Macromolecules

Carbohydrate ― polyhydroxy aldehydes and ketones sugars: monosaccharides & disaccharides e.g. glucose, fructose, sucrose, lactose polysaccharides: e.g. starch, glycogen, cellulose

Lipids ― soluble in nonpolar solvents fatty acid esters ― steroids ― prostaglanidns ― leukotrienes Protein ― polymers of amino acids enzymes ― transporters ― receptors ― immunoglobulins etc. Nucleic Acid ― polymers of nucleotides DNA: determines sequence RNA RNA: determines sequence of cellular proteins regulates gene expression

Do proteins wear out?Car analogy: lease vs. buy

Proteins in cells are on more of a lease system.They are degraded by a structure called the Proteasome …After being tagged for destruction by the protein ubiquitin.

Every Protein has a roughly constant half-life,But like radioactive isotopes their decay is somewhat random.The amino terminal amino acid determines the length of t½.

The rate of breakdown of most proteins balances the rate of synthesis (a steady state) but a change in either synthesis or breakdown can provide a means of regulating protein activity.

Glucose

AcetylCoA

Pyruvate

NADH/FADH2

KrebsCycle

C6

C4

C5

C4

ATP

ADP O2

NAD+/FAD

oxaloacetate

Protein

Amino Acids

Ubiquitin Protein digestion (t1/2)

Ubiquitin is a protein ‘tag’ that marks another protein for proteolytic destruction

UbiquitinUbiquitin activating enzyme (E1): ubiquitin + ATP ubiquitin-AMP + PPi

Ubiquitin-conjugating enzyme (E2): attaches to activated ubiquitin via SH

Ubiquitin-protein ligase (E3): transfers ubiquitin to e-amino of target protein t1/2 & N-terminal rule (e.g. R = 2 min. M = 20 hrs.)

Proteosome: (a 26s protease complex) digests ubiquitin-tagged proteins

Slow (>20 hr.) : Ala, Cys, Gly, Met, Pro, Ser, Thr, Val

Fast (2-20 min.) : Arg, Asx, Glx, His, Ile, Leu, Lys, Phe, Trp, Tyr

Processes regulated by protein destruction gene transcription circadian rhythms inflammatory response antigen processesing tumor supression

Ubiquitin activating enzyme (E1): ubiquitin + ATP ubiquitin-AMP + PPi

Ubiquitin-conjugating enzyme (E2): attaches to activated ubiquitin via SH

Ubiquitin-protein ligase (E3): transfers ubiquitin to e-amino of target protein t1/2 & N-terminal rule (e.g. R = 2 min. M = 20 hrs.)

Urea Cycle

NH4+ + CO2 + 3ATP + Asp + 2 H2O

urea + 2ADP, Pi + AMP, PPi + fumarate

||H2N – C – NH2

O

Detoxification of ammonia

Polymers of Amino AcidsPROTEINS

Protein sequenceYMGCFTSSGLIVVEHY...

Structure

Function

DNA (gene)

mRNA

NUCLEIC ACIDS

DNA RNAencodes genetic information

has both functional & informational rolesin gene expression

Genes code for Cell’s Proteins

polymers of nucleotides

NUCLEOTIDES

Base: Adenine, Guanine, Thymine (Uracil), Cytosine

Sugar: Ribose or deoxy-ribose

Phosphates: 1-3 via phosphate ester bonds

nucleoside = base + sugar

Base name Nucleoside Name Base type

Adenine A adenosine purine

Guanine G guanosine purine

cytosine C cytidine pyrimidine

thymine T thymidine pyrimidine

uracil U uridine pyrimidine

Nucleic Acid Bases

ThymineUracil

CH3

Cytosine

Adenine

Guanine

Pyrimidine Ring

N

N

Purine Ring

NN

N N 12

34

5

6

1

23 4

56

78

9

N2

NH3 or NO3-

soil bacteria

plantsAmino acids

Protein

N - Cpds

1anabolic

includes purine &pyrimidine bases

NADH

ATP

Glucose

Pyruvate

AcetylCoA

Krebs Cycle

C6

C4

C5

C4 FADH2

O2

ADP

Ribose-5-P

Amino Acids

DNARNA

bases

Nucleotides

Protein

Pyrimidine Ring

N

NC C

CC

1 2

34

5

6

Aspartate

carbamoylphosphate

O O || || H2N - C - O - P - O | O

Purine Ring

Glycine

Glutamine

tetrahydrofolate

Aspartate

CO2

NN

N N

CC

CC

C 1

23 4

5 6

78

9

Pyrimidines

N

N

H2N

O

Cytosine

N

NO

O

HUracil

N

NO

O

H CH3

Thymine

Purines

Guanine

NN

N NH2N

O

H

H2N

NN

N N

Adenine

OH

ribose - RNA

2-deoxyribose - DNA

Nucleotide Sugars

123

4

5 OOHHO

HO

OH

OHO

HO

N

N

H2N

O

Cytidine: a nucleosidedeoxycytidine

O O - P - O

dCMP

dCDP

O O - P - O

This structure is …. a) a purine b) a nucleoside c) a nucleotide d) DNA

This structure contains …. a) ribose b) 2´ deoxyribose c) 3´ deoxyribose d) a hemiacetal functional group

