bellipanni biochem exam 1

The theory of Oparin and Haldene of the primordial soup referring to the molecular evolution, was somehow confirmed by an experiment where scientists exposed C, H, O and N dissolved in water to extreme temperature, pH and energy and obtained__________

amino acids

Given that ΔG = ΔH - TΔS, under what condition is a reaction spontaneous only at temperatures that are below T = ΔH / ΔS?

- ΔS and – ΔH

T/F: The second law of thermodynamics does tell us what is the favored direction of a reaction

True

What happens to a living system when it reaches equilibrium with the environment?

It is dead

At constant pressure H is circa equal to _________

q

What general trait of cellular architecture allows for cellular protection, as well as storage of molecules and energy? 

Compartmentation

Which of the following is a correct statement about entropy?

Entropy is a measure of the disorder or randomness of a system

What does the first law of thermodynamics state?

Energy can neither be created nor destroyed

T/F: The hydrophobic effect mechanisms we studied is telling us that interactions between hydrophobic molecules are determined by a thermodynamic event of the surrounding hydrophilic environment (water-based solution) that tend to maximize its entropy S.

True

Water molecules are ______ because_________:

Polar because they have two free Sp3 orbitals that are partially negatively charged

Ionic-bond interactions are weaker than a ____________ but stronger than a   ______________

covalent bond/H- bond

Why weak interactions like H-bonds may have a biological effect like dissolving NaCl in water?

they are many and overcome the energy of interaction of the other bonds

What is biochemistry?

Biochemistry is the study of chemistry of living organisms

What relationship does biochemistry help us to understand?

the relationship between the structures of the molecules and their functions.

Where do biological molecules arise from?

Inorganic material

What is the most abundant and central element of our chemistry?

Carbon

Name the 4 most abundant elements in our body.

C (61.7%), N (11.0%), O (9.3%), H (5.7%)

What are some other less abundant, but present, elements in our body?

Ca (5.0%), P (3.3%), K (1.3%), S (1.0%), Cl (0.7%), Na (0.7%), Mg (0.3%)

What are covalent bonds, and how do they occur?

Covalent bonds are the forces that hold atoms together as molecules. A covalent bond occurs when two atoms share pairs of electrons.

What kind of bond holds the 2 O-H bonds in a water molecule together?

Covalent bond

What is the basic structure of a nucleotide?

a nitrogenous base (A, T, C, G), a pentose sugar, (ribose or deoxyribose), and a phosphate group

What is the basic structure of an amino acid?

An alpha-carbon, amino (-NH2) group, carboxyl (-COOH) group, a hydrogen (-H) atom, and an R-group (side chain)

What is the basic structure of a lipid?

A hydrophobic composition of carbon, hydrogen, and oxygen

What is the basic structure of a carbohydrate?

A composition of carbon, hydrogen, and oxygen following the CnH2nOn ratio

What is the convenience of compartmentation?

protection to adverse environment, ability to concentrate compounds, store energy

How do eukaryotes and prokaryotes differ in compartmentation?

Eukaryotes utilize membrane-bound organelles, whereas prokaryotes do not and keep most components free-floating in the cytoplasm

What was the shape of the first-living organisms?

Bacteria-like

Oparin-Haldane hypothesis

Inorganic molecules combined to form organic monomers, which accumulated in “the primordial soup” to make longer polymers. Then they developed primitive metabolic processes, becoming the first living organisms.

The Miller-Urey Experiment

Simulated the ancient water cycle and atmosphere to reveal that amino acids and other simple organic compounds developed from inorganic precursors.

Polymers

molecules formed by end-to-end combination of smaller units

How are polymers formed?

by repeated condensation reactions

How can the chemical versatility of a single large molecule increase?

Combination of multiple functional groups

What can electrostatic interactions lead to?

association of complementary molecules

Of the 4 major classes of biomolecules, which are not considered polymers?

lipids

What 3 things does the strength of association of ionic groups of opposite charges depend on?

1. the chemical nature of ions

2. the distance between them

3. The polarity of the medium

Where do Van der Waals forces arise from?

electrostatic interactions among permanent or induced dipoles

Dipole-dipole interactions are ________ than dipole-dipole-induced interactions

stronger

What kind of molecules have a small randomly oriented dipole moment?

Nonpolar molecules

What does the dipole moment result from?

the rapid fluctuating motion of their electrons

Where does London dispersion forces originate from?

from the transient dipole moment of nonpolar molecules that polarize the electrons in a neighboring group so that the groups are attracted to each other

1st law of thermodynamics

Energy cannot be created or destroyed, only changed from one form to another.

2nd law of thermodynamics

The entropy (disorder or spread of energy) of an isolated system always increases over time.

According to the 2nd law, how do organisms achieve order?

by breaking down the nutrients

Organisms ingest _____ S and ____ H nutrients and produce ____ H and ____ S waste with release of G

low, high, low, high

How are enzymes and ΔG related?

Enzymes accelerate biochemical reactions (catalyze) but can not promote reactions whose ΔG values are positive

isolated system

closed system

open system

variation of state function

ΔU= UF - UI

What does ΔU depend on in a closed system?

q (heat absorbed) and w (work done)
ΔU = q - w

What does work (w) equal when a system is in constant pressure?

PΔV

(P = pressure, V = volume)

What is Δq in a constant pressure reaction?

Becomes new quantity, H

H = U + PV

What happens to ΔH when the pressure of a system changes?

