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Biophysics 2022 > Part 1 > Flashcards

Part 1 Flashcards

1
Q

What are the three lineages of cells?

A
  • Bacteria
  • Archaea
  • Eukarya
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2
Q

What are the four main examples of Eukarya?

A
  • Animals
  • Plants
  • Fungi
  • Protists
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3
Q

Features of a Eukaryotic cell

A
  • Nucleus
  • Ribosomes
  • Golgi Complex
  • Endoplasmic reticulum
  • Plasma membrane
  • Mitochondria
  • Cytoplasm
  • Lysosome
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4
Q

Features of a prokaryotic cell

A
  • Capsule
  • Ribosomes
  • DNA
  • Cell wall
  • Plasma membrane
  • Cytoplasm
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5
Q

What are organelles?

A

Compartments within a cell that have specialised functions. They may be membrane bound or membraneless

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6
Q

What does the nucleus of a cell contain?

A

It contains genetic material surrounded by the nuclear envelope containing pores to allow messenger RNA diffusion in and out

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7
Q

Why do cells have differences in phenotypes?

A

The regulation of protein expression and degradation

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8
Q

How does DNA turn into proteins?

A
  • DNA is wound around histones in the nucleus of cells
  • RNA polymerase attaches to the start of the gene moving along the DNA making a strand of mRNA
  • Transcription occurs
  • Sections of RNA are removed and added
  • The mRNA moves into the cytoplasm
  • Ribosomes bind to the mRNA and read the code to produce an amino acid chain
  • tRNA molecules carry the amino acids into the ribosome
  • The chain folds into a protein
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9
Q

What is transcription?

A

The process whereby the DNA code determines the order in which the free basses are added to the mRNA

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10
Q

What is a nucleic acid?

A

A long chain molecule of repeating units called nucleotides

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11
Q

What is a nucleotide monomer composed of?

A

5 carbon sugar, phosphate, base

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12
Q

DNA and RNA are examples of what?

A

Nucleic acids

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13
Q

What is the only difference structurally between DNA and RNA?

A

The de-oxyribose has one less hydroxyl group

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14
Q

What ratios do concentrations of bases obey in DNA?

A

A/T = 1

C/G = 1

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15
Q

What is B-form DNA?

A

The canonical right handed DNA helix, most commonly found in nature. It has 10 residues per turn of the helix. The base pairs are planar and perpendicular to the helix axis.

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16
Q

What makes A-form different from B-form DNA?

A

The water content which changes the structure. It is a wider stubbier helix with 11 residues per turn of the helix. A form DNA in sodium occurs at lower relative humidity. They are however both right handed.

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17
Q

How is Z-form DNA different from other forms of DNA?

A

It is left handed and major and minor grooves show little difference in width.

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18
Q

What are chromosomes?

A

Thread-like structures of tightly packed DNA, located in the nucleus of cells.

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19
Q

What are histones?

A

A protein that DNA is wound around to give chromosomes their shape.
DNA + Histones = Chromatin

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20
Q

What is the process by which DNA replicates?

A
  • Double helix unzips along its backbone leaving unpaired bases
  • Free nucleotides in the nucleus match up with the unpaired bases (C&G, A&T) helped by enzymes called DNA polymerases
  • New strand of DNA identical to the original is formed
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21
Q

What are the three types of RNA and what their functions?

A

Messenger RNA: Reads information from DNA and is involved in protein synthesis

Transfer RNA: transfers specific amino acids onto a growing polypeptide sequence

Micro RNA/small interfering RNA: Breaks down mRNA or prevent it from going on to form proteins or can increase/decrease the transcription of certain genes

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22
Q

What are viruses?

A

Nucleic acids wrapped in a coating of protein to protect them and help them invade in a cell

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23
Q

What is a useful measure of DNA packing?

A

Ratio of volume taken up by the DNA to the volume of the region where DNA is stored

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24
Q

What are proteins?

A

Linear chains of amino acids that fold into precise 3D shapes to perform a wide range of processes

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25
Q

What is the Levinthal Paradox?

