Biochem thermo

Question 1

Primary source of protein stability

Answer 1

Hydrophobic interactions (H bond v important structural elements)

Question 2

Entropic forces involved in dimerization

Answer 2

Conformational entropy (freedom to move) +, hydrophobic effect and hydrogen bonding (-)

Question 3

What is ionization process influenced by

Answer 3

Special structural features of the protein (G intrinsic)
The charge of the protein created by other ionizable groups (G interaction)

Question 4

Ways to unfold a protein

Answer 4

Temperature, pH, chemical denaturant (acid, base, urea), enzyme

Question 5

Most common method for protein unfolding monitoring

Answer 5

Circular dichroism (abs spectroscopy method in the UV).

Question 6

What forces are at play in base stacking

Answer 6

pi electron interactions and hydrophobic interactions (water is most favorable solvent for stacking)

Question 7

Do all base pairs melt at same temp

Answer 7

No, AT has 2 bonds, GC 3
AT melts at lower temperatures

Question 8

What is RNA

Answer 8

A linear polymer made of four different types of nucleotide subunits linked together by phosphodiester bonds with several biological functions

Question 9

What is ELISA

Answer 9

The Enzyme-linked immunosorbent assay to quantify biological substances such as protein, antibodies, and hormones.

Question 10

PCR def

Answer 10

The Polymerase Chain Reaction molecular biological technique (to produce thousands to millions of copies of a particular DNA fragment).

Question 11

DNA rep

Answer 11

The biological process responsible for the synthesis of two identical copies of DNA from one copy.

Question 12

Steps in DNA replication

Answer 12

Initiation
Elongation
Termination

Question 13

Hess’s Law

Answer 13

the heat absorbed or evolved in a given reaction must always be constant
and independent of the manner in which the reaction takes place

Question 14

Standard-state free energy of formation

Answer 14

change in free energy that occurs when a compound is formed from its elements in their most thermodynamically stable states at standard-state conditions

(difference between free energy of a substance and the free energies of its constituents at standard-state conditions)

Question 15

Standard state conditions

Answer 15

1 M, 1 atm, 298 K, pH = 7

Question 16

Exergy

Answer 16

available energy to do work

State-condition

System in equilibrium with environment -> exergy = 0 (no useful work can be obtained)

Question 17

Catabolic reactions

Answer 17

Breakdown complex and higher E molecules into smaller ones
Release free E

Can be used to drive less favorable reactions

Question 18

Anabolic reactions

Answer 18

Energy consumed to build complex molecules (take up free E)
Ex: synthesis of proteins

Question 19

How can an unfavorable rxn be coupled with a favorable one

Answer 19

Enzymes directly couple energetically favorable rxns which release E and produce heat to unfavorable ones which produce biological order

Question 20

Enzyme

Answer 20

Protein that facilitates cellular metabolic processes by lower the activation energy levels to catalyze the chem rxns between biomolecules

Question 21

Activated carriers

Answer 21

Store E in easily exchangeable form as transferable chemical groups or electron at high E

They can be a source of E and chemical groups in biosynthetic reactions

-> coenzymes (ATP, NADH, NADPH)

Question 22

Phosphorylation of glucose by ATP

Answer 22

Phosphoryl group (PO32-) transfered from ATP to glu
Catalyzed by hexokinase
Unfavorable
Uses ATP ( -> ADP highly favorable rxn that releases E)

Question 23

Hydrolysis of ATP

Answer 23

ATP -> ADP highly favorable rxn that releases E

Question 24

Metabolic cycles

Answer 24

Metabolism = many sets of reaction to produce v specific molecules

rxns are coupled in that the product of one rxn = the reactant for the next reaction in the cycle

Question 25

Anaerobic glycolysis

Answer 25

Metabolic pathway that metabolizes glucose into lactate and produces ATP when limited O2 available

Question 26

Ionic strength

Answer 26

measure of salt concentration including all the ions present in a solution

Question 27

Membrane potential

Answer 27

Produces favorable gibbs energy for transport of K+ and unfavorable for transport of Na+ Membrane more permeable to K+ than to Na+

Question 28

Proteins

Answer 28

one or more polypeptide chain consisting of amino acids (side chains polar or nonpolar) whose sequence is coded from DNA

Question 29

Non polar groups of proteins

Answer 29

AA side chains containing methylene and methyl groups and aromatic residues

Question 30

Why does dissolving non polar protein in water correspond to positive gibbs

Answer 30

Enthalpy change is favorable but negative entropy change Normal water structure broken apart, ice-like structures form around HC, decreasing disorder

Question 31

Zwitterion

Answer 31

positive and negative charges in the same molecule

Question 32

Hydrophobicity of protein

Answer 32

Non-polar side chains prefer nonaqueous environment, so they aggregate in the interior of the protein

Question 33

Ionization entropy source

Answer 33

Negative entropy due to ordering of the water molecules around the ions Thermally neutral (enthalpy changes related to solvation of ions = enthalpic change due to breaking oxygen-hydrogen bonds)

Question 34

How do charged groups influence structure (pH)

Answer 34

High pH : negative charge interactions cause native structure to disappear Low pH: positive charge interactions cause disruption of native structure Salt linkage between opposite charge groups stabilize structure

Question 35

What is positive entropy and enthalpy due to in ionization

Answer 35

Positive entropy is due to the release of water of hydration of the ions when the ion pair is formed Positive enthalpy is a balance between negative enthalpy change from bringing the charges closer and positive enthalpy change associated with removing the hydration shell. The strength of the ion pair interactions will increase with temperature.

Question 36

Denaturation

Answer 36

Process where a structured biologically active molecule called the native form unfolds or becomes unstructured and biologically inactive

Question 37

Nucleotides

Answer 37

Subunits of nucleic acids 1. five C sugar (desoxyribose) 2. Nitrogen containing base ring (pyrimidine single ring T U C or purine - > double ring A, G)

Question 38

Why is H-bonding between bases (in DNA) in water solution weaker than in organic solvents

Answer 38

Competition for H-bond formation with water

Question 39

RNA

Answer 39

linear polymer made of four different types of nucleotide subunits linked together by phosphodiester bonds with fcts in bio systems

Question 40

What interactions determine RNA structure

Answer 40

hydrogen bonding between bases, stacking interactions, hydrophobic interactions