electric field applied to electrically charged particles or molecules.

A

TRUE

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25
Q

Common type of electrophoresis

A

gel electrophoresis

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26
Q

fluid that has a molecular structure that gives it properties similar to a solid

A

gel

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27
Q

TRUE OR FALSE

Larger molecules are more easily obstructed than smaller molecules.

A

TRUE

GEL INCREASES DIFFERENCES IN SEDIMENTATION

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28
Q

What affects the sedimentation in gel electrophoresis?

A

density of gel
size and shape of molecules
charge on molecules

Molecules with more charge = stronger force generated by electric field

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29
Q

enables the separation, identification, and purification of the components of a mixture for qualitative and quantitative analysis

A

CHROMATOGRAPHY

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30
Q

coined the term chromatography in 1906

A

Russian Botanist Mikhail Tswett

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31
Q

Who described the first analytical use of chromatography in gas for the analysis of fatty acid mixtures?

A

James and Martin in 1952

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32
Q

Chromatographic procedures involve

A

size
binding affinities
charge

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33
Q

powerful separation tool used in all branches of science, used to separate components from complex mixtures

A

CHROMATOGRAPHY

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34
Q

factors effective on Chromatography

A

adsorption (liquid-solid)
partition (solid-liquid)
affinity

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35
Q

Because of the differences in separation caused by chromatography, some components of the mixture stay longer in what phase?

A

stationary phase

move slowly in th system; mobile phase= move rapidly; leaves faster

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36
Q

Three components form the basIs of the chromatography technique

BASIC COMPONENT EFFECTIVE ON THE SEPARATION OF MOLECULES FROM EACH OTHER

A

STATIONARY PHASE
MOBILE PHASE
SEPARATED MOLECULES

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37
Q

composed of a solid phase or a layer of a liquid adsorbed on the surface solid support

A

STATIONARY PHASE

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38
Q

always composed of liquid or a gaseous component

A

MOBILE PHASE

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39
Q

Four separation techniques based on molecular characterisctics and interaction type

A

Ion exchange
Surface Adsorption
Partition
Size Exclusion

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40
Q

chromatography techniques based on the stationary bed

A

column
thin layer
paper chromatography

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41
Q

APPLICATION OF CHROMATOGRAPHY

  • identify and analyze samples for the presence of trace elements or chemicals
  • separation of compounds based on their molecular weight and element composition
  • detects the unknown compounds and purity of mixture
  • drug development
A

PHARMACEUTICAL SECTOR

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42
Q

APPLICATION OF CHROMATOGRAPHY

  • testing water samples and also checks air quality
  • HPLC and GC are very much used for detecting various contaminants such as polychlorinated biphenyl (PCBs) in pesticides and oils
  • life sciences applications
A

CHEMICAL INDUSTRY

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43
Q

APPLICATION OF CHROMATOGRAPHY

  • food spoilage and additive detection
  • determining the nutritional quality if food
A

FOOD INDUSTRY

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44
Q

APPLICATION OF CHROMATOGRAPHY

  • analyzing blood and hair samples of crime place
A

FORENSIC SCIENCE

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45
Q

Used in protein separation like insulin purification, plasma fractionism, and enzyme purification

A

HPLC

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46
Q

Routinely practiced in the biopharmaceutical industry, along with the vaccine development, and gene therapy vectors

A

Virus purification

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47
Q

APPLICATION OF CHROMATOGRAPHY

  • HPLC
  • Virus purification
A

Molecular Biology Studies

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48
Q

type of partition chromatography applied to isolate molecules with different molecular sizes

A

Size Exclusion Chromatography

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49
Q

it uses gravity and pressure to sediment a solution through gel

A

Size Exclusion Chromatography

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50
Q

tightly packed suspension of gel beads

A

SEC gels

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51
Q

TRUE OR FALSE

In SEC, it is the larger molecules that pass through the gel faster and the smaller molecules lag behind

A

TRUE

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52
Q

Using gels with different size pores can ——————–
different size molecules from the insides of the gel particles.

