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Biochemistry > Biochem Exam#1 Study Guide > Flashcards

Biochem Exam#1 Study Guide Flashcards

1
Q

Properties of atoms are defined by?

A

valence electrons

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2
Q

Octet Rule

A

Atoms try to have full outer shells either by giving up or receiving electrons

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3
Q

Electronegativity

A

Tendency of an atom to gain bonding pairs to fill/empty their outer shell

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4
Q

What is electronegativity based on?

A

atoms pull of electrons toward their nucleus

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5
Q

What are the 3 types of bonding?

A

covalent, polar covalent, ionic

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6
Q

Covalent Bond

A

equal sharing of electrons

EN<.4

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7
Q

Polar Covalent Bond

A

Unequal sharing of electrons

.5<1.2

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8
Q

Ionic Bond

A

Full on stealing of electrons from one atom by another

EN>1.21

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9
Q

What are the 4 types of molecule interactions?

A

Van der Waals
Hydrogen Bond
Hydrophobic Interactions
Electrostatic Interactions

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10
Q

Van der Waals

A
  • An uncharged molecule is induced with a charge, causing a charge on the neighboring molecule
  • Induced Dipole:Induced Dipole
  • weakest interactions
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11
Q

Hydrogen Bonds

A
  • Stronger than VDW
  • Sharing of a hydrogen atom
  • Bonding involves a donor and an acceptor
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12
Q

Electrostatic Interactions

A

Made with + or partial + and - or partial -

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13
Q

Hydrophobic Interactions

A
  • nonpolar molecules attempt to get away from water

* strongest IMF

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14
Q

Amphiles

A

a molecule that contains both polar and nonpolar parts

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15
Q

Intermolecular Forces are also known as

A

non covalent bonds

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16
Q

6 Characteristics as to why water is awesome

A 
Neutral
High Surface Tension
Universal Solvent
Liquid at room temp
High Specific Heat Capacity
High Dielectric Constant
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17
Q

What does “p” stand for?

A

-log

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18
Q

Strong Acid pH; Strong Base pH

A

Acid=1

Base=14

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19
Q

Acid

A

BL:donates protons
L: accepts electrons

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20
Q

Base

A

BL: accepts protons
L: donates electrons

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21
Q

Why are buffers needed?

A

to resist change in pH

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22
Q

LaChateliers Principle

A

equilibrium will shift in response to a change in concentration, pressure, temperature, or volume

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23
Q

What does it mean if the pka=pH

A

the amount of protonated to deprotonated molecules is 1:1

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24
Q

If the pka is higher than the pH, then…

A

there will be more protonated (HA) molecules

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25
Q

If the pka is lower than the pH, then…

A

there will be more deprotonated(A-) molecules

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26
Q

What type of buffer is used in the cell cytoplasm & blood

A 
phosphate buffer (cell cytoplasm)
carbonate (Blood)
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27
Q

Components of an amino acid

A

N:Amine
C:Carboxylate
R: Side Chain

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28
Q

What is the approximate pH of the C terminus?

A

~2

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29
Q

What is the approximate pH of the N terminus?

A

~9

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30
Q

Asp & Glu act as Nu at pH=7, what does this mean?

A

they act as a base, they want to accept protons and donate electrons

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31
Q

Lys & Arg act a E+ at pH=7, what does this mean

A

they act as an acid, they want to donate protons and accept electrons

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32
Q

Isoelectric point

A

pH where a majority of the species has a charge of 0

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33
Q

How are amino acids combined?

A

via dehydration synthesis

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34
Q

Dehydration

A

Bonds are formed from the release of water

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35
Q

Primary Amino Acid

A

Peptide Chain

36
Q

Secondary Amino Acid

A

Hydrogen bonds between amino acids

37
Q

What are the 2 types of secondary amino acids?

A

alpha helix & beta sheets

38
Q

Which type of beta sheet is more stable?

A

anti-parallel

39
Q

Tertiary Amino Acid

A

intermolecular forces between the amino acid side chains

40
Q

Quaternary Amino Acid

A

2 or more independent polypeptides come together

41
Q

Native Conformation

A

Final Structure

Can be tertiary or quaternary

42
Q

Motif

A

specific cluster of secondary structure units

43
Q

Domain

A

Structurally stable & independent unit with the native structure

44
Q

pH, substrate/enzyme, space/environment can result in…

A

a conformation change

45
Q

Who aids in folding of proteins in crowded spaces?

