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BBMB 316 > Exam 1 > Flashcards

Exam 1 Flashcards

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1
Q

What is the random molecular motion also known as?

A

Brownian Movement

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2
Q

After hydrogen and oxygen, the next most common element in the living system is what?

A

carbon

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3
Q

T/F: The three-dimensional structure of protein is dictated by the sequence of amino acids that constitute the protein

A

True

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4
Q

What three organelles have a double memebrane?

A

nucleus, mitochondria, and chloroplast

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5
Q

Identify the unbranched polymer that, when folded into its three-dimensional shape, performs much of the work of the cell.

A

Protein

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6
Q

What are the two groups that water can form hydrogen bonds with?

A

carbonyl and amine groups

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7
Q

What are the three interactions/bonds that are considered noncovalent bonds?

A

Van Der Waals interactions
hydrogen bonds
ionic interactions

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8
Q

What would be the effect of an organic solvent on electrostatic interactions, when compared with a polar solvent?

A

electrostatic interactions would be stronger

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9
Q

What is the attraction when hydrogen bonds are within liquid water?

A

the attraction is between H+ and OH- ions of the liquid

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10
Q

The loss of a proton (H+) from a water molecule is known as what?

A

dissociation

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11
Q

What does pKa mean?

A

the pH at which the concentration of the acid equals the concentration of the conjugate base

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12
Q

The polyportic molecule aspartic acid, with three ionizable acidic-side chains, has ________ potential buffering regions?

A

3

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13
Q

What is the Henderson-Hasselbach equation?

A

pH = pKa + log10 [A-]/[HA]

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14
Q

What are the two atoms commonly foudn in biological molecules that are often hydrogen-bond acceptors?

A

oxygen and nitrogen

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15
Q

What two amino acids contains an alkyl group side chain?

A

valine and isoleucine

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16
Q

T/F: for a single amino acid residue within a polypeptide chain, pure single bonds are formed between the a-carbon atom and its amino and carbonyl groups, allowing peptide unit rotation

A

True

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17
Q

What does the formation of an a-helix of B-sheet require?

A

hydrogen bonds between peptide - NH and C=O groups

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18
Q

What are nonregular, nonrepetitive secondary structures?

A

bends, loops, and turns that do not have a repeating element

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19
Q

What is the spatial arrangement of subunits and th enature of their interactions also known as?

A

quanternary structure

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20
Q

Two-dimensional electrophoresis is a combination of which two techniques?

A

isoelectric focusing and SDS-PAGE

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21
Q

What technique is based on separation of proteins due to size differences?

A

gel-filtration chromatography

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22
Q

What is the difference between a hypotheses and a theory?

A

hypotheses are usually narror in scope while theories ahve a broader explanatory power

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23
Q

T/F: most atoms in the universe were made by the process of nuclear fusion

A

true

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24
Q

What will you find if you break open a brain cell and a bacterial cell and analyze the contents?

A

they contain basically the same kinds of chemicals

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25
What did prebiotic ear contain little of?
dioxygen
26
What is responsible for initially poisoning the earth with dioxygen?
photosynthetic organisms
27
Entropy decreasing in a livign organism is offset by what?
entropy increasing in their surroudings
28
T/F: ionic bonds and hydrogen bonds have the same strength as covalent bonds
false
29
What is the length of an ideal hydrogen bond (as defined in th lectures)?
3Å
30
The boiling point and freezing point of water is ____ and ____ compared to other comparable small molecules
higher, higher
31
Of the following, which amino acid is most disruptive to an alpha helix? a) Pro b) Ala c) Glu d) Leu e) Met
a) Pro
32
How are parallel beta sheets distinguished from antiparallel sheets?
the pattern of H-bonding between strands and the relative directionality of the associated strands
33
What properties of a partien contribute to their absorbance of UV and visible light?
W and Y side chains and peptide bonds
34
T/F: the strength of the interaction between a protein and a hydrophobic interaction resin is increased by the addition of salt
True
35
What is the highest level of structure associated with a protein with two subunits in its active state?
quarternary
36
What does a Ramachandran plot tell you?
steric restrictions on combinations of Phi and Psi bond angles
37
What is important for the mechanism of protein folding?
folding progresses with retention of correct partial structure and the hydrophobic affect contributes to the energetics of the process
38
The phi bond angle is between which two atom types?
carbon and nitrogen
39
T/F: sodium dodecyl sulfate (SDS) is only used in PAGE analysis with folded proteins
False
40
Histidine-tags on recombinant protein is considered which type of purification chromatography?
affinity
41
What two things are used to reduce/break disulfide bonds?
dithiothreitol (DTT) and beta mercaptoethanol (BME)
42
In size exclusion chromatography, larger molecules will generally behave how, compared to smaller molecules? | 2
they will move faster through the column and they will not go into the pores of the beads, but will instead go around the beads
43
Why does DNA form a helix?
hydrophobic nitrogenous base pairs want to exclude water
44
What re nucleosomes and chromatin made up of?
DNA and histones
45
What is the role of DNA ligase?
to make phosphodiester bonds
46
What is the role of a restriction enzyme?
to cleave DNA specific sequence and is used to prepare DNA in a predictable, reproducible manner
47
What two enzymes are often used in forensic DNA analysis?
DNA polymerase and restriction enzymes
48
What does the Gibson syntehsis used for?
to synthesize very long strands of DNA
49
How do you read a DNA sequencing gel in order to figure out the sequence of the newly formed strand of DNA?
you start at the bottom and recored T, C, G, and A as they appear from the bottom to the top
50
What will happen if you leave out one of your primers while running a PCR reaction?
one DNA strand will be replicated with a linear dependence on cycles
51
What are the three methods used to synthesize DNA polymers in the laboratory?
gibson synthesis, PCR, and phosphoramidite synthesis
52
What 3 enzymes are used to build new nucleic acid polymers in the 5' to 3' direction?
DNA polymerase, RNA polymerase, and reverse transcription
53
T/F: uncharged polar functional groups can participate in dipole-dipole interactions with water
True
54
What is the thermodynamic force that drives hydrophobic interactions?
entropy
55
What are electrostatic interactions between atoms with opposite electrical charge called?
ionic bonds or salt bridges
56
What is the functional group that is most likely responsible for an organic molecule to act as an acid?
carboxyl group
57
What can carbon be oxidized by?
the loss of electrons by the addition of oxygen
58
What is the organelle that is the site for carbohydrate addition to protiens?
golgi complex
59
What determins how a protein folds?
the order of the amino acids found in the sequence
60
What do lysomes contain?
digestive enzymes
61
What does the entropy of a reaction refer to?
the tendency of the system to move toward maximal randomness
62
What does the hydrogen bond typically form between when a water molecule is with another biomolecule?
between a hydrogen atom and either a nitrogen, sulfur, or oxygen atom
63
What are the three groups that determines the Van Der Waals interaction in a biological system?
hydrophobic groups, polar groups, and nonpolar groups
64
What is the result of the addition of a proton to a water molecule?
hydronium ion
65
What type of ion does a buffer accept and donate?
hydrogen ion when in excess and donates hydrogen ions when they have been depleted
66
What does it mean if the pH of the solution is below the pKa?
the protonated form predominates and amino acids act as true acids capable of donating H+
67
What does it mean if the pH of the solution is above the pKa of the ionizable group?
the deprotonated form predominates and amino acids excist as conjugate bases, capable of accepting an H+
68
What are the seven common amino acids that have ionizable side chains (R groups) with additional pKa values?
tyrosine cysteine arginine lysine histidine apartic acid glutamic acid

BBMB 316 (1 decks)

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