A

Finding the native folded state of a protein by a random search among all possible configurations can take an enormously long time yet proteins fold in seconds or less

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26
Q

How is the Levinthal Paradox resolved?

A

By noting that it is not just random folding but rather protein sequences contain information on folding paths and the stability of the folding structure

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27
Q

What do we measure masses of proteins in?

A

Daltons (Da)

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28
Q

What is the primary structure of proteins?

A

The sequences of residues in the polypeptide chains. At the ends are amino acid and carboxyl groups.

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29
Q

How many standard amino acids are there?

A
  1. All proteins are built from the same 20 monomers.
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30
Q

What are Zwitterions?

A

Molecules that carry charged groups of opposite polarity.

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31
Q

Where are L and D amino acids produced respectively?

A

L by the ribosome and D during post-transitional modification.

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32
Q

Name some examples of amino acids?

A
  • Cysteine
  • Histidine
  • Prolene
  • Tryptophan and tyrosine
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33
Q

What is a peptide?

A

A compound consisting of two or more amino acids linked in a chain, the carboxyl group of each acid being joined to the amino group of the next by a bond of the type -OC-NH-.

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34
Q

What are the two possible planar configurations of the peptide unit?

A

Cis and trans

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35
Q

What is Ramachandran plot?

A

A plot used to represent allowed combinations of backbone dihedral angles of an amino acid. Shaded areas are those with minimal or no steric clashes.

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36
Q

What are the motifs of the peptide protein?

A
  • Alpha helixes
  • Beta sheets
  • Turns
  • Harpins
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37
Q

What is the entropy associated with the vast majority of configurations of a random coil?

A

It greatly outweighs any decrease in enthalpy associated with a particularly favourable packing arrangement

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38
Q

What are the differences between the Helix in DNA and in Proteins?

A
  • Alpha helix in a protein is formed from a singe polypeptide chain
  • Double helix of DNA is formed from 2 antiparallel DNA molecules
  • The protein alpha helix is held together by interactions between atoms of backbone which are on the inside the side chains are on the outside positioned to minimise interactions between them
  • The DNA double helix is held together by hydrogen bonding and stacking between bases negatively charged backbones are on the outside to minimise electrostatic repulsion
  • An alpha helix is often represented as a coiled ribbon in a diagram of a protein
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39
Q

What are beta pleated sheets?

A

Sheets formed from extended polypeptide strands running alongside each other held together by interstrand hydrogen bonds. They fall in the top left of the Ramachandran plot.

40
Q

Each folded polypeptide chain folded up making the quaternary structure is known as what?

A

A subunit

41
Q

What is the tertiary structure of proteins?

A

The folding of the full length of a polypeptide due to the packing of various secondary structure elements

42
Q

What is Gibbs free energy?

A

The maximum reversible work that may be performed by a system at constant temperature and pressure, equal to 0 at equilibrium

43
Q

What is enthalpy?

A

Total energy including chemical potential energy. An increase in entropy contributed to the spontaneity of a process

44
Q

What is entropy?

A

The number of ways to arrange the system (disorder). An increase in entropy contributes to the spontaneity of the process.

45
Q

What happens if a reaction occurs at high temperature?

A

The is a bigger effect on S

46
Q

What happens when ΔS > 0, ΔH < 0?

A

It is spontaneous

47
Q

What happens when ΔS < 0, ΔH > 0?

A

It is not spontaneous

48
Q

What happens when ΔS > 0, ΔH > 0?

A

It is spontaneous at high T but not spontaneous at low T

49
Q

What happens when ΔS < 0, ΔH < 0?

A

Spontaneous at low T but not spontaneous at high T

50
Q

What contributions to contacts are there?

A
  • Formulations of disulphide bridges
  • Electrostatic interactions
  • Hydrogen bonding
  • Van der Waals interaction
51
Q

What is hydrogen bonding?

A

Bonds that form between atoms such that one atom contains a bond to hydrogen and the other contains an available lone pair of electrons so the hydrogen is shared between two atoms.

52
Q

What condition must dipoles satisfy for hydrogen bonding? Why?

