Exam 1 Biochem

Question 1

Transcription

Answer 1

DNA copied into complementary RNA

Question 2

Translation

Answer 2

Adding nucleotides to ribosomes to grow polypeptide chain

Question 3

Most common essential elements for life

Answer 3

C, H, N, O, P, S

Question 4

Metal ions essential for life

Answer 4

K, Na, Ca, Mg, Zn, Fe, V, Cr, Mn, Co, Ni, Cu, Mo, W, Se, I

Question 5

ABCs of Life

Answer 5

(A) Amino acids
(B) Components of Nucleic Acids
(C) Components of lipids

Question 6

Components of Nucleic Acids

Answer 6

Nitrogenous bases (U/T, C, A, G)

5 Carbon sugars (Ribose or deoxyribose)

Phosphate (PO4H2)

Question 7

Stereoisomers function and properties

Answer 7

have different physical properties from each other

Question 8

Components of lipids

Answer 8

–Phosphate
–Glucose
–Carbon backbone

Question 9

Geometric isomers function and properties

Answer 9

(cis vs. trans or across double bonds)

have different physical and chemical properties

Question 10

Enantiomers (mirror images)
isomers function and properties

Answer 10

have identical physical properties (except with regard to polarized light) and react identically with achiral reagents

Question 11

Diastereomers (non-mirror images)
isomers function and properties

Answer 11

have different physical and chemical properties

Question 12

entropy

Answer 12

As the entropy of the universe increases, creating and maintaining order requires work and energy.

Question 13

How to Speed Reactions Up and Limitations (4)

Answer 13

Higher temperatures
− stability of macromolecules is limiting

Higher concentration of reactants
− costly, as more valuable starting material is needed

Changing the reaction by coupling to a fast one
− universally used by living organisms

Lower activation barrier by catalysis
− universally used by living organisms

Question 14

endergonic

Answer 14

Synthesis of complex molecules and many other metabolic reactions requires energy

Question 15

exergonic

Answer 15

The breakdown of some metabolites releases a significant amount of energy

Question 16

Why are some reactions endergonic?

Answer 16

A reaction might be thermodynamically unfavorable (delta G°> 0).
Creating order requires work and energy.
A metabolic reaction might have too high an energy barrier (delta G‡ > 0).
Metabolite is kinetically stable.

Question 17

How might some reactions be exergonic?

Answer 17

Such metabolites (ATP, NADH, NADPH) can be synthesized using the energy from sunlight and fuels.
Their cellular concentration is far higher than their equilibrium concentration.

Question 18

Energy Coupling

Answer 18

allows otherwise unfavorable reactions to occur

Question 19

Catalysis

Answer 19

a compound that increases the rate of a chemical reaction.
Catalysts lower the activation free energy G‡.
Catalysts do not alter G°.

Question 20

Enzymatic catalysis offers:

Answer 20

acceleration under mild conditions
high specificity
possibility for regulation

Question 21

Why is water the medium for life?

Answer 21

Life evolved in water (UV protection!)

Organisms typically contain 70–90% water.

Chemical reactions occur in aqueous solutions.

Water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes.

Question 22

Structure of the Water Molecule

Answer 22

-Four electrons around O
-Four sp3 orbitals
-O covalently bonded to H2
-2 lone pairs nonbonding
-VESPR is bent
-EN of oxygen is a net dipole
-Water is both H bond donor and acceptor

Question 23

Hydrogen Bonds

Answer 23

Hydrogen bonds are strong dipole-dipole or charge-dipole interactions that arise between a covalently bound hydrogen and lone pair of electrons.

They typically involve two electronegative atoms (looking for H connected to F,O, or N).

Hydrogen bonds are strongest when the bonded molecules allow for linear bonding patterns. (3 atoms hopefully)

Question 24

Up to four H-bonds per water molecule gives water its what three properties?

Answer 24

anomalously high boiling point
anomalously high melting point
unusually large surface tension

Question 25

Energy values of H2O bonds

Answer 25

Hydrogen bonds between neighboring molecules are weak (20 kJ/mol) relative to the H–O covalent bonds (420 kJ/mol)

Question 26

Ice: Water in a Solid State

Answer 26

different crystal forms; the hexagonal ice is the most common. Hexagonal ice forms an organized lattice and thus has a low entropy. maximal hydrogen bonds/ water molecules in equidistant arrangement (ice floats!!)

