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Biochemistry > Life, Water, Amino Acids, Proteins > Flashcards

Life, Water, Amino Acids, Proteins Flashcards

1
Q

What is the more complex of the cell types?

A

Eukaryotes

Enclosed organelles

Both have rhibosomes

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2
Q

What causes hydrogen bonding?

A

Electronegativity difference (dipoles)

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3
Q

What are the four weak forces?

A
  1. Hydrogen Bonds
  2. Van der Waals Forces
  3. Hydrophobic Interactions
  4. Electrostatic/Ionic Interactions
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4
Q

Which atom pulls the electron cloud towards itself resulting in a partial charge and giving rise to a dipole?

A

The more electronegative atom

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5
Q

Two atoms attract one another until they get too close

A

Van Der Waals foreces

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6
Q

Any interactions where there is a charge differential leading to an attractive force

A

electrostatic interaction

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7
Q

In an aqueous environment, non-polar molecules will gather together to reduce their surface area

A

Hydrophobic Interactions

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8
Q

These are used as buffers

A

weak acids or weak bases

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9
Q

proton donor

A

acid

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10
Q

proton acceptor

A

base

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11
Q

The _____ Ka is, the stronger the acid

A

larger

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12
Q

The _____ pKa is, the stronger the acid

A

lower

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13
Q

What is the equation for Ka?

A

HxA/HA

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14
Q

What is the equation for pKa?

A

-logKa

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15
Q

What is the equation for pH?

A

-log H

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16
Q

What is the Henderson-Hasselbalch equation?

A

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

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17
Q

R group is nonpolar

A

Hydrophobic/Nonpolar

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18
Q

R group has electronegative atoms that are not charged at normal pH ranges

A

Polar-Neutral

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19
Q

R group has electronegative atoms that are positively charged at physiological pH

A

Polar Charged/Positive

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20
Q

R group has electronegative atoms that are negatively charged at physiological pH

A

Polar Charged/Negative

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21
Q

What Amino Acid is this?

Polarity?

A

Glycine

Gly

G

Nonpolar

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22
Q

What Amino Acid is this?

Polarity?

A

Alanine

Ala

A

Nonpolar

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23
Q

What Amino Acid is this?

Polarity?

A

Valine

Val

V

Nonpolar

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24
Q

What Amino Acid is this?

Polarity?

A

Leucine

Leu

L

Nonpolar

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25
Q

What Amino Acid is this?

Polarity?

A

Isoleucine

Ile

I

Nonpolar

26
Q

What Amino Acid is this?

Polarity?

A

Methionine

Met

M

Nonpolar

27
Q

What Amino Acid is this?

Polarity?

A

Proline

Pro

P

Nonpolar

28
Q

What Amino Acid is this?

Polarity?

A

Phenylalanine

Phe

F

Nonpolar

29
Q

What Amino Acid is this?

Polarity?

A

Tryptophan

Trp

W

Nonpolar

30
Q

What Amino Acid is this?

Polarity?

A

Serine

Ser

S

Neutral Polar

31
Q

What Amino Acid is this?

Polarity?

A

Threonine

Thr

T

Neutral Polar

32
Q

What Amino Acid is this?

Polarity?

A

Tyrosine

Tyr

Y

Neutral Polar

33
Q

What Amino Acid is this?

Polarity?

A

Cysteine

Cys

C

Neutral Polar

34
Q

What Amino Acid is this?

Polarity?

A

Asparagine

Asn

N

Neutral Polar

35
Q

What Amino Acid is this?

Polarity?

A

Glutamine

Gln

Q

Neutral Polar

36
Q

What Amino Acid is this?

Polarity?

A

Lysine

Lys

K

Polar Positive

37
Q

What Amino Acid is this?

Polarity?

A

Arginine

Arg

R

Polar Positive

38
Q

What Amino Acid is this?

Polarity?

A

Histidine

His

H

Polar Positive

39
Q

What Amino Acid is this?

Polarity?

A

Aspartic Acid

Asp

D

Polar Negative

40
Q

What Amino Acid is this?

Polarity?

A

Glutamate

Glu

E

Polar Negative

41
Q

L is almost always __and D is almost always __

A

S, R

42
Q

What happens at conditions pH <2?

A

H3N+

CO2H

43
Q

What happens at conditions pH ~6?

A

H3N

CO2-

44
Q

What happens at conditions pH >10?

A

H2N

CO2-

45
Q

Simple linear structures that serve primarily as structural components in cells.

A

Fibrous proteins

46
Q

Roughly spherical with hydrophobic amino acids towards center and hydrophilic (polar) amino acids towards the outside

A

Globular proteins

47
Q

Found associated with membranes. Hydrophobic residues point outwards (to interact with hydrophobic lipid membrane) with hydrophobic inwards

A

Membrane proteins

48
Q

What configuration is this?

A

Staggered Anti

49
Q

What configuration is this?

A

Staggered Gauche

50
Q

What configuration is this?

A

Eclipsed

51
Q

What angle is this?

A

Phi Angle

52
Q

What angle is this?

A

Psi Angle

53
Q

Name a Mixed alpha and beta motif

A

Rossman Fold

TIM Barrel

Leucine Rich Repeat Protein

Flavodoxin Fold

Thioredoxin Fold

54
Q

Name an alpha helix motif

A

Coiled coil

Helix bundle

Globin fold

Homeodomain fold

55
Q

Name a Beta Motif

A

Greek key

Jellyroll

Beta Barrel

Beta propeller

56
Q

Structure: the amino acid sequence of the protein, read from the N- to C-terminus

A

Primary Structure

57
Q

Structure: alpha helices and beta sheets, induced by primary sequence and held together by weak forces

A

Secondary Structure

58
Q

Structure: overall 3D shape of the protein, stabilized by interactions of various R groups

A

Tertiary Structure

59
Q

Structure: interactions of multiple subunits in a complex

A

Quarternary Structure

60
Q

Overall 3-D architecture of a protein

A

Conformation

61
Q

Part of a polypeptide chain that can fold and possible function on its own.

A

Domain

62
Q

A recurring structural element found in various proteins that may or may not have an evolutionary relationship.

A

Motif

Biochemistry (12 decks)

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