Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MBB 222 > Topic 3 > Flashcards

Topic 3 Flashcards

1
Q

Intramolecular interactions

A

Atoms interacting both within the atoms

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

Intermolecular interactions

A

Atoms interact between molecules

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Covalent bonds

A
  • hold atoms together in a molecule (intramolecular)
    -formed by the sharing of electrons between atoms
  • strong bonds
    -short length
  • typical C-C bond distance is 1.54A
  • typical C-C bond energy is 357kJ/mol
  • the most stable of bonds
  • each atom type forms a characteristic number of covalent bonds with other atoms, depending on the number of free (bonding) electrons in the outer orbital
  • elements like N and O also have non-bonding electron pairs or “lone pairs”
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Noncovalent interactions

A
  • weaker, readily reversible - require 1-30 kJ.mol to break
  • distances between atoms is greater
  • intramolecular or intermolecular
    1. Hydrogen bond (weak forces)
    2. Electrostatic interaction (salt bridges)
    3. Van der Waals interaction
    4. Hydrophobic interaction (forcing water to be more disordered in system)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Bond energy

A
  • the amount of energy required to break a chemical bond (As well as the energy released when the bond is formed)
  • can be measure/reported in kJ/mol, kcal/mol
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What do covalent bonds hold together?

A

-hold atoms together in building blocks
- hold building blocks together in proteins and nuclei acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Phosphodiester Bonds

A
  • specialized covalent bond within molecules that hold phosphates together
  • also hold nucleotides together in DNA/RNA strands
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

glycosidic bond

A

Joins the ribose to the base in ATP

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Peptide bonds

A
  • covalent bonds that hold amino acids together in polypeptide or protein
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Disulfide bonds (disulfide bridges)

A
  • covalent bonds between thiol groups on the side chains of the amino acid cysteine that hold different parts of the polypeptide backbone together
  • stabilize the protein fold (usually most interactions that stabilize a protein fold are non-covalent)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

Weak chemical interactions

A
  • ie. non-covalent bonds
  • stabilize the fold of proteins
  • Hold DNA duplexes together
  • induce folding of RNA
  • bring macromolecules together for structures, reactions
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Weak bonds:

A
  • break and reform at room temp - are transient
  • require much less energy to break than fo covalent bonds
  • thermal energy at room temp = ~2.5 kJ/mol so weak bonds can be broken due to thermal motion
  • are crucial for most cellular processes ie DNA replication, protein folding, protein-protein interactions
  • transient interactions allow for very dynamic systems
  • individually these bonds are weak, but all together can be very strong
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Hydrogen Bonds

A
  • from between a H atom covalently attached to an electronegative atom ( a hydrogen bond donor, usually O or N) and a second electronegative atom that serves as H bond acceptor
  • the H-bond forms between the hydrogen atom on the donor and a lone electron pair on the acceptor
  • bond energies range from ~10 - 30 kJ/mol - strongest of the weak non-covalently interactions
  • the length of a H-bond is measured form the atom centres of the donor and the acceptor (~3A)
  • H-bonds have directional property - won’t form if atoms aren’t oriented properly (in line with non-bonding electrons on acceptor atom)
  • requiring a H bond donor and acceptor so are more specific than van der Waals bonds
  • a H-bond is partially covalent bond
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Hydrogen bonding in macro molecular structures

A
  • Example can be seen in proteins within the polypeptide backbone
  • H-bonds along the backbone hold the polypeptide in an helical conformation
  • such interactions are essential for protein folding
  • H-bonds hold bases together in duplex DNA, folded RNA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the key to water’s properties?

A
  • hydrogen bonds are key to water’s properties and this role as a solvent
  • water is highly polar: electrons are not shared equally between H and O in the covalent H-O bonds
  • electronegative O pulls the electrons toward it, giving it a partial negative charge and giving the H’s partial positive charge
  • the O has two lone pairs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What makes water different when compared to other solvents?

A
  • has a very high melting point, boiling point and heat of vaporization compared to other solvents
  • due to the hydrogen-bonding tendency which hold the molecules together requiring significant energy input to separate them
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What does each water molecule have in ice?

A

The potential to H-bond to 4 other water molecules
- one for each hydrogen, two for each oxygen (one for each lone pair) to create a crystal lattice

18
Q

Is water a solvent?

A

Yes
- is highly polar, thus an excellent solvent for ionic and nonionic-but-polar compounds
- water hydrates ions by electrostatic interactions

19
Q

Dipole interactions

A

its partially positivity-charges Hs interact with negatively-charged ions, its partially negatively-charges O’s interact with positively-charged ions

20
Q

The ability of water to hydrate ions is ______ than tendency to opposite ions to attract one another

A

Greater

21
Q

Dielectric constant, D

A
  • the ability of a solvent to interact with a solute and decrease the electrostatic interactions between ions is a measure of its dielectric constant, D
  • a measure is the ability of a solvent to surround ions in dipole interactions, diminishing their attraction to another
  • the greater is is, then lower that force between two charges in that particular solvent
22
Q

How can water solubilize polar compounds?

