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Biochemistry 405 > Midterm 1 > Flashcards

Midterm 1 Flashcards

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1
Q

• What are the three domains of life?

A

o Eukaryotes, Archea, and Bacteria

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2
Q

• What is the biggest difference between prokaryotes and Eukaryotes?

A

o Eukaryotes are larger and more compartmentalized into organelles

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3
Q

• Name three organelles for a plant cell and what the functions of it are?

A

o Chloroplast for photosynthesis, mitochondria for energy generation, and nucleus for genetic information storage

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4
Q

• Name three organelles for an animal cell and what the functions of it are?

A

o Lysosome which is the center for protein degradation, nucleus for genetic energy storage, and Mitochondria for energy generation

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5
Q

• What are some ways that organelles differ with each other?

A

o Cofactor content, protein content, DNA or RNA content, pH

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6
Q

• Name the two organelles important in malaria parasite invasion

A

o Microneme and Rhotry which both make proteins needed for entry into the red blood cells

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7
Q

• What is the biomembrane made out of?

A

o Lipids

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8
Q

• Why are lipid membranes important?

A

o They separate the exterior of the cell from the interior and they are a way of separating organelles from the rest of the cell.

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9
Q

• What are the advantages for a compartmentalized system in the Eukaryotes?

A

o Some events inside the organelle may be damaging to the rest of the cell if exposed, such as the processes that happen in the lysosome. Also, the organelle can use the membrane for specialized machinery for its function (such as ETC).

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10
Q

• What is the major component of the cell?

A

o Water

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11
Q

• Name the three major biopolymers and their building blocks

A

o Proteins which are made up of amino acids
o Nucleic acid which is made up of nucleotides
o Polysaccharides which are made up of sugars

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12
Q

• What is the function of DNA?

A

o Information storage and replication

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13
Q

• What is a transfer RNA (tRNA)?

A

o RNA that is attached to an amino acid at its 3’ terminus. With its anticodon attaching to a codon on regular RNA, it aids in the creation of an amino acid chain.

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14
Q

• What is the backbone of RNA called?

A

o The phospho-ribose backbone

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15
Q

• Name two common polysaccharides made up of glucose in plants and animals and their purpose

A

o Cellulose which provides rigidity for plant and glycogen which provides energy storage for animals

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16
Q

• If both glycogen and cellulose are made up of glucose, how are they different?

A

o Cellulose has only α 1-4 linkages while in glycogen, every so many glucose molecules there is an α1-6 linkage.

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17
Q

• What is the primary cellular energy currency?

A

o ATP which is made up of three phosphate groups, a ribose group and an adenine group.

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18
Q

• What is thermodynamics?

A

o The study of energy and its effects on matter

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19
Q

• Why is enthalpy used to look at biological processes instead of energy?

A

o Because the biological processes occur under constant pressure.

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20
Q

• What does entropy favor?

A

o More disorder or an increase in the amount of possibilities of a certain reaction

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21
Q

• What is Gibbs Free energy?

A

o An equation that takes into account both entropy and enthalpy in order to analyze if a reaction will spontaneously occur, it is exergonic. If ∆G is negative, then the reaction will occur spontaneously. If ∆G is positive, the reaction is not thermodynamically favorable, it is endergonic.
∆G=∆H-T∆S

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22
Q

• What does Gibbs Free Energy tell you about the rate of a certain process?

A

o Absolutely nothing, rate is independent of ∆G

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23
Q

• What is a covalent bond?

A

o Link between atoms where the electrons are shared

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24
Q

• What is a noncovalent bond?