A

Bonding angle must be more than 135 degrees as an unfavorable alignment of participating dipoles is repulsive

53
Q

What are the three types of Van der Waals interactions?

A
  • 2 Molecules with permanent diploes mutually orienting each other in such a way that on average attraction results
  • Dipolar molecules induce dipoles in other molecules so attraction results
  • Attractive forces are also operative between non-polar molecules (London dispersion forces)
54
Q

What is the hydrophilic effect?

A

When a hydrophilic molecule such as water becomes highly ordered around the non-polar surface forming the best possible hydrogen bonds (short, linear etc.)

55
Q

What are disulphide bonds?

A

Covalent crosslinks that stablise protein structures . They are stable in the extracellular environment and unstable outside it.

56
Q

What are integral membrane proteins?

A

Proteins with hydrophobic regions which allow them to span the cell membrane. These can function as channels and signal transducers.

57
Q

How many integral membrane proteins do we have?

A

300

58
Q

What techniques have been used to determine protein structures?

A

Xray crystallography was for a long time the main route but now cryoelectron microscopy plays a significant role

59
Q

What must the Gibbs free energy be for a process to be spontaneous?

A

Must be less than zero

60
Q

What are the major driving forces for the formation of well defined membrane structures?

A

Hydrophobic effect at hydrocarbon-water interface and hydrophilic forces between head groups

61
Q

In the self assembly of amphiphiles, how does the attractive interaction arise?

A

From artificial tension forces at the tail water interface

62
Q

What are geometric packing shapes determined by?

A
  • Optimal headgroup area
  • Volume of hydrocarbon tail
  • Maximum effective length of the hydrocarbon tail (critical length)
63
Q

What are the three shapes lipids can be divided into?

A

Type 1: Curved with heads pointing to centre of the arc
Type 2: Straight Line
Type 3: Curved with tails pointing towards centre of the arc

64
Q

What is lower energy, a flat or curved bilayer?

A

Flat

65
Q

What are vesicles?

A

They are self-contained structures consisting of fluid or gas surrounded and enclosed by an outer membrane called the lipid bilayer

66
Q

What approximation can be made for a lipid on a vesicle?

A

From the scale of the lipid, the vesicle is flat

67
Q

Why are membranes not flat?

A

Cells experience hydrodynamic forces such as when they flow in blood. The uptake and transport of molecules into the cell and between cellular compartments involves bending and budding off of membrane vesicles

68
Q

What are principle curvatures?

A

2 curvatures that characterise the shape at each point in space on a membrane

69
Q

What are principle radii of curvature?

A

The radii of the circular fragments from principle curvatures

70
Q

What conditions are needed for a membrane to transform from flat to curved?

A

The membrane elasticity determines the force which needs to be applied to deviate from the spontaneous shape. This elasticity is determined by the elastic modulus, the bending modulus and the modulus of the gaussian curvature.

71
Q

How do proteins enable a protein to bend?

A
  • A BAR protein with a rigid intrinsic curvature binds to the membrane and bends it
  • Coat proteins can bind to a membrane to stabilise the curvature
  • Proteins with amphipathic groups can insert into the head-tail region of the outer monolayer and mediate bending
72
Q

What are cubic phases?

A

3D structures which separate two discrete aqueous domains by a lipid bilayer. They are based around triply periodic minimal surfaces which have zero mean curvature and negative Gaussian curvature

73
Q

What do proteins need to be found in the lipid membrane?

A

A large hydrophobic core which sits amongst the lipid tails

74
Q

What are the conditions to use a lipid bilayer to stabilise the protein for crystallisation?

A
  • Its viscoelastic properties should be comparable to those existing in biological membranes
  • It should be capable of incorporating large amounts of proteins, detergents and precipitants without perturbation of the matrix
  • Membrane proteins incorporated into the system would retain there activity and structural integrity and these properties should be amendable to non-invasive spectroscopic tests
  • The system should provide a structured yet flexible matrix facilitating crystal nucleation and growth
75
Q

What is the endoplasmic reticulum?

A

A continuous membrane system taking up often the bulk of the cell interior. There are two types which are rough and smooth for protein synthesis.

