Fundamentals of Metabolism 3 - How cells work

Question 1

Essential Characteristics of Living Cells

Answer 1

1. Information of storage
2. Compartmentation
3. Controlled Reactions

Question 2

Essential Characteristics of Living Cells:

EXPLAIN INFORMATION STORAGE
HOW?

Answer 2

A mechanism for storing and using the information
required for the cell to work and passing it to offspring

→ NUCLEIC ACIDS

Question 3

Essential Characteristics of Living Cells:

COMPARTMENTATION = 2
HOW?

Answer 3

1. Keeping the contents of cells separate from their environment
2. Controlled interaction with environment

→ MEMBRANES WITH SELECTIVE PERMEABILITY

Question 4

Essential Characteristics of Living Cells: CONTROLLED REACTIONS

Answer 4

1. Reactions that occur in an aqueous environment under MILD conditions.

→ STEPWISE OXIDATION AND REDUCTASE REACTIONS AVOIDING LARGE CHANGES IN FREE SINGLE STEP

2. Made possible by the use of ENZYMES

Question 5

1. Storing information and passing to offspring = EXPLAIN HOW 3.

Answer 5

1 * DNA replication is SEMI-CONSERVATIVE
(each parent strand copied)

2 * PROTEIN STRUCTURE IS ENCODED BY DNA

3 * PROTEINS FOLD IN A MANNER DICTATED BY THIER PRIMARY STRUCTURE

Question 6

Molecular Composition of Cells:
6 - general

Answer 6

1. MAJOR ATOMS
2. MOLECULES
3. MARCROMOLECULES
4. SMALL MOLECULES
5. INORGANIC IONS
6. TRACE ELEMENTS

Question 7

Molecular Composition of Cells: MAJOR ATOMS

Answer 7

H

C

O

N

P

S

Question 8

Molecular Composition of Cells: MOLECULES

Answer 8

1. WATER (70%)
2. Macromolecules (23%)
   - Protein
   - Nucleic Acids (DNA and RNA)
   - Carbohydrates
3. SMALL MOLECULES (6%)
   - Amino acids
   - Sugars
   - Nucleotides
   - Lipids

Question 9

Molecular Composition of Cells: INORGANIC IONS

Answer 9

= 1% approx

Na+, Cl-, H2PO4-, HCO3-, Ca+2, K+

Question 10

Molecular Composition of Cells: TRACE ELEMENTS

Answer 10

Fe, Cu, Zn, Mg, Mn, Mo, Co, Se, I

Question 11

amino acids to

Answer 11

Proteins

Question 12

fatty acids to

Answer 12

Lipids

Question 13

Sugar residues to…

Answer 13

1. Glycerol
   to Lipids
2. Mono-saccharides
   to Carbohydrates

or

3. Sugar residues to monosaccharides to Nucleotides = DNA/RNA

Question 14

Nucleobases to

Answer 14

nucleotides to DNA/RNA

Question 15

Why is Water a solvent?

Answer 15

due to Hydrogen Bonds in Water

1 * Water forms H-bonds due to the interaction
between the δ+ on the H and the δ- on O

2 * Each water molecule can form up to 4 H-bonds
(4 in ice)

3 * Continually breaking and reforming

Question 16

Water’s polar nature and ability to H-bond gives water its unique solvent properties… WHAT ARE THEY?

Answer 16

1 – Polar (high dielectric constant)

2 – Dense

3 – High melting and boiling point

4 – Viscous with high surface tension

5 – Can act as proton donor or acceptor:

Question 17

Explain water Can act as proton donor or acceptor:

Answer 17

H2O ⇋ H+ + OH-

[H+][OH-] = 10^-14 M^2

H+ + H2O ⇋ H3O+ (hydronium ion)

Question 18

Water tends to exclude hydrophobic molecules because?

Answer 18

disrupt H-bonding

Question 19

EXPLAIN COMPARTMENTATION IN DETAIL….3

Answer 19

1 * Cells (and organelles) can maintain a SPECIALISED ENVIRONMENT consistent with the function of the cell- via phospholipid membranes

2 * Membranes have SELECTIVE PERMEABILITY to POLAR and CHARGED molecules via SPECIFIC TRANSPORTERS in their PLASMA and ORGANELLE MEMBRANES

3 * Energy (‘ATP’) must be used to MAINTAIN ORDER in a cell, including for TRANSPORT OF ESSENTIAL MOLECULES AGAINST A CONCENTRATION GRADIENT.