A

chaperones

46
Q

What is the systematic steps for folding?

A

denatured->molten globule->native conformation

47
Q

What causes a denatured protein to fold into a molten globule?

A

hydrophobic effect

48
Q

What causes a protein in its molten globular state to fold into its native conformation?

A

IMF between “R” groups

49
Q

Delta G

A

Gibbs Free Energy

50
Q

Delta H

A

Enthalpy

51
Q

Delta S

A

Entrophy

52
Q

Heat in___bonds, while Heat out____ bonds. Which is more stable?

A

Break/creates

Heat out

53
Q

Is a denatured peptide or a peptide in its native conformation considered disordered?

A

denatured

54
Q

Equation for Gibbs Free Energy?

A

Delta G=Delta H- temp(delta S)

55
Q

Protein Purification

A

isolating 1 protein from an entire organism

56
Q

What characteristics are important for isolation of a protein? (5)

A 
Size
pI
Solubility
Stability
Subject to Contamination
57
Q

What are the steps to isolate a protein?

A
  1. homogenize
  2. centrifuge
  3. precipitation (salt)
  4. chromatography
  5. analysis
58
Q

What is used to create a precipitate for protein isolation?

A

ammonium sulfate

59
Q

What is the purpose of (NH4)2SO4?

A

to move water away from the protein, so that proteins can bind proteins

60
Q

What process is used to separate the salt and water?

A

dialysis= buffer exchange

61
Q

What is the type of column based on for chromatography?

A

depends on the final globular protein on the resin

62
Q

The ion exchange separated based on_____.
+ resin=_____ exchange
- resin=______exchange

A

the charge
anion
cation

63
Q

During gel filtration what type of protein comes out first?Why?

A

heavy because the small go through the holes of the gel

64
Q

SDS page, the bigger proteins move____. And is based on protein___. The proteins move toward the ___ pole.

A

slower; size

65
Q

Myoglobin and Hemoglobin are not _____ instead they are _____

A

enzymes; globular proteins that carry oxygen

66
Q

All of the alpha helices of myoglobin are ___, while the heme is the ____

A

protein part; non protein part

67
Q

protein + non protein

A

holoprotein

68
Q

protein part

A

apoprotein

69
Q

non protein part

A

prosthetic group

70
Q

What is the purpose of myoglobin?

A

to store oxygen for the muscles

71
Q

What is the difference between Mb and Hb?

A

Hb is made up of 4 polypeptide chains that take oxygen from the lungs to O2 derived tissues

72
Q

What is in the middle of the heme? What kind does it need to be for oxygen to bind?

A

Fe (Iron); Fe2+

73
Q

How many coordination sites does hemoglobin have? What are they used for?

A

4 from heme
5th- proximal histidine (holds Fe)
6th- distal hisitidine (holds O2)

74
Q

When O2 binds, this causes______.

A

a conformational change in the proximal His

75
Q

How does Hb hind to O2?

A

with coopertivity

76
Q

Which has a better affinity for oxygen (Mb or Hb)?

A

myoglobin

77
Q

What are the 2 types of cooperative models?

A

concerted & sequential

78
Q

Concerted Model

A

Each heme is viewed together as a group

An equilibrium exists between T&R state

79
Q

Sequential Model

A

Each heme as viewed individually.

Each heme has better affinity

80
Q

Which model of cooperative is best?

A

Its is a combined model O2 makes Hb T->R and each heme is more exposed and those have better affinity for O2

81
Q

What does 23BPG do to Hb?

A

binds HbT and keeps in the T state until there are high levels of oxygen

82
Q

Bohr effect

A

pH changes the affinity of O2 to Hb

83
Q

What are the allosteric inhibitors of Hb?

A

2,3BPG inhibit T->R

CO2 & H+ inhibit R->T

84
Q

Steps to take O2 to O2 starved tissues?

A
  1. inhale O2 to increase concentration in lungs
  2. deoxyHb(T) converted to Hb(R)
  3. OxyHb(R) in blood find O2 starved tissue
85
Q

How does hemoglobin bind O2?

A

allosterically

Biochemistry (14 decks)

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