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BIOC384 > Module 1 - Biochem Principles > Flashcards

Module 1 - Biochem Principles Flashcards

1
Q

What are the 6 biochemical principles?

A

hierarchical organization, DNA is the basis for heredity, structure determines function, thermodynamics, life depends on water, and membranes are selective hydrophobic barriers

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2
Q

What is the hierarchy of molecular life? Describe each level.

A

elements and functional groups (C, N, O, CH3, NH2, COOH)
biomolecules (amino acids, nucleotides, simple sugars, and fatty acids)
macromolecules (proteins, DNA/RNA, carbs and lipids)
metabolism (glycolysis or citrate cycle)
cells (cell wall, plasma membrane, organelles)
organisms (tree, dog, person)
ecosystem (river, island, desert)

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3
Q

What are the main elements that make up 97% of organisms?

A

oxygen, carbon, hydrogen, nitrogen, phosphorus, and sulfur

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4
Q

How many lone electrons are on H, O, N, and C? How does this affect their bonding ability?

A

H: 1
O: 2
N: 3
C: 4
number of lone electrons is number of bonds that can form

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5
Q

What are the 6 most common chemical groups in biomolecules?

A

amino, hydroxyl, sulfhydryl, phosphoryl, carboxyl, and methyl

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6
Q

What are the 4 classes of biomolecules?

A

amino acid, nucleotide, simple sugar, and fatty acid

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7
Q

Describe the basic structure of amino acids and their primary functions

A

carbon with a amino group on one side (NH3+), a carboxyl group on the other (COOH) and an R group or hydrogens as the other bonds

protein function, neurotransmission, nutrient metabolism, and energy conversion

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8
Q

Describe the basic structure of nucleotides and their primary functions

A

5 carbon ribose or deoxyribose sugar with a nucleotide base on one carbon and phosphate groups on the other side

nucleic acid function, energy conversion, signal transduction, and enzyme catalysis

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9
Q

Describe the basic structure of simple sugars and their primary functions

A

6 carbon rings with H and OH groups on each carbon

energy conversion, cell wall structure, cell recognition, and nucleotide structure

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10
Q

Describe the basic structure of fatty acids and their primary functions

A

a chain of carbons with a COO- on one end (polar head and nonpolar tail)

cell membrane, energy conversion, cell signaling, and energy storage

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11
Q

What empirical chemical formula do all simple sugars follow?

A

CH2O

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12
Q

What is a polymer, and what are examples formed from the basic biomolecules? What links these polymers together?

A

large macromolecules formed from chains of small biomolecules

nucleic acids/DNA (from nucleotides, linked by phosphodiester bonds)

proteins (from amino acids, linked by peptide bonds)

starch/cellulose/chitin (from glucose, linked by covalent glycosidic bonds)

lipids/lipid membranes (from fatty acids, linked by ester bonds)

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13
Q

Macromolecules form when ATP is —- but break apart when ATP is —-.

A

form when high, break when low

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14
Q

Where is the peptide bond of a protein located?

A

between the amino acids (NCC - peptide bond - NCC - peptide bond - NCC, etc.)

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15
Q

Why can humans digest starch but not cellulose or chitin?

A

Humans have the enzyme to digest starch but not cellulose or chitin. Our enzyme can break an a(1-4) glycosidic bond but not a b(1-4) glycosidic bond.

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16
Q

What is the distinct feature of metabolic pathways?

A

they have linked reactions - the product of one is the reactant of another (and is called an intermediate)

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17
Q

What are the three types of metabolic pathways?

A

linear, forked, and cyclic

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18
Q

Describe signal transduction

A
  • when ligand levels are high, the ligand binds to receptor
  • conformational change to the active state is responsible for signal transduction into the cell
  • when ligand level lowers, the ligands release and the receptor returns to being inactive
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19
Q

What are the 3 key concepts of bioenergetics?

A
  • constant input of energy maintains homeostasis far from equilibrium
  • 3 Laws of Thermodynamics
  • energy charge is a measure of ATP, ADP, and AMP in the cell
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20
Q

What are oxidation and reduction?

A

oxidation is loss of electrons (and therefore loss of bonds, loss of hydrogens)
reduction is gain of electrons (and gain of bonds, gain of hydrogens)

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21
Q

Describe the basics of photosynthesis, carbon fixation, and aerobic respiration

A

photosynthesis: water + solar energy —> O2 + ATP
carbon fixation: CO2 —> glucose
aerobic respiration: glucose + O2 —-> CO2 and ATP

22
Q

What are the three common electron carriers and what are their reduced and oxidized forms?

A

NAD+ (oxidized) / NADH (reduced)

FAD (oxidize) / FADH (reduced)

Q (oxidized) / QH2 (reduced)

23
Q

What are the three laws of thermodynamics?

A

1 - total energy does not change, only converted
2 - everything tends toward disorder/entropy
3 - change in Gibbs Free Energy = change in standard free energy + RT ln (B/A)

24
Q

How does a bomb calorimeter work?

A

amount of heat to raise 1 kg of water from 14.5 C to 15.5 C at 1 atm is a Calorie (1 kcal or 4.184 kJ)

25
Q

Total potential energy of a gram of glucose is —– when different metabolic paths are taken

A

always the same

26
Q

Describe entropy and equilibrium regarding living systems

A
  • everything tends toward disorder, or increasing entropy
  • energy is needed to restrain this disorder
  • without energy input, a cell dies and entropy increases until the system equilibrates with the environment
  • to stay alive, the system cannot reach equilibrium with the environment
27
Q

What is the difference in energy conversion reactions and fermentation? What are they driven by?

A

energy conversion - redox
fermentation - enzyme catalyzed

28
Q

What does Gibbs Free energy tell us about a reaction?

