Jones Lehninger Biochemistry Exam 1

Front 1

What defines a cell?

Back 1

The plasma membrane that separates its contents from the surroundings. Enclosed in this membrane is cytoplasm.

Front 2

What are the key elements within the cytoplasm?

Back 2

1) Cytosol - concentrated aqueous solution with enzymes and RNA
2) metabolites - biosynthetic and degradative
3) coenzymes - enzyme-catalyzed reactions
4) ribosomes - protein synthesis
5) proteosomes - degrade unneeded proteins

Front 3

Two main families of organisms?

Back 3

1) Eukaryotes - contain a nuclear envelope; multicelled; DNA in nucleus; multi-compartmented
2) Prokaryotes - don't contain a nuclear envelope; DNA in nucleoid; plasmids
a. Arcahea - harsh environments (closer to eurkaryotes)
b. Bacteria - inhabit soils, surface H2O, and tissue

Front 4

What is compartmentalization?

Back 4

Prevents loss of compounds (diffusion) and pH change

Front 5

Why are large surface area-volume ratios important?

Back 5

1) Every part is easily accessible to outside molecules
2) Metabolism: allows faster O2 diffusion than consumption

Front 6

What is a cytoskeleton made up of?

Back 6

1) filaments
2) microtubules
3)intermediate filaments

Front 7

What are some important functions of cytoskeletons?

Back 7

1)endomembrane system: metabolic processes and ezyme-catalyzed reactions
2)exocytosis/endocytosis: fusion/fission which provides paths between cytoplasm and environment
3)noncovalent, reversible, subject to regulation

Front 8

Supermolecular compounds -> Macromolecules -> Monomeric Units

Back 8

Chromatin -> DNA -> Nucleotides
Plasma Membrane -> Protein -> Amino Acid
Cell Wall -> Cellulose -> Sugars

SPM) Noncovalent/hydrogen/ionic/hydrophobic/vanderwaals
MA) Noncovalent/hydrogen/ionic/hydrophobic/vanderwaals
MO) covalent

Front 9

What are the most abundant elements in a biological system?

Back 9

1) Hydrogen
2) Oxygen
3) Nitrogen
4) Carbon

Front 10

What are some additional things in cytosol?

Back 10

1) Amino acids, nucleotides, sugars, and their derivatives
a. polar, charged, water soluble, [micromolar-millimolar]
b. cell membrane impermeable to these

2) Secondary metabolites: plant smell, morphine, nicotine, caffeine

3)metabolomes

Front 11

What are some additional macromolecules?

Back 11

1) Polysaccharides: polomers of simple sugars (glucose)

2) Lipids: water-insoluble hydrocarbon dervatives
a. energy-rich fuel stores
b. pigments
c. intracellular signals
d. membranes
e. intracellular signals

Front 12

Why is it important that proteins and nucleic acids are linear polymers of monomeric subunits?

Back 12

This gives each molecule its three-dimensional structure which governs biological function and reactivity

Front 13

Why are stereoisomers important?

Back 13

Biological systems are stereospecific

Front 14

What are the three types of systems?

Back 14

1) isolated: no energy or mass exchange
2) closed: only energy exchange
3) open: both energy and mass exchange

Front 15

What does the sign on Gibbs free energy mean?

Back 15

-deltaG = exogernic = towards completion

+deltaG = endogernic = tends to run in the reverse

Front 16

What are the main sources of energy?

Back 16

1) Oxidizing environmental fuels
2) Absorption of sunlight

Front 17

What is an enzyme?

Back 17

A biological catalyst which determines how matter and energy are channeled into cellular activities

Front 18

What is catabolism?

Back 18

Free energy yielding reactions

Front 19

What does it mean to be chiral?

Back 19

To have at least two arrangements that are not superimposable onto each other.

Front 20

Important structures of:
1) amino acids
2) fatty acids
3) nucleotides

Back 20

1) Nitrogenous substituents
2) Long hydrocarbon chains
3) Nitrogen base, 5carbon Sugar, Phosphate

Front 21

What is activation energy?

Back 21

The amount of energy needed to convert 1 mol of molecules to the transition state

Front 22

What is required of a substance to be detected as different by the human body?

Back 22

The substance must be structurally different. The source of the substance does not matter

Front 23

What are some important characteristics of water?

Back 23

1) Difference in EN between Oxygen and Hydrogen create a net dipole, making water very polar
2) Has a strong ability to hydrogen with itself and other molecules which contain dipoles created by a difference in EN.
3) The above justify water as a good solvent for polar(hydrophilic) solutes

Front 24

What are the types of bonding ordered strongest to weakest?

