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BBMB 316 > Exam 1 > Flashcards

Exam 1 Flashcards

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
Q

What did prebiotic ear contain little of?

A

dioxygen

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26
Q

What is responsible for initially poisoning the earth with dioxygen?

A

photosynthetic organisms

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27
Q

Entropy decreasing in a livign organism is offset by what?

A

entropy increasing in their surroudings

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28
Q

T/F: ionic bonds and hydrogen bonds have the same strength as covalent bonds

A

false

29
Q

What is the length of an ideal hydrogen bond (as defined in th lectures)?

A

3Å

30
Q

The boiling point and freezing point of water is ____ and ____ compared to other comparable small molecules

A

higher, higher

31
Q

Of the following, which amino acid is most disruptive to an alpha helix?

a) Pro
b) Ala
c) Glu
d) Leu
e) Met

A

a) Pro

32
Q

How are parallel beta sheets distinguished from antiparallel sheets?

A

the pattern of H-bonding between strands and the relative directionality of the associated strands

33
Q

What properties of a partien contribute to their absorbance of UV and visible light?

A

W and Y side chains and peptide bonds

34
Q

T/F: the strength of the interaction between a protein and a hydrophobic interaction resin is increased by the addition of salt

A

True

35
Q

What is the highest level of structure associated with a protein with two subunits in its active state?

A

quarternary

36
Q

What does a Ramachandran plot tell you?

A

steric restrictions on combinations of Phi and Psi bond angles

37
Q

What is important for the mechanism of protein folding?

A

folding progresses with retention of correct partial structure and the hydrophobic affect contributes to the energetics of the process

38
Q

The phi bond angle is between which two atom types?

A

carbon and nitrogen

39
Q

T/F: sodium dodecyl sulfate (SDS) is only used in PAGE analysis with folded proteins

A

False

40
Q

Histidine-tags on recombinant protein is considered which type of purification chromatography?

A

affinity

41
Q

What two things are used to reduce/break disulfide bonds?

A

dithiothreitol (DTT) and beta mercaptoethanol (BME)

42
Q

In size exclusion chromatography, larger molecules will generally behave how, compared to smaller molecules?

2

A

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
Q

Why does DNA form a helix?

A

hydrophobic nitrogenous base pairs want to exclude water

44
Q

What re nucleosomes and chromatin made up of?

A

DNA and histones

45
Q

What is the role of DNA ligase?

A

to make phosphodiester bonds

46
Q

What is the role of a restriction enzyme?

A

to cleave DNA specific sequence and is used to prepare DNA in a predictable, reproducible manner

47
Q

What two enzymes are often used in forensic DNA analysis?

A

DNA polymerase and restriction enzymes

48
Q

What does the Gibson syntehsis used for?

A

to synthesize very long strands of DNA

49
Q

How do you read a DNA sequencing gel in order to figure out the sequence of the newly formed strand of DNA?

A

you start at the bottom and recored T, C, G, and A as they appear from the bottom to the top

50
Q

What will happen if you leave out one of your primers while running a PCR reaction?

A

one DNA strand will be replicated with a linear dependence on cycles

51
Q

What are the three methods used to synthesize DNA polymers in the laboratory?

A

gibson synthesis, PCR, and phosphoramidite synthesis

52
Q

What 3 enzymes are used to build new nucleic acid polymers in the 5’ to 3’ direction?

A

DNA polymerase, RNA polymerase, and reverse transcription

53
Q

T/F: uncharged polar functional groups can participate in dipole-dipole interactions with water

A

True

54
Q

What is the thermodynamic force that drives hydrophobic interactions?

A

entropy

55
Q

What are electrostatic interactions between atoms with opposite electrical charge called?

A

ionic bonds or salt bridges

56
Q

What is the functional group that is most likely responsible for an organic molecule to act as an acid?

A

carboxyl group

57
Q

What can carbon be oxidized by?

A

the loss of electrons by the addition of oxygen

58
Q

What is the organelle that is the site for carbohydrate addition to protiens?

A

golgi complex

59
Q

What determins how a protein folds?

A

the order of the amino acids found in the sequence

60
Q

What do lysomes contain?

A

digestive enzymes

61
Q

What does the entropy of a reaction refer to?

A

the tendency of the system to move toward maximal randomness

62
Q

What does the hydrogen bond typically form between when a water molecule is with another biomolecule?

A

between a hydrogen atom and either a nitrogen, sulfur, or oxygen atom

63
Q

What are the three groups that determines the Van Der Waals interaction in a biological system?

A

hydrophobic groups, polar groups, and nonpolar groups

64
Q

What is the result of the addition of a proton to a water molecule?

A

hydronium ion

65
Q

What type of ion does a buffer accept and donate?

A

hydrogen ion when in excess and donates hydrogen ions when they have been depleted

66
Q

What does it mean if the pH of the solution is below the pKa?

A

the protonated form predominates and amino acids act as true acids capable of donating H+

67
Q

What does it mean if the pH of the solution is above the pKa of the ionizable group?

A

the deprotonated form predominates and amino acids excist as conjugate bases, capable of accepting an H+

68
Q

What are the seven common amino acids that have ionizable side chains (R groups) with additional pKa values?

A

tyrosine
cysteine
arginine
lysine
histidine
apartic acid
glutamic acid

BBMB 316 (1 decks)

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