A

if it is favorable or unfavorable in the forward direction
dG<0 is favorable
dG>0 is unfavorable

29
Q

What are the differences between dG, dG knot, and dG knot prime?

A

dG: dG - T(dS)
dG knot: standard change, dG at a constant pressure (1 atm), temperature (298K), and each reactant starts at an equal concentration (1M)
dG knot prime: biochemical standard change, also constant pH (7), and water concentration (55.5 M)

30
Q

How can you describe the differences between actual change in free energy and standard change in free energy?

A

actual: changes in response to the environment, and depends on concentration of reactants and products
standard: constant for a given reaction, and reflects the potential energy in reactants and products independent of concentration

31
Q

What is Keq and how does it’s value correlate to dG and favorability?

A

Keq = conc. of products at equilibrium / conc. of reactants at equilibrium

Keq>1 = dG<0 = favorable
Keq<1 = dG>0 = unfavorable

32
Q

What is Q (or the mass action ratio)

A

ratio of the initial concentration of products / initial concentration of reactants

33
Q

What units do things need to be in for gibbs free energy calculations?

A

Kelvin, kJ, and moles
dG: kJ/mol
R: kJ/mol(K)
T: Kelvin
concentrations: Moles

34
Q

How do you find the dG value for a coupled reaction?

A

add the dG values for the seperate reactions (make sure they are going the direction that they would in the coupled reaction. if the reaction needs flipped around, then also flip the sign of the dG value)

35
Q

Why might coupled reactions be used instead of a direct reaction? Give an example.

A

The initial reaction might be unfavorable, but it creates a highly reactive intermediate with a very favorable second step so that the overall coupled reaction is favorable.
Example: transferring a phosphoryl is unfavorable, but it can generate a highly reactive intermediate that reacts very favorably.

36
Q

What is usually related to phosphoanhydride bond hydrolysis reactions?

A

protein conformational changes, like muscle contraction and ion transport against a gradient

37
Q

How does the cell maintain a very narrow range of ATP levels?

A

the adenylate system - excess ATP/AMP can be stored as ADP or ADP can be transformed into ATP when it is needed

38
Q

What is the energy charge of the cell? What is considered normal? How doe the energy charge impact cell activity?

A

ATP + 0.5(ADP) / ATP+ADP+AMP

normal is 0.7-0.9, with higher being more ATP/less ADP

when the energy charge is low, the cell catabolizes stored fuels to make more ATP.
when the energy charge is high, the cell uses ATP to anabolize energy from the environment into cellular biomolecules, replenishing the cell’s fuel stores

39
Q

Why does lack of water cause plants to wilt?

A

the central vacuole determines cell shape, and when it lacks water the pressure decreases allowing the cell to collapse

40
Q

What are the 4 colligative properties? What do all colligative properties have in common? Why is one more important than the others?

A

boiling point, vapor pressure, freezing point, and osmotic pressure

all depend on the number of solute particles in the solution, not the chemical properties of the particles

osmotic pressure is most important because most organisms do not live near O or 100C so they dont need to worry about the others

41
Q

Osmotic pressure is —— to solute concentration

A

proportional (aka, if solute concentration doubles than so does osmotic pressure)

42
Q

What happens to red blood cells in hypotonic and hypertonic solutions?

A

hypotonic: water flow into cells and they burst
hypertonic: water flow out of cells and they shrink

43
Q

How can you determine the concentration of H+ or OH- of normal water? How does that change for other solutions?

A

water is always 1x10^-14 = [H+][OH-], so in normal water the concentration of each is 1x10^-7

for a solution of 0.02 M NaOH, the [OH-] is 2x10^-2 M
if [H+][OH-] = 1x10^-14, then [H+] = 1x10^-14 / 2x10^-2 = 5x10^-13

44
Q

How can you determine pH from only [H+]? How do these two numbers relate to each other?

A

pH = log 1/[H+]

change in 1 pH is a 10 fold change in [H+]

45
Q

What information can you get from a titration curve?

A

the flat spot in the middle of the curve represents the pH at which acid=base, which is also the pKa of the solution

if a acid is polyprotic (has multiple dissociable protons) there are more than one curve and more than one pKa.

46
Q

How is blood pH maintained using a buffer system?

A

when pH levels drop, the blood H+ concentration is reduced by increasing breathing rate (increasing CO2 exhalation) and decreasing HCO3- secretion

47
Q

What are the three key concepts that make water essential for life?

A

less dense as a solid than as a liquid so the ocean’s dont completely freeze over, liquid over many temperatures (especially the ones on the surface of Earth), and it is a good solvent because of it’s polarity and ability to hydrogen bond

48
Q

How many hydrogen bonds can one molecule of water make? What is the hydrogen bond donor vs the hydrogen bond acceptor?

A

4
donor: the one with the hydrogen
acceptor: the one forming an H bond with another molecule’s hydrogen

49
Q

What is a water wire?

A

hydrogen-bonded water molecules in an electric field pass H+ ions from one molecule to the next through proton hopping
overall, a hydronium ion forms when a water molecule accepts a proton, then that proton hops down the chain until the very last water molecule becomes a hydronium ion

50
Q

What is the hydrophobic effect? What kinds of effects can it have on proteins?

A

when individual nonpolar molecules are surrounded by water, that water is more ordered and therefore has less entropy. since everything tends toward disorder, having a complex of nonpolar molecules reduces the surface area, meaning less water molecules are ordered, and entropy is increased.

hydrophobic regions on proteins interacts to reduce the size of the hydration later, causing proteins to fold so that hydrophobic parts are toward the interior

51
Q

Many protein complexes (like enzymes) are formed by —– —— ——- ——–.

A

reversible weak noncovalent interactions

BIOC384 (13 decks)

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