biophysics 1

Question 1

electromagnetic spectrum

Answer 1

types of radiation as a function of energy.
it is the distribution of EM radiation according to frequency or wavelength and their respective photon energies.
Order:
radio, microwave, infrared, visible light, ultraviolet, x ray, gamma ray.
highest wavelength is radio.
10^3, 10^-2, 10^-5, 0.5x10^-6, 10^-8, 10^-10, 10^-12
lowest frequency is radio
10^4, 10^8, 10^12, 10^15, 10^16, 10^18, 10^20

Question 2

**the photoelectric effect

Answer 2

-description of emission of electrons from a material when exposed to light or em radiation.
-occurs when photons (particles of light) strike a surface (typically metal)
-when the photons energy exceeds the threshold energy called the work function, they transfer their energy to electrons in material.
-if energy transferred is sufficient, this exceeds the binding force of the electrons to the material, so they are emitted from surface as photoelectrons.
MORE THEORY

Question 3

****ELECTRON MICROSCOPE

Question 4

photon energy, eV scale

Answer 4

photon energy is the energy carried by a single photon.
photon energy is directly proportional to frequency but inversely proportional to wavelength.
depends only on frequency not intensity.
E = hf =hc/wavelength
eV scale is unit of energy used to express energy values at atomic and subatomic levels
-the amount of KE gained or lost from an electron when it is accelerated by an electric field from an electric potential of 1 volt.
*anaolgy of ball rolling down a hill –> gravity is the driving force.
-the electric field is the driving forcing causing the electron to accelerate 1eV = 1.602x10^-19J
-eV scale allows scientists to describe energy values in a more practical manner

Question 5

interpretation of momentum of light: optical tweezers

Answer 5

optical tweezer traps particles using a high intensity laser beam.
-they utilise the momentum of light to create a force to trap and move these tiny particles (light can carry momentum due to its wave like properties)
the last beam focuses on a small region with high intense light
-when an object is placed in this region, it interacts with the photons, the photons bounce off or get absorbed and re emitted by the object, the transfer of momentum forms a force on the object.
-forces depend on the properties of the object such as size and shape and properties of laser beam such as intensity or focus
*forces can push or pull object allowing scientists to control movement and position

Question 6

*****models of atom

Question 7

wave nature of electron

Answer 7

based on concept of matter waves, electrons can behave as a waves
-davisson and germer created an apparatus and used it to fire a beam of electrons at a nickel crystal target under vacuum conditions
-they observed the electron exhibited a diffraction pattern similar to that of light waves.
-as the electrons interacted with the nickel crystals, they experienced scattering due to atomic arrangement, this led to a key observation, interference patterns in the scattered electrons displayed alternating white and black regions on screen behind nickel crystal, patterns were similar to those of produced by the diffraction of light waves passing through a narrow slit
*free electrons are electrons not bound to a nucleus of an atom, they are described by wave functions (are mathmatical representations that describe probability distribution of finding an electron at a particular position in space solutions to Schrödinger solution?

Question 8

***bound electron, quantum number

Question 9

*****Bohrs atomic model

Answer 9

-proposed by bills David Bohr in 1913
-assumed that electrons can occupy electron shells that have discrete values or energy states
-energy of electron is fixed at particular level and does not change unless it transitions to another level
*electrons positioned further from the nucleus have highest energy
-he proposed electrons absorb energy when they are excited from a ground state to a higher level (excited electrons have higher energy and are unstable)
-so they fall back to their ground state emitting energy in the form of photons of EM radiation
-he modelled this through an emission spectrum by investigating the hydrogen atom, however model couldn’t explain spectra of larger atoms with more complex structures
-final model was Schrödinger model based on quantum theory, electrons move by orbitals that have different shapes calling them electron clouds

Question 10

heinsenbergs uncertainty principle

Answer 10

-states one cannot know all the parameters of a particle at a given time
-the more precisely we try to measure one property in a particle, the less precisely we know its conjugate property
-the more accurately we try to determine position of a particle, the less accurately we know its momentum and vice versa
-this only applies to extremely small matter as uncertainties of ordinary objects are too small to be recognised

Question 11

physical foundations of the periodic table

Answer 11

table arrangement of all elements in order of increasing atomic number (the number of protons in that element)
-composed of:
groups (columns) - ones in the same group have the number of valence electrons so similar chemical properties
periods (rows)
-ionization across a period becomes higher as stronger electrostatic attraction but down a group becomes lower as further valence is further from the nucleus