Equals q

What can the 1st law of thermodynamics do AND not do?

The first law of thermodynamics lets us determine if a reaction is possible or

impossible. It does not let us determine what is the favorable direction of a reaction nor if it is reversible or not

What is the equation for entropy (S)?

S= kB ln W

(kB = Boltzmann constant; W = the number of energetically equivalent ways of arranging the components of a system)

What changes in a system tend to make a process more favorable?

A decrease in energy (-ΔH) and/or an increase i n entropy (+ΔS)

For a reaction to be spontaneous when both ΔH and ΔS are positive, T must be…

high

For a reaction to be spontaneous when both ΔH and ΔS are negative, T must be…

low

In a hydrogen bond:

D-H……A

D is a _______ and A is a _______

weak acidic “donor” group, weak basic “acceptor” atom

How many other molecules of water can one water molecule interact with?

4

What is formed in ice?

6-membered rings

Why does water expand on freezing?

the rigid position of each atom increases the volume and therefore make ice floating on water

What is formed in liquid water?

Three- to seven-membered rings

What are some of the consequences of the extensive hydrogen-bonded network of water?

1. High boiling point

2. High heat of vaporization

3. High viscosity

4. High surface tension

5. High dielectric constant

What does solubility depend on?

the ability of a solvent to interact with a solute more strongly than the solute particles interact with each other

The Hydrophobic Effect

the tendency of water to minimize its contact with hydrophobic molecules

How do water molecules maximize their number of hydrogen bonds?

they form a “cage” around the nonpolar solute. Thus, water molecules are more “ordered” when a nonpolar solute is dissolved in them.

Where, between a and b, water has more entropy?

b; In diagram (a), water molecules must form highly ordered, rigid "cages" around each separate nonpolar molecule. This restricted movement decreases the entropy of the water. Since water needs fewer molecules to cage the big drop in b, its entropy S increases so ΔS is positive

what is the entropy of water in a glass that has no oil, compared to these 2?

The highest entropy of all

Why do non-polar solutes tend to aggregate when dissolved in polar solvent?

The sum of 5 small drops = x; the surface of one single large drop < x. Thus, water uses less molecules to cage one single large oil drop

What kind of structures do amphipathic molecules tend to form in water?

ordered structures called micelles and bilayers.

What is a colligative property, and what is the big one we need to know?

physical properties that depend on the concentration of dissolved substances rather than on their chemical features; osmosis

osmosis

the movement of solvent, water in this example, from a region where it is highly concentrated (water in water) to a region of relatively low concentration (water + solute).

osmotic pressure

the pressure that must be applied to the solution to prevent the inward flow of water, and it is proportional to the concentration of the solute

How do living organisms overcome the problem of osmosis?

1. Surrounding the cells with liquids at similar osmotic

   pressure

2. Enveloping cell membranes with rigid cell walls (plants

   and bacteria)

diffusion

the random movements of solutes within a solvent

What is the basis for the laboratory technique of dialysis?

Diffusion of solutes

The equilibrium constant of a reaction: 

Is related to the change in standard free energy of the reaction.

Which of the following is the function of a buffer in a biological system?

To maintain a stable pH level

What is the primary function of ATP in living cells?

To provide energy for chemical reactions

Base staking interactions are:

combination of hydrophobic and van der Waals interactions

What is one function of topoisomerase?

To relieve tension caused by DNA supercoiling

When we consider a weak acid and the Handerson-hasselback equation, if  [A-] = [HA], then....

pk = pH

What is/are the differences between ΔG and ΔG ^'0 ? 

ΔG is a function of concentration of products and reactants while ΔG^'0 is a constant

For the generic reaction aA + bB —>cC + dD  you can calculate the mass action Q at time (i) by:

Q_i = [C]^c_i [D]^d_i / [A]^a_i [B]^b_i

Why weak interactions like those between water molecules and ions may have a biological effect like dissolving NaCl in water?

they are many and overcome the energy of interaction of the other bonds

How many molecules of water interact with a molecule of ethanol?

3

What is the purpose of DNA ligase in molecular cloning?

To ligate or join DNA fragments with a plasmid DNA

After double strand DNA denaturation by heat, DNA could spontaneously renaturate in its double strand conformation if____

If we let the sample to reach room temperature very slowly

In order to visualize DNA in a gel we use (add in the gel or samples)

Ethidium bromide

In CRISPR/Cas9 genome editing, what guides Cas9 to a specific DNA sequence?

A single-stranded RNA molecule

The denaturation of DNA by increasing temperature describes a sigmoidal curve, this indicates that this process is

Cooperative

Which atoms do purines form their bonds to a 5-carbon sugar?

N9

Which atoms do pyrimidines form their bonds to a 5-carbon sugar?

N1

In a ribonucleotide or in a deoxyribonucleotide one or more phosphate groups are bonded to atom ___ or ___

C3’, C5

What is it called when a phosphate group is absent from a ribo/deoxyribonucleotide

nucleoside

How is the energy potential of ATP is made available?

when one or two of its phosphate groups are transferred into another molecule

How does ATP provide energy for cellular work?

ATP diffuses through the cells via ATP hydrolysis in ADP

What explains the high free energies of ATP hydrolysis?

1. resonance stability of the phosphate products

2. electrostatic repulsion between charged products

3. additional hydration of the hydrolysis products

4. pH and ionic strength of the solutions

Describe RNA structures

They are chains of nucleotides whose phosphates bridge the 3’ and 5’ position of neighboring ribose units