Chapter 1: Foundations of Biochemistry

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1

Nucleus in

Eukaryotes

2

Nucleoid in

Bacteria

3

Nucleus and Nucleoid

Contain: genetic material, dna, proteins

Nucleus membrane bound

4

Chromatin

DNA + Protein

5

Plasma Membrane

Flexible Lipid Bilayer

Selectively permeable to polar

Membrane Proteins

Separates cell from enviro and regulates movement of material out of cell

6

Membrane Proteins

Functions:

  • Transport
  • Signal Reception
  • Act as enzymes
7

Cytoplasm

Contains:

  • Aqueous cell contents
  • Particles
  • Organelles
8

Supernatant Cytoplasm

Cytosol concentration solutions of enzymes

Contains:

  • RNA
  • Monomeric Subunits
  • Metabolites
  • Inorganic Ions

top in centrifuge

9

Pellet Cytoplasm

Contains:

  • Particles
  • Organelles
  • Ribosomes
  • Storage Granules
  • Mitochondria
  • Chloroplasts
  • Lysosomes
  • ER

bottom in centifruge

10

Animal Cell

Ribosomes

Peroxisomes

Cytoskeleton

Lysosomes

Transport vesicle

Golgi

Smooth and Rough ER

Nucleus

Nucleolus

Mitochondria

Plasma Membrane

Nuclear Envelope

11

Ribosomes (OF ANIMAL CELL)

Protein Sysnthesis

12

Peroxisomes

Destroy Peroxides

13

Cytoskeleton

Supports Cells

Aids in Movement

14

Lysosomes

Degrade Intracellular Debris

15

Transport Vesicle

Shuttles Lipids and Proteins b/w ER, Golgi and plasma membrane

16

Golgi

Complex Processes

PAckages and Target Proteins For Export

17

Smooth ER

Lipid Syn and Drug Metabolism

18

Rough ER

Protein Syn

19

Nucleus

Contains Genes (Chromatin)

20

Nucleolus

Ribosomal RNA syn

21

Mitochondria

oxidizes fuels to produce ATP

22

Nuclear Envelope

Segregates chromatin from cytoplams

23

Bacterial Cell

Nucleoid

Pilli

Flagella

Cell Envelope

Ribosomes

24

Nucleoid

Single, simple long circular DNA

25

Pilli

Provides Points of Adhesion To Surface Of Other Cells

26

Flagella

Movement

27

Cell Envelope

Structure varies w/ type

28

Ribosomes (OF BACTERIA)

smaller than eukaryotic ribosome

protein sys from RNA molecues

29

Nonpolar Amino Acids

Glucine

Alanine

Valine

Leucine

Isoleucine

Methionine

Tryptophan

Phenylalanine

Proline

30

Polar Amino Acids

Serine

Threonine

Cysteine

Tryosine

Asparagine

Glutamine

31

Electrically Charged Amino Acids: Acidic

Aspartic Acid

Glutamic Acid

32

Electrically Charger Amino Acids: Basic

Lysine

Arginine

Histidine

33

Nucleic Acids/ Nitrogenous Bases

Uracil

Thymine

Cytosine

Adenine

Guanine

34

Parent Sugar

alpha-d-glucose

35

5 Carbon Sugar

alpha-D-Ribose

2-proxy-alpha-d-Ribose

36

Lipids

Oleate

Palmitate

Glycerol

Choline

37

Alcohol + Acid=

Ester + H20

38

Monomeric Unit of Chromatin

Nucleotides

39

Macro Molecule of Chromatin

DNA

40

Monomeric Unit of Plasma Membrane

Amino Acids

41

Macro Molecules of Plasma Membrane

Proteins

42

Monomeric Unit of Cell Wall

Sugars

43

Macro Molecule of Cell Wall

Cellulose

44

Bond Strength

triple bond > double bond > single bond

*takes less energy to break single bond*

45

Metal Ions

K+

Na+

Ca ++

Mg++

Zn++

Fe++

46

Bulk Elements

H

Na

K

Ca

C

N

O

P

S

Cl

47

Trace Elements

Mg

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Se

Mo

I

48

Steroisomer

Different Physical Properties

Enantiomers + Diastereomers

49

Geometric Isomers

cis vs. trans

Different Physical and Chemical Properties

50

Enantiomers

Non-super imposable on mirror image

Identical Physical Properties

React Identically w/ achiral reagents

51

Diastereomers

Different Physical and Chemical Properties

Stereoisomers that are not mirror images

need 2 chiral centers

52

Cis

same side

53

Trans

opposite side

54

Chiral

Rotated cannot be superimposed on mirror image

carbon w 4 different things on it

55

Achiral

rotated can be superimposed on mirror image

56

SAR: Isoproterenol + Propanolol

Isoproterenol --> increase heart rate

Propanolol --> decrease heart rate

*structure looks very similar but parts different therefore different functions

57

SAR: Testosterone + Estradiol

*structure looks very similar but parts different therefore different functions

58

SAR: Allopurinol + Hypoxanthine

Allopurinol --> Decrease Uric Acid levels

Hypoxanthine --> Converted to Uric Acid

*structure looks very similar but parts different therefore different functions

59

SSRI: Citalopram vs. Escitalopram

Citalopram --> 20mg/day

-R + S enantiomers

Escitalopram --> 10mg/day

-S enantiomer

*not pure + racemate need higher dose*

60

Living Organisms

maintain themselves w energy from fuel or light

exist in a dynamic steady state, never at equilibirum

interdependent

61

Equilibrium =

DEATH

62

1st Law of Thermodynamics

Total amount of energy in universe remains constant

Form may change

"conservation of energy"