A

By forming H-bonds with these solutes

23
Q

What does water form around ions, proteins, and other macromolecules?

A

Hydration spheres

24
Q

Hydrophilic

A

Love water

25
Q

Why does water have one of the highest dielectric constants of any pure liquid?

A

Due to its polar nature

26
Q

How do D constants indicate the reduction in attraction?

A
  • indicate the reduction in attraction between two oppositely-charged ions in a given solvent relative to heir attraction in vacuum
27
Q

Electrostatic interactions

A
  • transient electrostatic interactions between opposite charges
  • also called an ionic bond or a salt bridge
  • electrostatic interactions between charged amino acid side chains contribute to stabilizing a protein structure
  • specific interaction -> amino acid sequence drives protein folding
28
Q

What does the attraction between two charged species depend on?

A

The nature (ie charge) of interacting species, q1 and q2, and the distance, r, between them

29
Q

Coulomb’s Law

A

The energy of an electrostatic interaction between two point charges is directly proportional to the magnitudes of each charge and inversely proportional to the distance between the charges

30
Q

The strong the energy of the interaction is when

A

The larger the (opposite charges) and the smaller the distance

31
Q

What is also effected by the solvent, hence the D constant

A

Energy

32
Q

Van der Waals

A
  • include all intermolecular forces that act between electrically neutral molecules
  • create interactions that are constantly forming and breaking at physiological temperatures in less their cumulative number imparts stability by collective action (ie in the case of hydrogen bonding and base stacking to hold the DNA duplex together)
  • exist because the electron cloud of every atom fluctuates, yielding a transient electric dipole
33
Q

Transient dipole

A
  • the dipoles of one atom can influence the electron distribution in another, inducing a transient dipole in that atom
34
Q

Dipole interactions - permanent dipoles

A
  • polar molecules interact weakly with negative poles attracted to positive poles
  • H-bonds are a specialized type of dipole-dipole interaction
35
Q

Dipole-induced dipole interactions

A

A permanent dipole (or a charged group) can induce a dipole in a neighbouring group that’s neutral by distorting its electron distribution

36
Q

London dispersion forces

A
  • nonpolar groups can polarize electrons in a neighbouring group due to rapid fluctuation of their electron -> attraction
  • extremely weak, transient, fall off rapidly with distance
37
Q

What are van der Waals forces?

A
  • the same of dipole-dipole attraction and repulsion
38
Q

Van der Waals contact distance

A
  • the attraction between the two atoms increase as r between the atoms decreases until they each optimal distance (van der Waals contact distance)
  • at this distance the attractive forces are highest
  • if atoms get closer than this optimal distance they will repel each other due to overlap between their electron clouds
    -rw = 0.5r
  • r is longer than ac valent bond radius where orbitals overlap in a covalent bond radius
  • each atoms has one that reflects the volume the atom -neutron, protons, electrons- occupies
39
Q

Hydrophobic interactions

A
  • not a true force but a consequence of the energy needed to insert a nonpolar molecule unto water
  • water naturally forms a hydrogen bond network
  • these bonds must be broken in order to insert nonpolar molecules
  • nonpolar molecules form can der Waals interactions among themselves and do not H-bond with water - difficult to solvate/solubilize
  • dissolving such nonpolar solutes requires organization of water molecules which surround them, resulting in cage-like structures known as clathrates
  • this ordered arrangement of water molecules around each hydrophobic molecule is thermodynamically unfavourable - when the hydrophobic molecules associate with each other, this liberates part of the hydration shell, increasing the entropy (disorder) of the system, which is thermodynamically favorable
40
Q

clathrates

A

Structure in which water molecules under certain conditions bond to form complex networks of molecules forming cage-like structures that encapsulate a guest molecule, which is a gas

41
Q

Hydrophobic effect

A
  • the attraction between non-polar molecules in an aqueous environment
  • not so much an attraction but a default to a lower energy state
  • draws non-polar molecules together in aqueous solution
  • nonpolar molecules spontaneously aggregate in an aqueous solution, reducing the number of H2O molecules involved in ordered clathrate structures, thereby, increasing the disorder or entropy of the system -> more favourable situation energetically
42
Q

Protein folding

A
  • driven in part by the hydrophobic effect
  • in unfolded protein nonpolar or hydrophobic regions are exposed to water, which much organize inter self around them
  • in folded protein hydrophobic regions often associate with each other and are thus shielded from the aqueous solvent
  • less order is required for the water molecules to solubilize the protein, which is more favourable energetically
  • thus, protein folding occurs because a orderly folded protein is more thermodynamically stable than an unfolded protein in aqueous solution

MBB 222 (5 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions