Week 2 - Molecular Forces

Question 1

What is a covalent bond?

Answer 1

when two atoms with unfilled electronic shells overlap, increasing the electron density, and forming a bond.

Question 2

Is H+ or H2 more stable? and why?

Answer 2

H2 because it is covalently bonded with itself to make it nonpolar, therefor strengthening its stature among other molecules.

Question 3

What is hydrogen bonding?

Answer 3

The force of attraction between a hydrogen atom in one molecule and a small atom of high electronegativity in another molecule; O, F, N.

Question 4

Is hydrogen a proton donor?

Answer 4

Yes

Question 5

What is Ionic bonding?

Answer 5

When atoms of opposite ionic charge attract each other by donating or receiving electrons (E.g. Na and Cl to form NaCl (sodium chloride)).

Question 6

What is a polar covalent bond?

Answer 6

Where the pair of electrons is shared unequally between two attoms. - H2O: The electrons are unequally shared, with the oxygen atom spending more time with the electrons than the hydrogen atom.

Question 7

What does the term dipole mean?

Answer 7

Dipoles occur when two atoms in a molecule have different electronegativity

Question 8

What are Dipole-Dipole forces?

Answer 8

Dipole‐dipole forces are attractive forces between the positive end of one polar molecule and the negative end of another polar molecule.

Question 9

What type of interaction does a hydrogen bond contain?

Answer 9

A hydrogen bond can be considered to be a type of dipole‐dipole interaction.

Question 10

What are Van Der Waals forces?

Answer 10

These are weak forces between atoms and/or molecules that can either be attractive or repulsive.

Question 11

What are Hydrophobic interactions?

Answer 11

Hydrophobic interaction involves bulk water molecules excluding non-polar molecules and is an affect of an increase in entropy rather than an effect of enthalpy.

Hydrophobic forces in combination with dispersion forces keep non-polar molecules together in water but a separate phase may form

Question 12

What are some Biochemical examples of hydrophobic interactions?

Answer 12

• Cell membranes - Protein folding - Insertion of membrane proteins into the nonpolar lipid environment

Question 13

What is an Ion-Induced dipole attraction?

Answer 13

When a permanent charge, or other dipole, induces polarization in another molecule. Results in electrostatic attraction between the permanent charge and the partial charges induced in the other molecules.

Question 14

What type of interaction occurs between H and Cl?

Answer 14

Dipole-Dipole interaction, the positive end of the Hydrogen atom attracts the negative end of the Chlorine atom and influences the position.

Question 15

Why do atoms or molecules interact?

Answer 15

Electrons distribute, and rearrange, within atomic and molecular orbitals to maintain a combination of the lowest possible potential energy and greatest dispersion of energy. This leads to greater stability.

Question 16

Ethane is an example of what type of interaction?

Answer 16

A Covalent interaction

Question 17

Why are covalent bonds important in biomolecules?

Answer 17

Essential in forming biomolecules and form the polymer ‘backbones’ of macromolecules from monomer units.

Question 18

What is an Isomer?

Answer 18

Two or more compounds with the same formula but a different arrangement of atoms in the molecule and different properties.

Question 19

What would be meant if a carbon was chiral?

Answer 19

That the Carbon was attached to 4 different groups. If you were to draw a mirror image of the molecule and it is the same, it would be ACHIRAL if it was different, it would be CHIRAL

Question 20

What is a stereoisomer?

Answer 20

2 or more molecules that have the same chemical formula, the same connections, BUT the three dimensional configuration is different.

Question 21

What are geometric (Cis-Trans) Isomers?

Answer 21

Double or triple bonds that prevent or restrict rotation of functional groups or hydrogen atoms around the bond. - Cis configuration: Functional groups and hydrogen atoms are of the same side of the double bond respectively. - Trans Configuration: Functional groups and hydrogen atoms are on opposite sides of the double bond respectively.

Question 22

What are Chiral Isomers (enantiomers)?

Answer 22

• have a Non superimposable mirror image. - 4 Different types of atoms attached to the carbon atom - Same chemical properties but a difference in interactions.

Question 23

Why are chiral isomers important?

Answer 23

Many interactions in biochemistry are stereospecific. For example: - Enzyme to substrate - Protein to Ligand Stereoisomers can elicit different biological responses.

Question 24

What is the relationship between Stereoisomers and Configuration?

Answer 24

• A sterioisomer defines a particular configuration of the atoms. - Can only convert from one arrangement to another by breaking one or more covalent bonds.

Question 25

What is Conformational Isomerism (Conformation)?

Answer 25

A form of stereoisomerism in which the isomers can be interconverted exclusively by ROTATIONS about formally SINGLE bonds.

Question 26

What is polarity?

Answer 26

• An unequal distribution of electrons that causes slight differences in charge over throughout the molecule.

Question 27

How is a dipole indicated between two atoms?

Answer 27

With an arrow pointing FROM the positive charge TOWARDS the negative charge.

Question 28

What is a molecule with a permanent dipole moment known as?

Answer 28

A polar molecule.

Question 29

How are permanent dipoles formed?

Answer 29

When there is a large difference in electronegativity between two atoms bonded together in a covalent bond. This causes the shared pair of electrons to be shared unequally. They are pulled towards the more electronegative atom.

Question 30

True or False: Not all molecules that contain a polar bond are polar

Answer 30

True: They can be overall non-polar. Generally, a molecule needs to be asymmetric to have a dipole.

Question 31

Are hydrocarbons polar or non-polar?

Answer 31

hydrocarbons are non polar. This is due to the hydrogen that is covalently bound to the carbon being non polar.

Question 32

what are the two different types of Van Der Waals forces?

Answer 32

Repulsion interactions and dipole interactions

Question 33

List the 4 main characteristics of covalent interactions

Answer 33

• Effective at small internuclear distances less than 2Å (2 angstrom = 0.2nm) - Electron clouds overlap, exchange, or share electrons between two particular atoms - Mainly intramolecular - Higher bond energy

Question 34

List the 4 main characteristics of non-covalent interactions

Answer 34

• Effective up to 10Å or more but increases in strength at small distances between molecules - Little or no overlap, exchange, or sharing electrons between atoms - Mainly intermolecular - Lower bond energy

Question 35

What is the “rough” strength of the bonds in kJ/mol for Non-Covalent, Ionic and Covalent bonds?

Answer 35

• Non-Covalent: between about 350 and 400kJ/mol - Ionic: About 250kJ/mol - Non-Covalent: Hydrogen bonds ~ 20, Dispersion ~ 2, and Dipole-Dipole ~ 2 (kJ/mol)

Question 36

how are non-covalent bond interactions important when it comes to DNA?

Answer 36

Non-Covalent hydrogen bonds are important for helix base pairing in the DNA double helix.

Question 37

How can Non-Covalent interactions be strong?

Answer 37

In quantity lots of non-covalent molecules can be collectively strong.

Question 38

Do non-polar molecules increase or decrease macromolecular flexibility?

Answer 38

Increase

Question 39

What does the term “Salt bridge” mean?

Answer 39

The attractive interaction between oppositely charged amino acids in a protein structure

Question 40

How do you calculate the attractive or repulsive force between 2 charged atoms?

Answer 40

By using the Coulombs law equation: F = k q(one)q(two) / r^2

Question 41

What is does Coulomb’s law calculate?

Answer 41

How strong the force will be between two electrostatic charges

Question 42

what is the van der waal radius?

Answer 42

Van der Waals radii is the closest distance of approach for another atom with an atom (without electron clouds overlapping)

Question 43

What happens to the van der waal radii in a covalent bond?

Answer 43

They overlap

Question 44

What are dispersion forces?

Answer 44

weak Temporary attractions due to opposite charges induced in each molecule over relatively short distances

Question 45

How are dispersion forces influenced?

Answer 45

• Shape of the molecule (E.g regular or planar shapes have greater dispersion forces due to more contact points) - Size of the molecule (E.g. Large molecules have more contact points than smaller molecules)

Question 46

What is repulsion?

Answer 46

Electrostatic repulsion between molecules that prevents them from getting too close to each other

Question 47

What is interaction is being demonstrated here?

Answer 47

Ion-Induced Dipole interaction; the Fe2+ molecule is a positive ion inducing the polerization (distortion of the electron cloud) of the O2 (nonpolar) molecule.

Question 48

What interactions are being demonstrated by the blue dashes?

Answer 48

Hydrogen bonding