63

Interdependent

Exchange energy and matter through enviro

64

Temp at which living cells function

room temp

65

Energy Needs of All Organisms Provided By

solar energy

66

Energy Transduction

Flow of electrons in oxidation/reduction reaction

67

Potential Energy

Energy Stored In Bonds

Get from: Foods--> Nutrients in enviro

  • Sugars, Fats
  • Sunlight
68

When Bonds Broken

Energy Is Available

69

Energy Transductions Accomplish

Work

70

Energy Used For

  1. Chemical Transformation Within Cells
  2. Heat
  3. Increase Entropy of Surrounding
  4. Decrease Entropy of System
71

Chemical Transformations Within Cells

Cellular Work:

  • Chemical Synthesis --> Ex. Produce Fatty Acid from AA
  • Mechanical Work
  • Osmotic + Electrical Gradient --> Pump Against Gradient
  • Genetic Info Transfer --> Syn. of DNA and RNA
72

Increase Entropy of Surroundings

Breaking Things Down

** DISORDER **

- CO2, NH3, H2O, HPO4-

Metabolism

73

Decrease Entropy of System

Building Things Up

** ORDER **

-Polymerize to Produce: DNA, RNA + Proteins

74

ATP

Chemical Currency of Energy

Universal Carrier of Metabolic Energy

Linking Catabolic + Anabolic Pathways

75

High Energy Bond *First Bond of P In P-P-P Adenosine (ATP)

Increase P.E.

Very hard to make that bond

76

High Energy Bond Broken *First Bond of P In P-P-P Adenosine (ATP)

A lot more E released

77

Cleaving off Phosphate from ATP

ATP

(-P)--> ADP

(-P)--> AMP

78

How To Speed Up RXN

Higher Temp

Higher Conc Of Reactants

Coupling to Fast RXN ****

Catalysis --> Lower Activation Energy ****

79

Endergonic

Syn REQUIRES E

RXN Unfavorable ( G = +)

  • creating work requires Work + E

Metabolic RXN to increase energy barrier

  • metabolite stable
80

Exergonic

Breakdown RELEASES E

RXN Favorable (G = -)

metabolites (ATP, NADH, NADPH) syn w E from Sunlight and Fuels

Cellular con higher than equilibirum conc

81

Favorable

G= -

82

Unfavorable

G = +

83

Coupling

-G + +G= -G

84

Energy Coupling

Coupling of exergonic and endergonic RXN allow what would be an unfavorable rxn to occur

High E molecule (ATP) reacts directly w metabolite that needs "activation"

85

Exothermic + Endothermic

Changes In Enthalpy

H --> Heat

86

Exergonic + Endergonic

Changes In Gibbs Free E

G --> Energy

87

Changes In Gibbs Free Energy

G= H-TS

88

Spontaneous

-G

89

Nonspontaneous

+G

90

Exothermic + Exergonic

-H + +S = -G

Spontaneous

91

Endothermic + Endergonic

+H + -S = +G

Nonspontaneous

92

Low Temp: +H + +S

Endothermic + Endergonic

+G

NonSpon

93

High Temp: +H + +S

Endothermic + Exergonic

-G

Spontaneous

94

Low Temp: -H + -S

Exothermic + Exergonic

-G

Spontaneous

95

High Temple: -H + -S

Exothermic + Endergonic

+G

Nonspontaneous

96

Exothermic

-H

97

Endothermic

+H

98

Catalyst

Increase Rate of RXN

Decrease Activation Energy

Does Not Alter Free Energy

99

Enzymatic Catalysis

Accelaration Under Mild Conditions

High Specificity

Possibility for Regulation

100

Enzymes

Protein Catalyst

Lower Activation Energy to Increase RXN rate

101

Catabolic

Breaking

Metabolize

Exergonic

Produces E

102

Anabolic

Making

Biosynthesis

Endergonic

Produces Valuable Materials

103

Negative Feedback

Product Inhibition

104

Parsimony of Nature

Good Regulatory Sys

DOES NOT WASTE

105

Living Cells

Self Regulating Chemical Engines

Continually adjusting for MAX ECONOMY

106

DNA --> RNA --> Protein

1. Replication

2. Transcription (of DNA to Complementary RNA)

3. Translation (of RNA on ribosome to polypeptide chain)

107

Central "Dogma" Of Biochem

DNA --> mRNA --> Unfolded Hexokinase --> Catalytically Active Hexokinase

108

Protimer

Genes (RNA) + Proteins come together to form complex molecule

109

Mutation

Random Event

*Mutations Evolve*

110

Substrate

Reactant of Enzymes

111

Gene Mutations

CF

Sickle Cell

112

RNA WORLD

Evolving into DNA/ RNA world