Week 2 - Biochemical bonds, Free energy, and biochemical reactions

Question 1

Different forms of chemical bonds

Answer 1

1

Question 2

concept of free energy

Answer 2

1

Question 3

chemical reactions involve changes in free energy

Answer 3

1

Question 4

ATP is the main source of energy in cells

Answer 4

1

Question 5

Chemical bond?

Answer 5

attraction between atoms brought about by a sharing of electrons or a complete transfer of electrons between atoms

Question 6

in aqueous solutions: strong bonds

Answer 6

covalent bond

Question 7

in aqueous solutions: weak bonds

Answer 7

ionic bond
hydrogen bond
van der waals interaction
hydrophobic interaction

Question 8

covalent bond

Answer 8

strong bonds
short
hold atoms close together
sharing of an electron pair (or multiple)
valence of an atom determines the number of covalent bonds it can form

Question 9

covalent bonds and electrical polarity

Answer 9

polar; differences in electronegativity between two atoms bonded together; electrical dipole(polar bond); unequal sharing

non-polar; equal sharing

Question 10

Covalent bond and rotation

Answer 10

single; allow rotation

double and triple; do not allow freedom of rotation

Question 11

geometry of molecule; covalent bond

Answer 11

number and types of bonds determine the geometry of molecule

- bond angles determined to minimize the proximity of different atoms’ electrons to each other

Question 12

non-covalent bond

Answer 12

ionic bond
hydrogen bond
hydrophobic interaction
van der waals attraction

Question 13

ionic bond

Answer 13

electrostatic attraction between ions;
strongest of non-covalent interactions
dissociate in solution
* ionic bond very strong unless put in water
* weak acid and base are very strong bonded

Question 14

hydrogen bond

Answer 14

formed between electronegative atom (N,O) and hydrogen atom (covalently attached to another atom; N,O)
stabilize biological molecules

• H+ covalently bonded to Carbon will NOT participate in hydrogen bond
• There is ONE hydrogen atom in a hydrogen bond

Question 15

hydrophobic interaction

Answer 15

between hydrophobic molecules because they are repelled by water; between non-polar molecules

Question 16

van der waals attraction

Answer 16

between all molecules as a result of permanent and transient dipoles (unequal distribution of electrons); random fluctuation induced transient dipoles
very weak force
non-specific attractive force
* 10A=weak van der Waals
* 5A = very strong attraction
* 4A = balanced by repulsive forces, owing to interpenetration of outer electron shells

Question 17

pH dependent carboxyl group charge (ionization state)

Answer 17

depending on the pH of the solution,
acidic and basic groups may be protonated or deprotonated
* pH = measure of the [H+]
at its pKa, concentration of the two forms will be equal and there will be no net charge

Question 18

Water and hydrogen bonding lattice

Answer 18

crystal molecules in regular fashion; tetrahedron; 육각수

Question 19

multiple weak bonds

Answer 19

stabilize associations between macromolecules;
surface complementary
stable and less stable complex

Question 20

specific interaction

Answer 20

complementary molecular surfaces
lock and key model; substrate has a fit shape
antibody-antigen interaction
enzyme and substrate complex

Question 21

making and breaking chemical bonds, and energy

Answer 21

making - consume energy
breaking - release energy

strong bond - harder/ greater E
weaker bond - easier/ lesser E

Question 22

free energy; G

Answer 22

amount of energy available for atoms and molecules to do work; ex. thermal energy
can interconvert between thermal energy (kinetic) and bond energy (potential)

Question 23

delta G determine direction of chemical reaction

Answer 23

A+B -><0 is spontaneous; toward product

delta G = 0 is at equilibrium

Question 24

activation energy

Answer 24

required for initiation of a reaction
leads to activated state
lowered by enzyme

Question 25

ATP

Answer 25

adenosine triphosphate
main cellular energy source; phosphate and adenylate donor; building block in RNA; precursor of dATP; majorallosteric regulator of proteins

adenine + rybose + 3 phosphate

Question 26

ATP hydrolysis

Answer 26

phosphoanhydride bonds
provides much of the free energy
energy used in many enzymatic reactions

Question 27

DNA

Answer 27

deoxynucleotide = phosphoric acid, 2’ deoxyribose, base

2 condensation reactions

Question 28

neucleic acid synthesis

Answer 28

Hydrolysis of high energy phosphate bonds

* P-P : pyrophosphate