A

o A force of attraction between atoms that are not from the sharing of electrons

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25
• What is a dipole molecule?
o When there is a partial positive charge on one area of the molecule and a partial negative charge on another part of the molecule, but this is on neutral molecules and is only due to the chemical properties of the atoms attached to the molecule
26
• Who is awesome?
o Diana *high five self for answering correctly*
27
• What is the weakest non-covalent interaction?
o Van der Waals interaction
28
• What is the strongest Non-covalent interaction?
o Dipole-dipole interactions
29
• Name the basic property of the water molecule that allows it to be such a wonderous molecule.
o It is a non-linear molecule that has a permanent dipole due to the oxygen. Also, the hydrogen non-covalently bonded to oxygen comes closer than the Van der Waals radius which is very uncommon
30
• How close can two molecules come close to each other?
o The sum of the Van der Waals radii between the two atoms
31
• How many water molecules does each ice molecule interact with? What about water?
o Four water molecules for ice and less than that for water because water is very dynamic and is constantly moving
32
• Identify the hydrogen bond donor and the hydrogen bond acceptor between water molecules?
o The oxygen carrying the hydrogen bond non covalently bonded to the other oxygen is the hydrogen bond donor, while that Non-covalently bound oxygen to the hydrogen is the hydrogen bond acceptor
33
• Name some good hydrogen bond acceptors
o The carbonyl oxygen on a carbonyl group | o A nitrogen with two free electrons
34
• What property of the water molecule allows for Ions in solution to be easily dissolved by water?
o The permanent dipole on water interacting with the ion charge
35
• What is a hydration shell?
o When you have ions in a solution of water and the water molecules form all the way around the ion. Because water is very dynamic, the position of the water changes all the time in the hydration shell
36
• What are hydrophobic interactions?
o When non-polar molecules that do not react with water are placed in water
37
• What happens during hydrophobic interactions?
o Proteins will begin to fold o Hydrophobic molecules with tend to clump together to increase the entropy of the water o The placement of hydrophobic molecules into an aqueous environment also aids in the formation of DNA and RNA and well as lipid Bilayers in cells
38
• Describe the enthalpy and entropy of placing a hydrophobic molecule in water
o Since this reaction does not involve any heat, there is no enthalpy change, but because the formation and clumping of hydrophobic molecules increase the space water has to move, therefor increasing disorder, the entropy is positive and high.
39
• What drives the reaction of the grouping of hydrophobic molecules in water?
o Since there is no enthalpy change, the entire reaction is entropy driven
40
• What is an amphiphilic molecule?
o A molecule with both a polar and non-polar end (hydrophobic and hydrophilic)
41
• What are micelles?
o A formation of amphipathic molecules where it looks like a sphere with the polar head interacting with the water and the nonpolar region away from the water and clustered on the inside.
42
• What determines whether a lipid bilayer forms or a micelle?
o Properties of amphiphile, pH, temperature, and ion concentration It is very energetically unfavored for the water to be within the center of the miscelle (hydrophobic effect). That is the problem of it getting bigger because water becomes to appear in the center. To counter this energetically unfavored interactions, the miscelle caves in and forms the bilipid layer.
43
• Define the Bronsted Lowry acids and base
o The acid is a proton donor while the base is a proton acceptor
44
• What is the Henderson Hasselbalch equation?
o pH=pKa+log([Base]/[Acid]) | o when concentrations are the same, the pH is the same as the pKa
45
• What is Ka?
o This dissociation constant of an acid (b for base)
46
• Why is pH so important and how it is it controlled by organisms?
o pH determines many things such as the structure of the protein as well as the function. Organisms and scientist can control pH by using buffers Buffers keep the pH under the organisms livable conditions.
47
• What does the influenza virus depend on in order to infect the host?
o The lower pH found in some organelles of the cell allowing for the virus to undergo a conformational change resulting in the injection of genetic material
48
• Can protein cross a lipid membrane?
o No It is highly energetically unfavorable. But their are integral membrane proteins that have nonpolar segments that are in the lipid membrane. They typically have polar regions that stick outside of the cell.
49
• What is an ATPase?
o The big protein complex that sits in the lipid membrane that uses a proton gradient in order to generate ATP. This ATPase uses the rotation from the proton motive force to phosphorylate ADP. It acts like a dam. As the hydrogen passes through the ATPase, it causes a portion of the protein to rotate and induce phosphorlation of ADP.
50
• What are the bonds that hold amino acids together?
o Peptide bonds They are very rigid due to resonance compared to the rest of the bonds. So they do not allow free rotation. But the other bonds along the peptide backbone do allowing alpha helices and beta pleated sheets to form.
51
• What synthesizes a protein?
o Ribosomes
52
• What is it called when there are charges on an amino acid (or molecule in general), but the net charge is zero?
o The molecule is a zwitterion
53
• At what pH does a zwitterion on an amino acid usually form?
o Neutral pH
54
• Name the amino acids with an aliphatic nonpolar side chain
``` o Glycine o Alanine o Proline o Valine o Leucine o Isoleucine o Methionine ```
55
• Why is proline unique?
o Its side chain is bonded to the amine group. Giving it a rigid character compared to other residues (amino acids on the protein,, not a single amino acid)
56
• Why is glycine unique?
o It has no side chain It has an H as a side chain. This allows it to be a more flexible molecule, and least sterically restricted.
57
• What are the two amino acids with a chiral center in its side chain?
o Isoleucine and threonine
58
• What are the amino acids with an uncharged polar side chain?
``` o Serine o Threonine o Cysteine o Asparagine o Glutamine ```
59
• What is a key function for the uncharged polar side chain group amino acids?
o Their side chains can play a role in hydrogen bonding aiding in the formation of protein structure.
60
• What are the amino acids with a positively charged side chain?
o Lysine o Arginine o Histidine
61
• Why is histidine special?
o Due to its strange ring formation, it is helpful in catalysis as well as metal interactions. It has a lower pH compared to its other positively charged side chain group members.
62
• What are the amino acids with a negatively charged side chain?
o Aspartate | o Glutamate
63
• What are the amino acids with an aromatic ring?
o Phenylalanine o Tyrosine o Tryptophan Phenylalanine is a tyrant that be tryppen.
64
• Which side chains in the aromatic amino acid group are amphiphilic?
o Tyrosine and tryptophan
65
• What is special about aromatic amino group side chains?
o They absorb wavelengths at 258 nm. Phenylalanine although absorbs much less that Tyrosine or Tryptophan
66
• What is the pKr of arginine?
o 12.5
67
• What is the pKr of aspartic acid?
o 3.9
68
• What is the pKa of Cysteine?
o 8.3

Biochemistry 405 (2 decks)

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