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Biophysics > Module 2 (C & D) > Flashcards

Module 2 (C & D) Flashcards

(97 cards)

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1
Q

Are involved in nearly every biological process within the cell

A

Protein

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2
Q

Example of biological process

A

Catalyzing biochemical reactions
Regulating (turning on and off) biochemical processes
Transporting molecules across cell membranes from cell to cell, or from cell to another part)

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3
Q

Proteins are also involved in _____ (self- induced movement of the cell)

A

Cell motility

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4
Q

Protein roles

A
  • Physics of protein folding
  • Conformational transitions
  • Binding is crucial to understand
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5
Q

Process by which a protein structure assumes its functional shape or conformation

A

Protein folding

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6
Q

All protein molecules are _____

A

Heterogeneous unbranched chains of amino acids

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7
Q

Protein folding is a process by which

A

A polypeptide chain folds to become a biologically active protein in its native 3D structure

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8
Q

The structure of a protein is hierarchically arranged from a ____ to ____ structure

A

Primary to Quarternary

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9
Q

Refers to the linear sequence of amino acid residues in the polypeptide chain

A

Primary structure

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10
Q

Generated by formation of hydrogen bonds between atoms in the polypeptide backbone

A

Secondary structure

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11
Q

Secondary structure folds the chains into either ____ or ____

A

Alpha helices or beta sheets

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12
Q

Formed by the folding of the secondary structure sheets or helices into one another

A

Tertiary structure

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13
Q

Usually a geometric shape and has polypeptide chain as a backbone

A

Tertiary structure

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14
Q

Determined by the interactions and bonding of the amino acid side chains in the protein

A

Tertiary structure

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15
Q

Results from folded amin-acids chains in tertiary structures interacting further with each other to give rise to functional protein like hemoglobin or DNA polymerase

A

Quarternary structure

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16
Q

Primary structure is also known as

A

Amino acid structure

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17
Q

Secondary structure is also known as

A

Regular sub- structures

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18
Q

Tertiary structure is also known as

A

Three- dimensional structure

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19
Q

Quaternary structure is also known as

A

Complex of protein molecule

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20
Q

External factors influencing the sensitive process of protein folding

A
  • Electric and Magnetic field
  • Temperature
  • pH
  • Chemicals
  • Space Limitation
  • Molecular crowding
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21
Q

The hydrophobic effect constrains the _____ ____ of a protein to escape water

A

Apolar residues

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22
Q

The apolar residues converge to form an apolar core of the protein leaving more ______

A

Polar residues at the surface where they form hydrogen bonds with water molecules (upper panel)

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23
Q

The ____ contribution to the folding reaction is illustrated in the lower panel

A

Enthalpic

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24
Q

Lower panel is

A

electrostatic interaction between the positive N- terminus and the negative C- terminus