Question 27

Water is a good solvent for...

Answer 27

charged and polar substances: -amino acids and peptides -small alcohols -carbohydrates

Question 28

Water is a poor solvent for

Answer 28

nonpolar substances: -nonpolar gases -aromatic moieties -aliphatic chains

Question 29

Noncovalent Interactions

Answer 29

Ionic (Coulombic) interactions Dipole interactions van der Waals interactions Hydrophobic Effect

Question 30

Ionic (Coulombic) interactions

Answer 30

electrostatic interactions between permanently charged species, or between the ion and a permanent dipole

Question 31

Dipole interactions

Answer 31

electrostatic interactions between uncharged but polar molecules

Question 32

van der Waals interactions

Answer 32

weak interactions between all atoms, regardless of polarity attractive (dispersion) and repulsive (steric) component

Question 33

Hydrophobic Effect

Answer 33

complex phenomenon associated with the ordering of water molecules around nonpolar substances

Question 34

van der Waals Interactions

Answer 34

-attractive force (London dispersion), which depends on the polarizability -repulsive force (Steric repulsion), which depends on the size of atoms Attraction dominates at longer distances (typically 0.4–0.7 nm). Repulsion dominates at very short distances.

Question 35

Biochemical Significance of van der Waals Interactions

Answer 35

Weak individually Universal Importance -determines steric complementarity -stabilizes biological macromolecules (stacking in DNA) -facilitates binding of polarizable ligands

Question 36

The Hydrophobic Effect

Answer 36

association or interaction of nonpolar molecules or components of molecules in the aqueous solution Is one of the main factors behind: protein folding protein-protein association formation of lipid micelles binding of steroid hormones to their receptors Does not arise because of some attractive direct force between two nonpolar molecules

Question 37

Solute Effects on Colligative properties of Water:

Answer 37

-boiling point, melting point, and osmolarity -do not depend on the nature of the solute, just the concentration

Question 38

Solute Effects on noncolligative properties of Water:

Answer 38

-viscosity, surface tension, taste, and color -depend on the chemical nature of the solute

Question 39

Osmotic Pressure (Concentration effects)

Answer 39

Water moves from areas of high water concentration (low solute concentration) to areas of low water concentration (high solute concentration). Osmotic pressure (π) is the force necessary to resist the movement.

Question 40

Cell in isotonic solution

Answer 40

No net water movement

Question 41

Cell in hypertonic solution

Answer 41

Water moves out of cell and cell shrinks

Question 42

Cell in hypotonic solution

Answer 42

Water moves in creating outward pressure, cell swells and may burst

Question 43

Ionization of Water

Answer 43

H20 <<<<---> OH - and H+ Products are a proton (H+) and a hydroxide ion (OH–). Dissociation of water is a rapid reversible process. Most water molecules remain un-ionized, thus pure water has very low electrical Low Keq Value

Question 44

Proton Hydration

Answer 44

Protons do not exist free in solution. They are immediately hydrated to form hydronium ions (H3O) The covalent and hydrogen bonds are interchangeable. This allows for an extremely fast mobility of protons in water via “proton hopping.”

Question 45

Dissociation of Weak Electrolytes: Principle

Answer 45

Weak electrolytes dissociate only partially in water. The extent of dissociation is determined by the acid dissociation constant Ka. We can calculate the pH if the Ka is known. But some algebra is needed!

Question 46

Buffers

Answer 46

Mixtures of Weak Acids and Their Anions (Conjugate Base) Buffers resist change in pH. pH = PK 1:1 mix of acid/base

Question 47

Henderson–Hasselbalch Equation: Derivation

Answer 47

Know it

Question 48

Maintenance of intracellular pH is vital to all cells. Why?

Answer 48

Enzyme-catalyzed reactions have optimal pH. Solubility of polar molecules depends on H-bond donors and acceptors. Equilibrium between CO2 gas and dissolved HCO3– depends on pH.

Question 49

Buffer systems in vivo are mainly based on:

Answer 49

phosphate, concentration in millimolar range bicarbonate, important for blood plasma histidine, efficient buffer at neutral pH

Question 50

Buffer systems in vitro are often based on sulfonic acids of cyclic amines.

Answer 50

Sulfur is often not used metabolically by bacteria so buffer systems last longer!!