A

exclude

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53
Q

study of the interaction between radiation and matter

A

spectroscopy

54
Q

measure the intensity of the emergent radiation

A

spectroscopy

55
Q

comon properties of spectroscopy

A

direction of the emitted radiation
polarity

56
Q

resulting plot that has the function of the wavelength or the frequency of radiation

57
Q

Formula for frequency

A

f = c/λ

c = speed of light
λ = wavelength

58
Q

Formula for Energy

A

E = hf

h = Planck’s constant: 6.626068 x 10^(-34) kg m^2/s or J/s

59
Q

techniques of spectroscopy were developed using

A

visible light (380 to 750 nm)

60
Q

spectroscopic techniques are classified according to

A
  • type of light used (EM)
  • properties of the emergent light measured
61
Q

measure the amount of light absorbed as we control and slowly vary the temperature of a sample

A

temperature absorbance spectroscopy

62
Q

Techniques that do not involve EM Rad

A
  • Electron Spectroscopy
  • Mass spectroscopy
63
Q

measures the kinetoc energy of electrons that emerge from the sample

A

Electron Spectroscopy

64
Q

produces a spectrum as a function of a mass

A

Mass spectroscopy

65
Q

provide information about the identity of biological molecules, their structure, conformational transitions, binding and kinetics

A

Spectroscopic techniques

66
Q

frequencies and amplitudes are perceive as ————– respectively

A

color and intensity/brightness

67
Q

measurement of the interaction between radiation and matter

A

Spectrometry

68
Q

instrument which performs the measurements

A

Spectrometer or Spectrograph

69
Q

TRUE OR FALSE

EM is treated as photons or particles and waves

70
Q

Exhibit elastic collisions, bouncing and scattering off of objects

71
Q

Exhibits reflection, refraction, and interference

72
Q

also called absorbance spectroscopy

A

ABSORPTION SPECTROSCOPY

73
Q

light of a specific wavelength is incident through a sample and measure the intesnity of the light that comes out the other side

A

ABSORPTION SPECTROSCOPY

74
Q

In absorption spectroscopy, light is converted into

A

kinetic energy; higher or excited energy state

75
Q

the absorbance of a given sample depends on three things

A
  1. intrinsic ability of molecules in solution to absorb light
  2. concentration of the molecules in solution
  3. path length of the light
76
Q

measure that accounts for both concentration and thickness

A

molar extinction coefficient

77
Q

it is used to determine the proportion of hemoglobin with oxygen bound to it

A

absorbance spectroscopy

78
Q

graph of the absorbance versus the wavelength or frequency of light

A

absorption spectrum

79
Q
  • used to identify types of molecules in a sample
  • used to measure concentration of molecules in solution (once the identity of the molecule is known)
A

absorption spectrum

80
Q

used to folloe conformational transitions and ligand binding

A

absorption spectroscopy

81
Q

measures absorbance across a range of temperatures; useful for studying temperature-induced conformational transitions

A

temperature scanning absorption spectroscopy

82
Q

electrons drop down from their excited state, emitting light in the process

A

FLUORESCENCE

83
Q

caused by absorption

A

Fluorescence

84
Q

TRUE OR FALSE

Emitted light is longer than the absorbed light.

85
Q

Can be used to characterize molecules and to measure and follow conformational transitions and ligand binding

A

FLUORESCENCE SPECTROSCOPY

86
Q

a small molecule or the specific part of a molecule that is responsible for the fluorescence

A

fluorophore

87
Q

technique in which a fluorophore is attached to another molecule in order to track that molecule through some biological process

A

FLUORESCENT TAGGING

88
Q

used to determine the sequence of residues in DNA

A

FLUORESCENT TAGGING

89
Q

uses genetic tag that produces a stoichiometric ratio of a fluorescent protein reporter and the protein of interest during protein translation

A

PROTEIN QUANTITATION RATIOING (PQR)

90
Q

Distinct Characteristics of NMR

A
  • involves interaction of light (EM) with the nuclei of atoms in a molecule
  • provide structural details (higher resolution)
  • strong magnetic field that alters and limits some of the energy states available to the nuclei
  • uses RF
91
Q

Absorption and Fluorescent spectroscopy rely on EM in

A

UV
Visible
Infrared

92
Q

TRUE OR FALSE

The frequency of the EM radiation will be proportional to the energy difference between the two spin states.

93
Q

TRUE OR FALSE

the smaller energy difference between spin states means that these nuclei will resonate with lower frequencies (less energy) of EM

94
Q

TRUE OR FALSE

Nuclei that are less shielded by electrons will be more exposed to the magnetic field; thus, these nuclei resonate with higher-frequency EM

95
Q

Molecules of parts of molecules are ionized and then passed through a magnetic field

A

Mass Spectroscopy

96
Q

used both for determining molecular weights and identifying molecules (once the molecular weight is known)

A

MASS SPECTROSCOPY

97
Q

technique for determining the relative positions of atoms within a crystal

A

X-RAY CRYSTALLOGRAPHY

98
Q

orderly, three-dimensional, repeating arrangement of atoms or molecules

99
Q

provides precise, high resolution structural information for molecules in a crystal