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25
Disappears from the surface when the protein folds
Apolar surfaces
26
Apolar means
No charge
27
An example of neurodegenerative condition cause by protein misfolding
Alzheimers, Huntingtons, Parkinsons
28
This branch of biophysics studies the energy flow in living systems
Bioenergenetics
29
Most life forms get their energy from
Sun
30
Cellular processes such as the building and breaking down of complex molecules occur through ___
Stepwise chemical reactions
31
During the light reactions of photosynthesis, energy is provided by a molecule called
Adenosine Triphosphate (ATP)
32
Describe how energy behaves in physical systems and biological
Law s of thermodynamics
33
States that energy cannot be created nor destroyed
First law of thermodynamics ( can be transferred from place to place)
34
States that in a closed system the orderliness (entropy) of the system can never increase but only decrease over time
Second law of thermodynamics
35
High disorder and low energy =
High entropy
36
______ increases as molecules at a ____ concentration in one place diffuse and spread out
Entropy at a high
37
Living thighs are highly ordered, requiring constant energy to be maintained at ____
State of low entropy
38
Application of probability and statistics to large populations of molecules
Statistical mechanics
39
A mathematical description of how the molecules move
Model
40
Allows us to interpret the things we can measure in terms of what specific molecules are doing
Statistical mechanics
41
Branch that deals with measuring the rate or speed of biological process
Kinetics
42
Biological processes examples
- Biochemical reactions - Conformational transitions - Binding or unbinding of biomolecules
43
Tells us whether a given process or biochemical reaction will occur
Thermodynamics
44
How fast this process will occur
Kinetics
45
This model is a hypothesis as to what the molecular mechanisms is that causes some process
Models in statistical thermodynamics
46
A device that can alter the direction or size of a force
Machine
47
Examples of machine
Pulley, lever or an inclined plane
47
Is a type of machine that also has the ability to convert potential energy into mechanical energy into a mechanical force or motion
Motor
47
Uses our bones as levers to redirect and in some cases magnify or decrease the forces they apply
Muscles
48
These are hairlike projections on the surface of some cells that move, allowing the cell to swim,
Cillia
49
Longer, whiplike stricture that stick out from the body of some cells and move to proper the cell forward
Flagella
50
Some cells move by temporarily pushing out their membrane at one or more location
Pseudopodia
51
Cells that manufacture proteins or other substances to be used elsewhere in the body
Secretions
52
Have various mechanisms for packaging and moving the substances they make
Secretory cells
53
When a cell is getting ready to divide it first duplicates its chromosmes
Separation of chromosomes (DNA) during cell divisions
54
Binding in one part of a molecule affects activity in another part of the same molecule
Allosterics
55
Allostery from the greek word ____ meaning ___
allos - other stereos - object / solid object
56
Allostery allows two things to take place
Allosteric regulation and cooperativity
57
The control of a biological process by a cell or organism
Regulation
58
Directly involved in carrying out the protein's function
Active site
59
Usually happens simply by controlling binding directly at the molecule's active site
Regulation of the process
60
Regulation of a process is achieved through binding somewhere other than the active site
Allosteric site
61
When a biochemical process is controlled via long distance
Exhibits allosteric regulation
62
Sites behave as active sites and as allosteric sites at the same time it is called
Cooperativity
63
The occurrence of separate events together in a nonindependent manner
Cooperativity
64
Events occur only slightly more together than they would if they were completely independent
Slightly cooperative process
65
A set of otherwise independent events occurs in a mostly all or none manner
Highly cooperative process
66
Regulates the substrates to bind
Regulatory molecule
67
No rejection happened
Allosteric inhibitor
68
Rejection of substrate happened
Allosteric inhibition
69
Regulates substrates to bind
Regulatory molecule
70
There's binding at active site
Allosteric activator
71
This branch of biophysics studies the physics of DNA and RNA
DNA and Nucleic Acid Biophysics
72
DNA and RNA stands for
alam mo n dapat to beh
73
Can act as a catalyst for certain chemical reactions
RNA
74
Controls our physical heriditary
DBA
75
Can bend and twist to form a helix as wel
Double helix
76
Helix of a helix is called a
Superhelix
77
Process of forming a superhelix in DNA is known as
Supercoiling
78
A quarternary structure in DNA occurs when the DNA Superhelix wraps itself around protein complexes known as
Histones
79
Function of DNA
Long term storage of genetic information; transmission of genetic infos to make other cells and new organisms
80
Function of RNA
Used to transfer the genetic code from the nucleus to the ribosomes to make proteins
81
RNA is used to
Transmit genetic information in some organisms and may have been the molecule used to store genetic blueprints in primitive organisms
82
DNA is
responsible for storing and transferring genetic informations
83
RNA directly codes
For amino acids and acts as a messenger between DNA and ribosomes to make proteins
84
Structural features of DNA
B- form double helix - double stranded molecule consisting of a long chain of nucleotides
85
Structure features of RNA
A- form helix, single stranded helix - shorter chains of nucleotides
86
Composition of Bases and Sugars
Deoxyribose sugar phosphate backbone Adenine Guanine Cytosine Thymine bases
87
Composition of Bases and Sugars
Ribose sugar Phosphate backbone Adenine Guanine Cytosine Uracil bases
88
Propagation of DNA
Self- replicating
89
Propagation of RNA
Synthesized from DNA on an as needed basis
90
Base Pairing of DNA
AT (Adenine - Thymine) GC (Guanine - Cytosine)
91
Base pairing of RNA
AU (Adenine- Uracil) GC ( Guanine - Cytosine)
92
Reactivity of DNA
Reactivity of C-H bonds in DNA make it fairly stable, plus the body destroys enzymes that would attack DNA, the small grooves in the helix also serves as protection, providing minimal space for enzymes to attach
93
Reactivity of RNA
The O-H bond in the ribose of RNA makes the molecule more reactive, not stable under alkaline conditions, the large grooves in the molecule make it susceptible to enzyme attack, It is constantly produced, used, degraded, and recycled
94
Ultraviolet Damage of DNA
DNA is susceptible to UV damage
95
Ultraviolet Damage of RNA
Compared with DNA, RNA is relatively resistant to UV damage

Biophysics (2 decks)

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