Question 12

frank hertz experiment

Answer 12

1- a vacuum tube with an anode and a cathode is filled with mercury gas at low pressure
2-a grid is put between and and cathode
3-the cathode is heated to provide energy for electrons to leave cathode
4-the emitted accelerated electrons move towards positive grid
5-the negative voltage of the anode will slow down the electrons and only some electrons with enough energy will be able to reach anode
conclusion - energy cannot change continuously, but rather with discrete energy values called quanta so electrons can only occupy discrete energy levels

Question 13

potential energy of interatomic interactions

Answer 13

atoms and subatomic particles experience atomic interactions
-repulsion - between particles of same charge
-attraction - between parties of opposite charge
interactions between particles can be short range (effective only over short distance) or long range (effective over long distance)
-coulombic attractions will occur: electrostatic attractive forces between charged particles
the potential energy of the system is equal to the sum of the attractive and repulsive forces
*when atoms are far apart, the potential energy between them is negligible
*as the atoms come closer to each other, potential energy decreases if interaction is attractive so stable configuration
*if interaction is repulsive, potential energy increases as atoms approach each other indicating unstable or energetically unfavourable configuration

Epot → potential energy of the system
o Eattraction→contribution of the attractive forces o Erepulsion → contribution of the repulsive forces o A,B→interaction-specific constants (atom
dependent)
o n(attraction) < m(repulsion) o r: distance of atomic nuclei

Question 14

electronegativITY

Answer 14

Electronegativity is the ability of an atom to attract a shared electron pair in a covalent bond
o It increases across a period from left to right
▪ This is because the atomic number increases and so the nucleus is
more positively charged, and thus can attract negatively charged
electrons more strongly o It decreases down a group
▪ This is because the number of occupied main energy levels increases, and so there will be a greater shielding effect between the nucleus and the shared pair of electrons
- The fluorine atom → most electronegative
- Electronegativity values are important for bond polarity:
o Ionic Bond: the difference in electronegativity values between the two atoms is > 1.7 (in some resources >2.1)
o Covalent Bond:
▪ Polar Covalent→difference in electronegativity between atoms is
0 (or 0.6) < EN < 1.8 (or 2.1)
▪ Non-polar Covalent→little to no difference in electronegativity
between atoms
* Bonding electrons are shared equally

Question 15

Primary and secondary bonds

Answer 15

• Intramolecular Interactions→between atoms in a molecule/compound
• Intermolecular Interactions→between molecules or between compounds
• Primary bonds are strong intramolecular interactions
  o Ionic bonds: oppositely charged ions are held together by coulombic forces ▪ Eb>1eV
  ▪ Typically occurs between metals and non-metals
  o Metallic bonds: attraction forces between positively charged nuclei and
  delocalized electrons (multi-atomic system)
  ▪ Electrons can carry charge→metals are good electrical conductors
  o Covalent bonds: electrons are shared between two non-metals
  ▪ Non-polar covalent: electrons are shared equally between atoms ▪ Polar covalent: one atom has a stronger pull on the electrons
• Secondary bonds are generally weaker intermolecular interactions
  o Dipole-dipole interactions: between partially + and – segments (dipoles) of 2
  polar molecules→permanent dipoleso Van der Waals interaction: occurs between 2 non-polar participants where there is an induced (temporary) dipole
  ▪ Hydrophobic interactions are Van der Waals interactions → aggregation between non-polar structures to exclude polar H2O molecules
  o Hydrogen Bond: occurs between a hydrogen atom and a highly electronegative atom (N, O, F)
  ▪ Water and DNA have hydrogen bonding ▪ Considered the strongest of the
  secondary bonds

Question 16

*****Resolving power of the atomic force microscope

Question 17

The ideal gas

Answer 17

PERFECT GAS
- The features of an ideal gas:
o All particles in the gas are identical
o Volume of particles is neglected
o There is no interaction between the particles
▪ Only elastic collisions→sum of energies is constant (Ekin and momentum are conserved)
o Particle motion follows Newton’s laws
The ideal gas law is based on several key assumptions about the nature of gases:

Point Particles: Gas particles are considered to be point particles with no volume.
No Intermolecular Forces: There are no attractive or repulsive forces between gas particles.
Elastic Collisions: Collisions between gas particles, and between particles and the walls of the container, are perfectly elastic, meaning there is no loss of kinetic energy.
Random Motion: Gas particles are in constant, random motion.
Large Number of Particles: The number of gas particles is large enough that statistical averages apply.