Question 20

Understanding SELECTIVELY MEMBRANE TRANSPORT…

EXAMPLE K+ channel = 5

Answer 20

1. Hydrated K+ and Na+ ions in Solution, ENTRY AT PORE
2. Na+ is smaller than K+
3. K+ (but not Na+) co-ordinate perfectly with carbonyl ( -C=O) oxygens in channel
4. ACTIVATION ENERGY = for K+ to MOVE THROUGH PORE IS LOW.

ACTIVATION for Na+ to MOVE THROUGH PORE REMAINS HIGH

5. K+ transported 1000 x faster than Na+

Question 21

CONTROLLED REACTIONS:

AIM? HOW?

Answer 21

AIM: avoid a large release in free energy in a single step

∴ Fuels oxidized stepwise (e.g. β-oxidation)

• Enzymes permit reactions to proceed RAPIDLY in the aqueous environment of
  cells under mild conditions

Question 22

Controlled Reactions: SPEED UP REACTION BY: 2

Answer 22

a) Holding reactants in correct ORIENTATION

b) Promoting attainment of the TRANSITION STATE

Question 23

Specificity in Binding - BETWEEN MACROMOLECULES

Answer 23

1. Between a macromolecule and a SMALL MOLECULE
   eg. ENZYME BINDING TO ITS SUBSTRATE

2.SPECIFIC MATCHING of FUNCTIONAL GROUPS ENABLES SPECIFIC PROTEIN-PROTEIN INTERACTION

3. Collective bond energies –> strong interaction;

• N bond, Ionic bond, Hydrophobic and van der Waals interactions

Question 24

Chemical ENERGY in Cells …

Understanding ATP - the energy currency in cells

Answer 24

A large release of free energy accompanies ATP HYDROLYSIS

1.* Can be COUPLED to REACTIONS that NEED ENERGY to PROCEED in
the FORWARD DIRECTION:

e. g.
glucose + Pi ⇀, <——– glucose-6-P

2* COUPLED to ATP HYDROLYSIS, PHOSPHORYLATION of GLUCOSE proceeds in the
FORWARD DIRECTION:

glucose + ATP <↽, ——-> glucose-6-P + ADP

Question 25

Phosphoanhydride bond ….

Answer 25

ADENOSINE = (Phosphoanhydride bond + phospanhydride bond) = PHOSPHATE + RIBOSE + ADENINE

ADENOSINE TRIPHOSPHATE (ATP)

—–H2O—–>

ADP + Orthophosphate (Pi)

NEW BOND FORMED, ENERGY RELEASED

Question 26

Energy is extracted from

Answer 26

fuels by oxidation reactions

Question 27

C-C → C=C

Answer 27

β-oxidation,
Citric acid cycle

Question 28

C-OH → C=O

Answer 28

β -oxidation,
Citric acid cycle,
Pentose phosphate pathway

The two electrons
from these oxidations
are used to reduce
cofactors:
NAD+ à NADH
FAD à FADH2

Question 29

R-C-OH → R-CH=O

Answer 29

Pentose phosphate pathway

The two electrons
from these oxidations
are used to reduce
cofactors:
NAD+ à NADH
FAD à FADH2

Question 30

R-CH=O → R-COOH

Answer 30

Glycolysis,
Citric acid cycle

Question 31

NADH and NADPH – Mobile Electron Carriers

Answer 31

1 * Carry 2 electrons (= energy) from one site to another

2 * NADH and NADPH bind reversibly to their enzymes, can be made (reduced) by one enzyme, dissociate and diffuse to another enzyme and be oxidized, releasing their energy (note, FADH2 remains enzyme bound).

Question 32

n mammals, NAD+ and NADP+ are made from

Answer 32

Niacin (= vitamin B3 = nicotinic acid)

Question 33

NADPH drives
biosynthesis of organic
molecules,

Answer 33

e. g. fatty
acids and cholesterol.