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Biochemistry I > Chapter 1: The Foundations of Biochemistry > Flashcards

Chapter 1: The Foundations of Biochemistry Flashcards

1
Q

What are the defining characteristics of living things?

A

Living things can:
1. Extract, store, and use matter and energy from the environment.
2. Generate chemical complexity.
3. Sense and respond to environmental changes.
4. Change over time by gradual evolution.
5. Make order out of chaos.
6. Use energy derived from thermodynamically favorable processes to drive thermodynamically unfavorable processes.

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2
Q

What are the four major classes of biological molecules?

A
  1. Amino acids
  2. Monosaccharides
  3. Nucleotides
  4. Fatty acids
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3
Q

What are most biological functions carried out by?

A

Proteins

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4
Q

What is the “Central Dogma?”

A

DNA -> RNA -> Protein

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5
Q

What is metabolism?

A

The overall process through which organisms acquire and use the free energy and matter they need to carry out the functions of life; the sum of all of the chemical transformations taking place in life form.
- Ex. glycolysis

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6
Q

What are common features of all cells?

A
  1. Plasma membrane
    - Hydrophobic barrier, defines boundary, maintains integrity
  2. Cytoplasm
    - Highly concentrated cytosol
    - Ribosomes and other large insoluble macromolecules assemblies suspended in cytosol
  3. Chromosome(s)
    - Genetic material in the form of one or more molecules of DNA
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7
Q

What are the differences between prokaryotic cells and eukaryotic cells?

A

Prokaryotic cells: No nucleus or other organelles, smaller, always unicellular.
Eukaryotic cells: Larger, contain membrane-enclosed organelles, may be unicellular or multicellular.

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8
Q

What is biochemical function determined by?

A

Three-dimensional molecular structure.

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9
Q

What is biological change (evolution) driven by?

A

Mutation, gene duplication, and natural selection.

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10
Q

What are amino acids linked by?

A

Peptide bonds.

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11
Q

What kind of reactions are peptide bond formation and peptide bond cleavage?

A

Formation: Condensation reaction (water lost)
Cleavage: Hydrolysis (water added as nucleophile)

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12
Q

What does N-terminal and C-terminal mean on an amino acid?

A

N-terminal: The amino end of the chain.
C-terminal: The carboxyl end of the chain.

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13
Q

What is the empirical formula of carbohydrates?

A

C(H2O)

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14
Q

What functional group(s) is/are present in saccharides?

A

They are polyhydroxy aldehyde or ketone.

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15
Q

What are monosaccharides linked together by?

A

Glycosidic linkages.

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16
Q

What are the three components that make up a nucleotide?

A
  1. Pentose (D-ribose or 2’-D-deoxyribose)
  2. Nitrogenous base (purine or pyrimidine)
  3. Phosphoryl group.
17
Q

What bonds together nucleotides?

A

Phosphodiester bonds.

18
Q

What does 5’ and 3’ mean in nucleotides?

A

5’: End with free 5’ phosphate group (the “start” of the chain).
3’: End with free 3’ OH group (the “end” of the chain).

19
Q

What are three important aspects of lipids that make them special?

A
  1. Diverse non-polar/amphipathic molecules.
  2. Hydrophobic, associates with one another noncovalently.
  3. Makes up membranes, high in energy, useful in signaling.
20
Q

What are the important building blocks for many lipids?

A
  1. Fatty acids (long carboxylic acids).
  2. Glycerol (C3H8O3).
  3. Sphingosine (long chain amino alcohol).
  4. Isoprene (C5H8).
21
Q

What are fatty acids?

A

Carboxylic acids with long-chain linear hydrocarbon tails; usually found in nature as esters.

22
Q

What are saturated fatty acids and unsaturated fatty acids?

A

Saturated fatty acids: All C-C single bonds.
Unsaturated fatty acids: Contain double bonds.

23
Q

What are the most prominent elements in biomolecules?

A

C, H, O, N, S, and P.

24
Q

What is the first law of thermodynamics?

A

Conservation of energy; energy cannot be created nor destroyed, only transformed from one form to another.

25
Q

What is the second law of thermodynamics?

A

Increase in local order of organisms must be offset by greater increase in disorder of surroundings.

26
Q

What is Gibbs free energy?

A

Amount of energy that can be used to do work.
- Negative: spontaneous, exergonic.
- Positive: non-spontaneous, endergonic.
G = H-TS

27
Q

What happens if living things reach equilibrium?

A

They will die. If equilibrium is reached, no work is being done.

28
Q

What determines a spontaneous reaction/process?

A

Gibbs free energy is less than 0.
Q < K
Exergonic.

29
Q

What is homeostasis?

A

A non-equilibrium steady state where flows of matter and energy are constant (balanced).

30
Q

What’s the similarities/differences between equilibrium and homeostasis?

A

Equilibrium:
- No net free energy in or out
- System and surroundings at similar S
- Conditions stable within system
Homeostasis:
- Net influx of free energy into system
- System more ordered (lower S) than surroundings
- Conditions stable within system

31
Q

What are photoautotrophs?

A

Organisms where free energy is harvested from sunlight (photosynthesis).
- Ex. Vascular plants, single cell algae, photosynthetic bacteria
- Redox reactions (water oxidized to O2, CO2 reduced to glucose) powered by solar energy result in chemical energy in the form of glucose.
- Organisms oxidize this stored fuel at night to sustain cellular energy needs (glucose -> ATP).

32
Q

What are chemoheterotrophs?

A

Organisms that cannot capture solar energy and must rely on oxidation of glucose and other reduced organic compounds (ex. fatty acids) obtained from other organisms (ultimately photoautotrophs).

33
Q

What are enzymes?

A

Enzymes:
1. Almost always proteins
2. Provide an alternative pathway/mechanism for a reaction
3. Work under mild reaction conditions (atmospheric pressure, moderate temperature, neutral pH)
4. Excellent reaction selectivity and specificity
5. Capacity for regulation

34
Q

What are covalent bonds?

A

Covalent bonds: atoms joined together by shared electron pairs.

35
Q

What are noncovalent interactions?

A

Attractive and repulsive forces between one molecule/ion and another based on electrostatics (also known as intermolecular forces).

36
Q

Is energy released or absorbed when covalent bonds form? What about when they break?

A

Formation: Energy released
Cleavage: Energy absorbed

37
Q

What are the three noncovalent interactions?

A
  1. Ionic (Coulombic, electrostatic) interactions.
    - Charge-charge, charge-dipole
  2. Van der Waals interactions.
    - Dipole-dipole, dipole-induced dipole, London dispersion forces
  3. Hydrogen bonding
    - Hydrogen shared by two electronegative atoms (usually O or N)
38
Q

What determines the strength of hydrogen bonds?

A

Distance and direction (angle)

Biochemistry I (5 decks)

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