Back 24

1) covalent: sharing of electrons
2) ionic: involves formal charges
3/4) hydrogen: differences in EN
3/4) hydrophobic: results when nonpolar and polar are mixed; nonpolar minimizes exposure to polar (shifts towards disorder rather than order)
5) Van der Waals: attractive force between two atoms, becomes repulsive if too close

Front 25

If noncovalent bonds are so weak, why are they found in biological systems?

Back 25

Within the big picture, the sum of all the noncovalent interactions is quite large. Noncovalent interactions are largely responsible for the way macromolecules "fold" into their 3-dimensional shape

Front 26

What is osmotic pressure?

Back 26

When water moves across the barrier between two aqueous layers to equalize osmolarity.

Front 27

What are the products of the ionization of water?

Back 27

H3O+ and OH-

Front 28

As pka increases acidity ___?

Back 28

Decreases

Front 29

What is a buffer?

Back 29

Combination of weak acid/base and their conjugate which resists change by reacting with any additional acid/base added

Front 30

Hinderson-Haselbach equation?

Back 30

pH = pka + log[A-]/[HA]

Front 31

Calculating changes upon addition of....
1) acid
2) base

Back 31

1) [A-] - [Added Acid] ; [HA] + [Added Acid]
2) [A-] + [Added Base] ; [HA] - [Added Base]

Front 32

Back 32

I would choose (d) because it involves a nonionic compound with a long hydrocarbon chain which is insoluble in water. In order to dissolve we must first deprotonate with base (sodium bicarbonate).

Front 33

What happens when pH >> pka of a particular substituent?

Back 33

The substituent becomes deprotonated

Front 34

What do all 21 amino acids have in common?

Back 34

1) alpha-carbonyl group
2) alpha-amino group
3) alpha-carbon substituent

Front 35

What is unique only to glycine?

Back 35

The alpha-carbon is symmetric = no stereoisomers

Front 36

What are the 21 amino acids?

Back 36

Major Roles:
1) monomers
2) chemical messengers
3) energy (oxidation)
4) buffer
5) allergies
6) protection
7) osmosis modulators

Front 37

Aromatic Amino Acids

Back 37

1)Phenyalanine
2) Tyrosine
3) Tryptophan

Relatively nonpolar
Participate in hydrophobic reactions
Hydroxyl groups can hydrogen bond
T's more polar than Phenylalanine
Absorb UV light

Front 38

Polar Uncharged Amino Acid

Back 38

1) Serine
2) Threonine
3) Cysteine
4) Selenocysteine
5) Asparagine
6) Glutamine

More soluble in water b/c of H-bond
Disulfide bonds create covalent links between polypeptides

Front 39

Positively Charged Amino Acids

Back 39

1) Lysine
2) Arginine
3) Histidine

Very soluble in water (charged)
Histidine both charged and uncharged @ pH7
Histidine serves as proton donator/acceptor

Front 40

Negatively Charged Amino Acids

Back 40

1) Aspartate
2) Glutamate

2 carboxyl groups

Front 41

How are peptides and proteins formed?

Back 41

Through covalent peptide bonds between multiple amino acids

Front 42

How are peptide bonds formed?

Back 42

Removal of elements of water from alpha-carboxyl group of one amino acid and the alpha-amino group of another. This requires energy input!

Front 43

What is the function of a peptide?

Back 43

There are several, but the most general is being a building block for protein

Front 44

What are some common separation techniques?

Back 44

1) Column Chromatography: charge/polarity/affinity
2) TLC: polarity
3) Centrifuge: size/density
4) Electrophoresis: charge/size/viscosity
5) Sodium Dodecyl Sulfate (PAGE): charge/size/viscosity ; impedes movement of large molecules ; protein reduced and denatured

PAGE = polyacrylamide gel electophoresis

Front 45

How are amino acids analyzed?

Back 45

Complete hydrolysis of polypeptides/proteins

Front 46

Nonpolar, alipathic Amino Acids

Back 46

1) Glycine
2) Alanine
3) Proline
4) Valine
5) Leucine
6) Isoleucine
7) Methionine

Front 47

Nonpolar, nonaromatic

Back 47

1) Glycine
2) Alanine
3) Proline
4) Valine
5) Leucine
6) Isoleucine
7) Methionine

Front 48

What are the four levels of protein structure?

Back 48

1) Primary: simple AA sequence
2) Secondary: interaction of closely linked primary AA
3) Tertiary: interactions of far away primary AA
4) Quaternary: interactions of subunits; more than one protein

Front 49

What are some secondary protein shapes?

Back 49

1) helix (slinky)
2) sheets (accordion)
3) random (inconsistent bond angles)