Question 18

Maxwell boltzman velocity distribution

Answer 18

The Maxwell-Boltzmann velocity distribution describes the probability of finding particles with different velocities in an ideal gas
o In a gas, the particles are constantly moving, and they can move at different speeds
▪ The Maxwell-Boltzmann distribution tells us the chances of finding particles with different speeds
▪ The graph is usually a bell curve, with the highest point at the speed that is most likely to be observed in the gas
* This means that most particles have speeds close to the average, and fewer particles have extremely high or low speeds
o Temperature affects the speed at which the particles are moving→as particles gain kinetic energy upon increasing temperature
▪ Upon increasing the temperature, the curve will shift to the right
* This shift indicates an increase in the average velocity of the gas particles
▪ The area under the curve represents the number of molecules
* The total number of particles stays constant but the shift
indicates that more particles (from the total) have velocities closer to the new, higher average velocity
The Maxwell-Boltzmann distribution is often visualized as a curve that shows the number of particles having different speeds at a given temperature. Key points to note:

The peak of the curve corresponds to the most probable speed
v
m
p
v
mp
​
.
The area under the curve represents the total number of particles.
At higher temperatures, the curve flattens and broadens, indicating a wider range of speeds and a higher average speed.

Question 19

****Applications of the Boltzmann distribution Nernst

Answer 19

ompartments of an electrochemical concentration cell (the compartments have different concentrations of charged particles)
▪ 𝑐𝐴 → concentration of charged particles at point A
▪ 𝑐𝐵 → concentration of
charged particles at point B

Question 20

real gas

Answer 20

Particles are not point-like→have a finite size and occupy a certain volume (volume is not negligible)
o This is in contrast to the ideal gas model, where particles are considered to have negligible volume
o Consequence: the volume available for particle motion in a real gas is reduced by the volume occupied by the gas particles themselves → 𝑉 − 𝑁𝑏
▪ This reduction is represented by the term “Nb” in the equation, where “N” represents the number of gas particles and “b” represents the effective volume of each particle
- Interactions arise between the particles
o In an ideal gas, particles are assumed to have no interactions with each other
▪ However, in real gases, particles do interact due to forces such as intermolecular attraction or repulsion
o Consequence: The presence of interactions between particles in a real gas reduces the overall pressure compared to what would be expected in an ideal gas without such interactions

Question 21

**state equation of Real gases

Question 22

Application of Boltzmann Arrhenius plot

Answer 22

Boltzmann distribution can be applied to
understand the equilibrium and rate of the reaction
o Equilibrium: a state where the rates of the forward and reverse reactions are
equal, and there is no net change in the concentrations of reactants and products
▪ The Boltzmann distribution helps us understand the distribution of particles among different energy states involved in the reaction
* The equilibrium state is reached when the relative differences in energy levels between reactants and products are balanced
o Reaction Rate: refers to the speed at which the reactants are converted into products
▪ It depends on the energy barrier that needs to be overcome for the reaction to occur
▪ If the energy barrier is high (the reaction requires a large amount of energy for the molecules to transform) only a small fraction of molecules will have enough energy, and the reaction will proceed slowly
▪ On the other hand, if the energy barrier for the reaction is low, a larger fraction of molecules will possess that amount of energy, leading to a faster reaction rate
* Catalysts work by lowering the energy barrier of reactions
𝑅𝑇
- Arrhenius equation: 𝑘 = 𝐴𝑒−𝐸𝑎 →𝑙𝑛𝑘 = 𝑙𝑛𝐴 − 𝐸𝑎
𝑅𝑇
o The Arrhenius plot is a graphical representation of the relationship between the rate constant (k) of a chemical reaction and the temperature (T) at which the reaction occurs
▪ When we plot the ln(k) versus 1/T on the Arrhenius plot, we often observe a linear relationship
▪ The slope of the line represents the activation energy (Ea) of the reaction, and the intercept corresponds to the natural logarithm of the pre- exponential factor (A) in the Arrhenius equation

Question 23

macro state and microstate in thermodynamics

Question 24

A system is a portion of the universe that is the subject under study where changes in reactions occur due to varying conditions
- The system may be categorized:
o Macroscopically→macrostate characteristics
▪ Determines the state of the system as a whole
* Thermal properties→Temperature (T)
* Concentration (c)
* Volume (v)
* Pressure (p)
* Number of particles per unit volume (N/V) o Microscopically→microstate characteristics
▪ Describing the characteristics (e.g., energy) of each particle in the system at a single instant in time
* Energy * Location * Velocity
o In thermal equilibrium, the macrostates are usually constant and the microstates are changing
- Types of systems:
o Open: exchange of matter and energy between system and the surroundings o Closed: exchange of only energy between system and the surroundings
o Isolated: exchange of neither matter or energy between system and the
surroundings
▪ Diathermic: allows exchange of heat ▪ Adiabatic: no exchange of heat