76
Q

What is the total volume of the ER?

A

The difference between the volume taken up by the outermost sphere and the volume of the innermost concentric sphere.

77
Q

What is the function of the Golgi?

A

They take proteins made in the ER, package them and sends them where they are needed. They also modify proteins with carbs or phosphates

78
Q

What are Lysosomes?

A

membrane enclosed organelles that bud from the Golgi and contain enzymes which digest food, cell debris and waste materials. They have a low pH monitored by proton pumps and chloride ion channels across the cell membrane.

79
Q

What do the enzymes lipase, amylase, protease and nuclease digest respectively?

A

Lipase - Lipids
Amylase - Starch
Protease - Proteins
Nuclease - Nucleic acids

80
Q

What are mitrochondria?

A

The main energy source of cells. Adenosine triphosphate (ATP) is made in the mitochondria via the Krebs cycle.

81
Q

Where are non-membrane bound organelles found? and what are they for?

A

Throughout the cells and are formed by phase separation of protein and RNA, often associated with stress responses of cells.

82
Q

How does cellular mechanics play a role in gene expression and protein production?

A

Cells exert forces on surroundings. Motility and adhesion require dynamic control of cell architecture

83
Q

What is growth rate of microtubules affected by? What does growth rate determine?

A

Mechanical forces and concentration of monomer in solution. Growth rate determines tube strength

84
Q

How does the cytoskeleton behave in microtubules?

A

Microtubules which are typically arranged radially in the cell enable control over the transport of molecules in the cell. They are stiff enough to resist compression and play a key role in moving 2 copies of the genetic material to opposite sides of a cell when cell division takes place.

85
Q

How does the cytoskeleton behave in actin?

A

Individual actin filaments are too soft to push effectively against other cellular structures but they link with each other via other proteins that act as crosslinkers. The network formed in this way is strong enough to pull in/out the external cell membrane.

85
Q

Where do active forces come from?

A

Protein assemblies called motor proteins

86
Q

What do molecular motors do?

A

They transform chemical energy (ATP) into conformational changes (mechanical energy)

87
Q

What examples of motor proteins are there?

A

Kinesin and dyesin

88
Q

What is enthalpic elasticity?

A

When the internal energy of component of a systems free energy is changed

89
Q

What are microtubials?

A

Rigid, hollow rods (roughly 25nm in diameter) and are dynamic structures that undergo continual assembly and disassembly within the cell. They function to determine cell shape and cell movements.

90
Q

What are microtubules composed of?

A

Tubulin (a dimer consisting of 2 closely related polypeptides)

91
Q

What are protofilaments?

A

Head to tail arrays of tubulin dimers arranged in parallel with a fast growing plus end and a slow growing minus end to determine direction of movement along microtubules.

92
Q

What is the process of treadmilling of microtubules?

A

Tubulin molecules bound to GDP are continually lost from the minus end and are replaced by the addition of tubulin molecules bound to GTP to the plus end of the same microtubule. This gives the effect that the microtubule is moving.

93
Q

Why is there polarity in microtubules?

A

Due to the dimeric nature of tubulin subunits. This polarisation is recognised by motor proteins such as kinesin which know which way to walk along the microtubule

93
Q

What causes dynamic instability in microtubules?

A

GTP hydrolysis where individual microtubules alternate between cycles of growth and shrinkage. This causes the rapid turnover of most microtubules with half-lives of only minutes within a cell.

94
Q

How is copied genetic material equally distributed in the 2 daughter cells in cell division?

A

When 2 parallel microtubules are bound to a motor complex, the complex will pull the microtubules together into a bundle as it moves along them. When 2 antiparallel microtubules are bound to the same motor complex, they will be slid apart by the action of the motors pushed in opposite directions.

95
Q

How is copied genetic material equally distributed in the 2 daughter cells in cell division?

A

When 2 parallel microtubules are bound to a motor complex, the complex will pull the microtubules together into a bundle as it moves along them. When 2 antiparallel microtubules are bound to the same motor complex, they will be slid apart by the action of the motors pushed in opposite directions.

Biophysics 2022 (2 decks)

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