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Biochem MCAT > Biochemistry Basics > Flashcards

Biochemistry Basics Flashcards

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MCAT flashcards
1
Q

Is the backbone of DNA negatively or positively charged? Why?

A

Negatively because of the 3 phosphate groups with a negative charge (Overall charge is -4)

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2
Q

H+ might also be written as…?

A

Protons

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3
Q

What is the main source of energy in the cell?

A

ATP

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4
Q

Is breaking off an inorganic phosphate group from ATP energetically favorable or unfavorable?

A

Energetically favorable.

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5
Q

Why are energetically favorable reactions important for our cells.

A

Energetically favorable reactions can be coupled to unfavorable ones to drive them forward.

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6
Q

What is the general process of the electron transport chain?

A

H+ atoms from NADH are pumped into the intermembrane space of the mitochondria . The protons then diffuse down their concentration gradients into the mitochondrial matrix. This powers ATP synthase which produces ATP.

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7
Q

What do electrons do in the electron transport chain?

A

The electrons are used to help pump H+ (protons) into the intermembrane space. At the end, they are attached to oxygen and released as water (H20).

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8
Q

What does redox stand for?

A

Reduction and Oxidation

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9
Q

How can one study pathways?

A

Look for how electrons get passed from one compound to another.

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10
Q

What happens to glucose and fatty acid alkane units in energy-producing pathways?

A

These reduced biomolecules are oxidized (lose electrons) in energy-producing pathways.

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11
Q

Out of hydrocarbons, which are the most reduced and which are the most oxidized?

A

Alkanes are the most reduced and Alkynes are the most oxidized.

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12
Q

Out of oxygen containing organic compounds, which are the most reduced and which are the most oxidized?

A

Alcohols are the most reduced and Carboxylic Acids are the most oxidized.

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13
Q

What are examples of redox half reactions?

A

A —> A+ + e-

B + e- —> B-

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14
Q

Is the formation of ATP from ADP energetically favorable?

A

NO!

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15
Q

What is polarity?

A

Distribution of charge

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16
Q

What are polar covalent bonds?

A

The electron density is distributed unevenly between atoms.

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17
Q

What happens when the asymmetry of a polar covalent bond is very strong?

A

Hydrogen bonding takes place.

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18
Q

What elements are involved in hydrogen bonding?

A

Between H and FON atoms.

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19
Q

List popular compounds from most polar to least polar.

A
  1. Charged molecules
  2. Carboxylic Acids
  3. Alcohols
  4. Amines
  5. Ketons and Aldehydes
  6. Hydrocarbons (Aromatics) (Non-polar)
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20
Q

What compounds are the most polar?

A

CHARGED compounds (ions)

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21
Q

What is an Amphipathic molecule?

A

A molecule with a highly polar head and a non-polar hydrocarbon tail.

22
Q

What do polar covalent bonds form?

A

Charge dipoles.

23
Q

What does asymmetric charge distribution form?

A

Vectors

24
Q

Is CO2 polar or non-polar? Why?

A

Non-polar because the dipole moments cancel out (if all dipoles cancel out, the molecule is non-polar)

25
Q

Why is polarity linked to solubility?

A

Like dissolves like

26
Q

Polar molecules traits.

A

Hydrophilic and Lipophobic (like aqueous solutions)

27
Q

Non-polar molecules traits.

A

Hydrophobic and Lipophilic (like lipid rich environments)

28
Q

What usually dictates protein function?

A

Structure!

29
Q

What are some ways protein structure dictates function? does

A

The 3-dimensional shape determine which molecules fit together with other molecules. And charged based interactions are very important (polarity).

30
Q

What are three common scenarios where polarity has major implications?

A

Enzymes
Transmembrane Proteins
Protein Folding

31
Q

How could you disrupt enzyme function?

A

By substituting an amino acid residue in the active site with another amino acid that has different properties (polar vs non-polar or positive vs negative charge)

32
Q

How to determine what will make a good substrate for a given active site?

A

Look for a combination of amino acid properties that result in attractive interactions.

33
Q

Describe a transmembrane protein.

A

It has a central membrane spanning domain (hydrophobic) and intracellular (facing inward, hydrophilic) and extracellur (facing outward, hydrophilic) domains

34
Q

What is protein folding?

A

It shapes the 3D structure of protein which determines their function. Primarily affected by tertiary structure.

35
Q

How would the tertiary structure of a protein be affected by an amino acid substitution?

A

Substituting an amino acid residue with one that has different polarity properties will be more likely to change the 3D form of a protein. Whereas an amino acid with similar properties would be more likely to preserve overall structure.

36
Q

What can diffuse through the permeable plasma membrane?

A

Very small uncharged molecules and lipid-soluble/ non-polar molecules.

37
Q

What are hormones?

A

Signaling molecules that travel through the circulatory system to induce various effects on their target tissues. Play a major role in regulatory homeostasis, and mediate the body’s response to various stimuli.

38
Q

What are the two major types of hormones?

A

Peptide hormones (polar) and Steroid hormones (non-polar).

39
Q

What are peptide hormones ?

A

They are composed of chains of amino acids. Large and polar. Interact with target cells via membrane bound receptors and then engage in secondary messenger systems within the cell. Which can amplify a signal within a short amount of time. Quick onset and short-lasting effects.

40
Q

What are steroid hormones?

A

derived from the lipid cholesterol. Small and non-polar. Exerts effects by interaction with nuclear receptors that regulate gene transcription. Longer- onset and longer duration effects.

41
Q

How do histones interact with DNA?

A

DNA is negatively charged due to the phosphate groups in its backbone. Histones which are rich in positive/basic amino acids form a non-covalent interaction with DNA due to this. Histones function as scaffolding that packages DNA.

42
Q

How can histone modifications impact DNA expression?

A

If covalent additions of methyl, phosphate, or acetyl groups are made to histones, it removes the positive charge which weakens the interactions between the histone and DNA. When this process is repeated, it loosens the DNA which creates more space for transcription factors to actively transcribe it. (Upregulates Gene Expression).

43
Q

Is moving a membrane phospholipid from one side of the membrane to another energetically favorable or unfavorable ? Why?

A

Energetically unfavorable because it requires energy to move the polar phosphate head through the inner non-polar layer.

44
Q

What does the enzyme flippase do?

A

Catalyzes movement form the external side of the cell to the internal side. (opposite of floppase)

45
Q

What does the enzyme floppase do?

A

Catalyzes movement form the internal side of the cell to the external side. (opposite of flippase)

46
Q

What are popular metabolic pathways?

A

Glycolysis
Gluconeogenesis
Citric Acid Cycle (Krebs Cycle)
Beta-Oxidation

47
Q

What are the especially important steps of a metabolic pathway and why?

A
  1. Highly energetically unfavorable steps
    tend to be regulated.
  2. Early steps tend to be regulated as part of
    negative feedback processes
  3. Final steps can be regulated. It allows
    cells to keep a close eye on end product
    concentration.
48
Q

What is isomerization?

A

The process by which one molecule is transformed into another molecule which has exactly the same atoms but different arrangement.

49
Q

What are some important questions to ask about metabolic pathways?

A

What’s the point? Where does this happen? What goes in and comes out? Which are the most important steps and why? How is this process regulated?

50
Q

What is metabolism?

A

How cells produce energy. Relies on electron transfers.

Biochem MCAT (7 decks)

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