Dental Biochemistry

Front 1

1. What is demineralization and mineralization in the dental enamel?

How is re-mineralization sustained?

Back 1

Leaching of calcium and phosphate ions

Re-deposition of them

Calcium and phosphate ions are present in the salivia

Front 2

2. What is demineralization dependent on?

Back 2

H+ concentration

Acidity promotes demineralization

Major source of acidity in mouth anaerobic metabolism of carbs by bacteria embedded in dental plaque

*saliva contains a buffer to help stabilize pH of mouth

Front 3

3. How are bonds under physiological conditions?

Back 3

Covalent bonds are very stable

Most biochemical reactions do not react spontaneously under physiological conditions

Front 4

4. What is the energy currency of the cell?

Where is the the energy stored?

Back 4

ATP
-it cannot get out of the cell (intracellular)

Store energy in phosphate anhydride bonds

Front 5

5. What are the properties of covalent bonds?

Three points

Back 5

1. Pair of electrons are shared

2. Stable under physiological conditions
-to break or reform requires catalysts at physiological conditions

3. Well defined geometry
-characteristic length
-characteristic direction in space

Front 6

6. Six atoms to study metabolic chemistry

Back 6

Carbon
Hydrogen
Oxygen
Nitrogen
Sulfur
Phosphorus

Front 7

7. What is valence?

Back 7

Number of covalent bonds at atom usually forms

Valence is determined by number of unpaired electrons atoms possesses

Front 8

8. What is the valence for the six atoms to know?

Back 8

H - 1
C - 4
S - 2
O - 2
N - 3
P - 5

Front 9

9. What is electronegativity?

What are the relative electronegativities?

Why are they important?

Back 9

Affinity for electrons

P ~ H < C ~ S < N << O

Determine distribution of electrons and hence electrical charge within a covalent bond

Front 10

10. What is atomic geometry?

What is carbons atomic geometry?

Why this shaper?

Back 10

Bond angles

Tetrahedral 109.5 degrees

Maximum separation of bonding electrons pairs

Front 11

11. What is N atomic geometry?

Back 11

Puckered tetrahedron configuration with three single bonds and one non-bonded pair of electrons

107 degrees

Front 12

12. What is O and S atomic geometry?

Back 12

Bent tetrahedron configuration

Two single bonds and two non-bonded pair of electrons

105 degrees

Front 13

13. What are the geometries of single vs. double bonds?

Back 13

Atoms with only single bonds are tetrahedral

Atoms in double bonds are flat and planar
-bonded and non-bonded electron pairs point toward corners of equilateral triangle

Front 14

14. What are the bond rotations of single and double bonds?

Back 14

Single bonds form flexible structure with zig-zag shape

Double bonds create flat, rigid structures

Front 15

15. What role do non-bonded electron pairs in N, O, and S play in acid-base reactions?

Back 15

Capture a hydrogen ion (H+) to form additional covalent bond

Resulting molecule now has a net charge of +1

*O holds electrons tighter so keeps electron as non-bonded pair

Front 16

16. What is electron resonance?

Why is delocalization important in resonance structures?

Back 16

Electrons are delocalized

Electrons shared by 3 or more atoms

Delocalization of electron pair lowers its energy stabilizing the resonant structure

Front 17

17. What do hydrogen bonds form between?

What does the strength of hydrogen bonds depend on?

Back 17

O, N, and H

Strong H-bond maximized electrostatic interactions

Strength depends on precise distance and orientation bwt participating atoms
-H and 2 atoms should be in straight line

*Also don't want to be in aqueous soln b/c water competes for H-bonds

Front 18

18. Where are ionic bonds only stable and why?

Back 18

In non-aqueous environments

Because water readily dissolves ions

Front 19

19. What types of structures do molecules that are partly polar and non-polar form?

Back 19

1. Keep polar parts in contact with water

2. Keep non-polar parts away from water

3. Leave a minimum of empty space
-densest packing of atoms

Front 20

20. Definition of acid and base.

Back 20

Acid can donate or release H+
-proton donor

Base can accept or react with H+
-proton acceptor

Front 21

21. How is a molecule classified as an acid or base?

Back 21

Acid if uncharged form is a proton donor
*many acids exist as conjugate base at physiological pH

Base if uncharged form is proton acceptor
*many bases exist as conjugate acid at physiological pH

Front 22

22. How is pH and H+ related?

How does [H+] change with pH?

What is physiological pH?

Back 22

Inverse relationship

Higher pH means lower [H+]

Lower pH mean higher [H+]

*[H+] changes 10-fold when pH changes by 1 unit

7.4

Front 23

23. Why are [H+] and pH so important?

Which conditions favor protonated form and vice versa?

Back 23

Function molecules depend on whether they are protonated or unprotonated

High [H+] favor protonation (AH form)

Low [H+] favors deprotonation (A- formation)

Front 24

24. How does pH affect proteins?

Back 24

Function is very sensitive to pH
-decrease function
-irreversible structural changes (denaturation)

This is main reason why pH is critical biological systems

Front 25

25. What is Ka?

Back 25

Acid dissociation constant

concentration of dissociation products / concentration of protonated species

Front 26

26. What does is mean when Ka equal [H+]?

What does a large or small Ka mean?

Back 26

[A] = [HA]

Larger Ka = stronger acid (greater tendency to dissociate)
Smaller Ka = weaker acid

Front 27

27. How is pKa and pH related?

Back 27

pKa = -logKa

Higher Ka then lower pKa
(inverse relationship)

Front 28

28. What is the Henderson Hasselbalch equation?

What are some important points about it?