A

X-RAY CRYSTALLOGRAPHY

100
Q

used to discover that DNA is a double helix

A

X-ray Crystallography

101
Q

disadvantage of X-ray crystallography

A

molecules must be in crystalline form

102
Q

occurs when light waves pass through an ordered arrangement of openings and interfere with each other on the other side

A

DIFFRACTION

103
Q

Waves meet in phase with one another, the peaks from one wave come together with peaks from the other wave

peaks become higherand troughs become lower

A

CONSTRUCTIVE INTERFERENCE

104
Q

Meet out of phase, a peak and trough come together

waves flatten out and lower the intensity of radiation

A

DESTRUCTIVE INTERFERENCE

105
Q

Technical field of using microscopes to view objects and areas of objects that cannot be seen with the naked eye

A

Microscopy

106
Q

Who built the first electron microscope?

A

Ruska and Max Knoll

107
Q

use a beam of highly accelerated electrond

A

ELECTRON MICROSCOPES

108
Q

the beam passes through a very thinly sliced sample to provide an image on the other side; the image is made by focusing the electron beam onto a view screen coated with some material that fluoresces in response to the incoming electrons

A

TRANSMISSION ELECTRON MICROSCOPY

109
Q

gradually scanned across the surface of the specimen

some of the intensity of the elctron beam is lost

A

SCANNING ELECTRON MICROSCOPY

1/10 as powerful as TEM,but provides 3-dimensional image of the specimen

110
Q

provides magnified images similar to those of SEM, but with resolution similar to those of TEM (10 times better than SEM)

A

ATOMIC FORCE MICROSCOPY

111
Q

It works by moving a mechanical probe across the surface of the object being scanned

provides true, three-dimensional information about the object

A

ATOMIC FORCE MICROSCOPY

112
Q

More advanced techniques of —————— and —————–keep the probe a constant distance from the object’s surface in order to avoid the possibility of the probe damaging or deforming the surface of the object being scanned

113
Q

Instrument that uses focused laser beams to create piconewton size forces that can be used to hold and manipulate microscopic particles anywher from 0.1 nm (size of an atom) to 10000 nm (size of bacterium)

A

optical tweezers

114
Q

the phenomenon of focused laser beams holding a single particle in place in three dimensions

A

OPTICAL TRAP

115
Q

useful for investigationg the mechanics of and forces associated with molecular motors

A

OPTICAL TWEEZERS

116
Q

Used for sorting and separating cells of various types or for measuring the forces necessary for bending or breaking a DNA molecule

A

OPTICAL TRAP

117
Q

Measure and characterize electric currents in cells, particularly in excitable tissue cells such as neurons

A

VOLTAGE CLAMP

118
Q

The basis of this technique is the ability to insert a very fine microelectrode into the cell, with another electrode in contact with the fluid around the outside of the cell.

A

VOLTAGE CLAMP

119
Q

Voltage is clamped, or held constant, through feedback mechanisk

A

VOLTAGE CLAMP

120
Q

value of voltage that is held constant

A

command voltage

121
Q

allows to measure the cell’s electric current under a variety of conditions; useful to discover and characterize volatge-gated ion channels which are proteins found in cell membranes

A

VOLTAGE CLAMP

122
Q

Used to keep the current constant while allowing voltage to vary

A

CURRENT CLAMP

123
Q

The electrode is placed inside a micropipette filled with an electrolyte solution, and the micropipette is placed against the cell membrane

ALLOWS TO INVESTIGATE THE BEHAVIOR OF A SINGLE ION CHANNEL

A

PATCH CLAMP

124
Q

SIMILARITIES OF VOLTAGE CLAMP, CURRENT CLAMP, AND PATCH CLAMP

A

they all consist of an electrode, some wires, and electronic feedback unit capable of measuring and manipulating volatges and currents

125
Q

difference among current clamp, voltage clamp, and patch clamp

A

settings on the device:
MEASURE CURRENT OR VOLTAGE
HOLD FIXED
MANIPULATE VIA FEEDBACK MECHANISM

126
Q

Measure of energy changes in the form of heat

A

CALORIMETRY

127
Q

instrument that measures heat energy

A

CALORIMETER

128
Q

used to measure the amount of energy absorbed or released

A

CALORIMETRY

129
Q
  • Used to determine the amount of energy necessary to unwind a piece of DNA helix
  • Used to measure the binding strength of various drugs to a particular protein
A

CALORIMETRY

130
Q

useful for measuring the very small amounts of energy

A

MICROCALORIMETERS

FINALS! BIOPHYSICS LECTURE (2 decks)

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