This nucleotide is…. a) adenine monophosphate b) guanine monophosphate c) guanosine monophosphate d) AMP

Sugar

Phosphate

Base

1´

2´3´

5´

4´

↓

This bond indicated by the ↓ is … a) covalent b) phosphate ester c) both d) neither

Phosphate ester bonds are also found in a) phosphoglycerides b) activated phosphorylase c) both d) neither

Base name

Nucleoside Name

Base type information

Adenine A adenosine purine D – A – X

Guanine G guanosine purine A – D – D

cytosine C cytidine pyrimidine D – A – A

thymine T thymidine pyrimidine A – D – A

uracil U uridine pyrimidine A – D – A

Nucleic Acid Bases

ThymineUracil

CH3

Cytosine

Adenine

GuanineH

Nucleotides & DNA

Protein sequenceYMGCFTSSGLIVVEHY...

Structure

Function

DNA (gene)

mRNA

O

OH

OA |

O || O - P - | O_

O || O - P - | O_

O ||-O - P - | O_

O-(H+) | O - P - || O

O-

| O - P - || O

O-

|-O - P - || O

O

OH

OC |

Phosphodiester bond formation

3 hydroxyl3

5 phosphate

5

|_ O - P - | O_

O || O - P - O-

| O_

O ||-O - P - | O_

O

O

OA |

O || O - P - | O_

O || O - P - | O_

O ||-O - P - | O_

O

OH

OC |

Phosphodiester bond formation

dinucleotide5’ end

3’ end3-5 phosphodiester bond

P-P-P C S P G

SP A

SP T

SP T

SOH

5

3

1950 ― Erwin Chargaff

In DNA isolated from any species # A = # T & # G = # C A-T : G-C ratio varies

1953 ― Franklin and Wilkins ― Watson & Crick

DNA has double helix structureBases paired in center A=T & GCComplementary strands progress in opposite directions.

5’- C G A T T C AG C - 3’3’- G C T A A G T C G - 5’

P-P-P C S P G

SP A

SP T

SP T

SP

P-P-P A S P A

SP T

SP C

SP G

SP

5

35

3

H2N

NN

N N

AN

N O

O

HCH3

Thymine

NNO

OH

CH

3

ThymineN

NO

O

H CH3

Thymine

H2N

NN

N NNN

O

OH

CH

3 A

T

T A

H2N

NN

N N

A

C

NN

NH2

O

X

X

C A

G

NN

N NH2N

O

H

O

N

NH2

N

C

C G

Can’t have 2 pyrimidines paired :too far apart for H-bonds

T C

2 purines don’t fit inside helix

11 Ao

DNAdouble helix B Form

majorgroove

minor groove

N

NN

N NNN

O

OH

CH

3 A

T

H H

DNA binding proteins that recognize specific sequences of DNA.Transcription factors, RNA Polymerase, restriction endonucleases ….Use amino acid side chains to form specific H-bonds with paired sequences through the major or minor grooves.

G

NN

N N N

O

HO

N

N

N

C

H

H

H

H

Lambda Phage Repressor Protein

Gene Expression

DNA (gene)↓

mRNA↓

Polypeptide chain↓

Folded polypeptide↓

Functional protein

Thymine has an equilibrium between keto & enol forms

N

NO

O

H CH3

ketoN

NO

HO

CH3

enol

1

10,000 or 104

H2N

NN

N N

A

T (enol)

X

X

H3C

NN

O

OH

G

NN

N NH2N

O

H

T (enol)

H3C

NN

O

OH

P-P-P A S P A

SP T

SP C

SP G

SP

P-P-P C S P G

SP G

SP T

SP T

SP

5

35

3

T

G

DNA Pol has proof reading capability

There is a DNA repair system in place in cells to repair DNA structural anomalies that Arise due to replication errors or DNA damage

If a cell cannot keep up with DNA repair – apoptosis (programmed cell death) pathways should prevent cell growth and division.

dsDNA ↔ ssDNA

Which form is favored at elevated temperatures? Why? a) dsDNA b) ssDNA c) the equilibrium will not change with T

DG = DH - TDS

GC richA260

T (ºC)40 50 60 70 80

A=T rich

ssDNA

dsDNA

dsDNA ↔ ssDNA Lower A260 higher A260

DNAdouble helix B Form

majorgroove

minor groove

DNA forms supercoilsExample shown is bacterial plasmid DNA

Supercoiling compacts DNA to take up less spaceThe structural form of DNA influences expression

Eukaryotic DNA forms chromosome structuresThese contain DNA binding protein called histones

NucleosomesDNA wrapped around a histone core structure

NucleosomesDNA wrapped around a histone core structure