Back 28

Using pKa to get in terms of pH

1. pH = pKa at midpoint
2. At midpoint [HA] = [A]

Front 29

29. What are the two situations with pH and pKa being different?

Back 29

1. pH is higher than pKa
-lower [H+]
-favor dissociation

2. pH is lower than pKa
-higher [H+]
-favor protonation

Front 30

30. What is a buffer?

Back 30

Substance acts as a buffer if it can react with either added H+ or added -OH to get rid of at least some
*not all removed

Buffer minimizes pH change

Front 31

31. When do buffers work well?

Back 31

When the pH is near their pKa

Work poorly at pH's far from their pKa

Front 32

32. What is carbonic anhydrase?

Back 32

Catalyizes the reaction

CO2 + H2O -> H2CO3

Front 33

33. What is the pK of the bicarbonate system?

Why does it still work?

Back 33

6.41 - that's more than 1 pH unit away from pH of blood (7.4)

System still works b/c it is an open system
-natural presence of CO2 gas at partial pressure of 40 mm Hg in lungs maintains the CO2(d) at a fairly constant level

Front 34

34. General structure of amino acid

Back 34

1. Alpha carbon

2. Side chain (R)

3. Amino Group (NH2)

4. Carboxylic acid (COOH)

Front 35

35. What are the 8 amino acids in the nonpolar group?

Back 35

1. Alanine
2. Valine
3. Leucine
4. Isoleucine
5. Methionine
6. Proline
7. Phenylalanine
8. Tryptophan

Front 36

36. What are the 7 amino acids in the polar, uncharged group?

Back 36

1. Serine
2. Threonine
3. Tyrosine
4. Glutamine
5. Asparagine
6. Glycine (no R group)
7. Cysteine

Front 37

37. What are the 2 acidic amino acids?

Back 37

1. Glutamate

2. Aspartate

Front 38

38. What are the 3 basic amino acids?

Back 38

1. Arginine

2. Lysine

3. Histidine

Front 39

39. What ionizable groups in amino acids are always negative and why?

Back 39

Terminal carboxyl group: 3.1

Aspartic and glutamic acid: 4.2

*Always negative b/c pK is so low

Front 40

40. Which amino acid is useful as a proton exchanger and why?

Back 40

Histidine

pK is near physiological pH

Front 41

41. Which ionizable groups in amino acids are always positive and why?

Back 41

Tyrosine
Lysine
Arginine (most basic)

Always protonated at physiological pH b/c they have high pK's

Front 42

42. What is an alpha helix?

What is a beta sheet?

Back 42

In peptide backbone, Hydrogen bonds bwt each carbonyl oxygen atom and amide hydrogen of amino acid reside

Bonding is between adjacent strands
*antiparallel beta sheets have nice linear bonds
*parallel have distorted H-bonds and are less stable

Front 43

43. How does the tertiary structure of proteins fold?

Back 43

Hydrophobic interior

*hydrophobic interactions are most powerful driving force of tertiary folding

Also have ionic bonds between oppositely charges sides chains
-can be strong b/c of the absence of water

Front 44

44. How does the pH change when a person eats candy?

Back 44

Sugar increases metabolic acids
BUT
Sweet, chewy, or tarty taste will increase bicarbonate buffer reaction

Can have either increase or decrease in pH if one process increases more than another

Front 45

45. How are these local processes?

Back 45

Feeding bacteria is most significant where there is abundant dental plaque (that's where they live)

Neutralization occurs best where there is more saliva

Front 46

46. Where is the most risk for demineralization?

Back 46

At areas sequestered with plaque that saliva cannot reach

Front 47

47. Why does lemon juice not raise the oral cavity pH greatly?

Back 47

Ingest citric acid directly so acidity is easy to neutralize b/c mixes with saliva (readily buffer it)

Front 48

48. Why was swallowable vitamin C more acidic than chewable?

Back 48

Swallowable had only ascorbic acid
so mostly HA

Chewable had ascorbic acid and sodium ascorbate (more of this to raise pH)

Front 49

49. Where do disulfide bonds exist in proteins?

Back 49

Only exist in proteins that are for outside the cell

At air interface disulfide bonds are present b/c don't have H-bonds and can't rely on hydrophobic bonds to stabilize protein

Front 50

50. Summary of essential points on enzymes.

Five points

Back 50

1. All reactions are reversible

2. Every reaction has characteristic equilibrium described by Keq and G

3. Enzymes don't change Keq and G

4. Enzymes accelerate both forward and reverse reactions

5. Enzymes accelerate reactions by stabilizing T.S

Front 51

51. Summary of essential concepts of enzyme catalysis.

Five points

Back 51

1. Enzymes bind substrate into ES complex via non-covalent interactions

2. Binding energy provides force to distort conformation of S and E

3. S forces into shape resembling TS

4. Non-covalent bonding by S atoms far from the reactive bond(s) accounts for substrate specificity

5. Several catalyic residues account for ability of enzymes to pull apart strong bonds

Front 52

52. Enzyme kinetics and reaction rates

Back 52

Uncatalyzed - depends on [R] in linear fashion

Catalyzed - rate leels out at high [S] (saturation or hyperbolic kinetics)

Front 53

53. Vmax measures what?

Km measures what?

Back 53

Max capacity of enzyme
-depends on how much E is present

Intrinsic property of E
-measures affinity of E for S

Km is [S] at which activity of enzyme is half of Vmax

Front 54

54. Isozymes

Back 54

Enzymes that catalyze the same reaction but have different amino acid sequences