The chemistry of life

The chemistry of life


Cell chemistry is hierarchical
Inorganic precursors

Small organic molecules

Macromolecules

Supramolecular structures

Organelles/structures

Cell
BIO 1140 – SLIDE 1

Review of macromolecules
Carbohydrates
 Polymers of monosaccharides (polysaccharides)



Energy storage
Structural
chitin

starch glycogen Purple pages F23



cellulose

BIO 1140 – SLIDE 2

http://www.mpie.de/index.php?id=2957

Monosaccharides


CnH2nOn






n = 3 to 7
Trioses, pentoses and hexoses most common

Linear vs ring configuration
Asymmetrical C  isomers

glyceraldehyde

ribose
D-glucose

-D-glucose

ß-D-glucose

Fig. 2.13

BIO 1140 – SLIDE 3

Purple pages F20-21

 Polysaccharides


Glycosidic bond



C1 to C4
 vs ß

starch

glycogen

Purple pages F22-23 cellulose chitin

NH

BIO 1140 – SLIDE 4



NH

NH

NH

C=O

C=O

C=O

C=O

CH3

CH3

CH3

CH3

Fig. 2.17 Karp 2010

Test your recall:
Distinguish between a polymer and a polysaccharide.
Provide an example of a carbohydrate used for energy storage.
 Glucose is a 6-carbon sugar or __________________.
 Why are there  and ß forms of glucose in the ring configuration but not in the linear configuration?
 What carbohydrate is formed from repeated units of ß-glucose? Can humans digest this carbohydrate?



BIO 1140 – SLIDE 5

Nucleic acids
 Polymers of nucleotides





Informational
DNA vs RNA

Nucleotides



5C sugar – ribose or deoxyribose nitrogenous base



Purine: adenine, guanine
Pyrimidine: cytosine, cytosine thymine thymine, uracil

Sugar + base = nucleoside
Up to 3 phosphate groups  nucleotide
 Several different roles in cell...

Fig. 4.12




BIO 1140 – SLIDE 6

H
(deoxyribose)

Purple pages F29-30

Nucleic acids
 Polymers of nucleotides





Informational
DNA vs RNA

Nucleotides



5C sugar – ribose or deoxyribose nitrogenous base



Purine: adenine, guanine
Pyrimidine: cytosine, cytosine thymine thymine, uracil

Fig. 4.12

Sugar + base = nucleoside
 Up to 3 phosphate groups  nucleotide
 Several different roles in cell...


(deoxyribose)

Adenosine

Base

Nucleoside

Adenine
Guanine
Cytosine
Thymine
Uracil

Adenosine or deoxyadenosine
Guanosine or deoxyguanosine
Cytidine or deoxycytidine
Deoxythymidine
Uridine

Adenosine monophosphate (AMP)
Adenosine diphosphate (ADP)

BIO 1140 – SLIDE 7



H

Adenosine triphosphate (ATP)

Sugar-phosphate backbone

Nucleic acids
Phosphodiester bond
RNA  single-stranded
 DNA  double-stranded


5’ end






Double helix
James Watson & Francis
Crick, Nature 1953

Fig. 2.53 Karp 2010
3’ end

BIO 1140 – SLIDE 8



Sugar-phosphate backbone

Nucleic acids
Phosphodiester bond
 RNA  single-stranded
 DNA  double-stranded





Purple pages F30

5’ end

3’ end

Double helix
James Watson & Francis
Crick, Nature 1953 (see http://www.nature.com/nature/dna50/archive.html) 3’ end

BIO 1140 – SLIDE 9

5’ end
Purple pages F30



Nucleic acids
Phosphodiester bond
RNA  single-stranded
 DNA  double-stranded






Double helix
James Watson & Francis
Crick, Nature 1953 (see http://www.nature.com/nature/dna50/archive.html) BIO 1140 – SLIDE 10



Purple pages F31

Test your recall:
Distinguish between a nucleic acid and a nucleotide.
True or false – cytosine is a purine.
 Use the blocks at right to construct a nucleoside.
 List three differences between DNA and RNA.
 Describe the structure of dGTP.
 Who elucidated the structure of DNA?
 Nucleic acid sequences are always presented in the order _____ to _____.



BIO 1140 – SLIDE 11

Proteins
 Polymers of amino acids



Informational
Wide array of functions:
Enzymes (e.g. carbonic anhydrase)
Structural (e.g. keratin, collagen)
 Motility (e.g. actin)
 Transport (e.g. Na+-K+-ATPase)





Regulatory (e.g. transcription factors, hormones) Receptors (e.g. ß-adrenoreceptors)
 Defensive (e.g. antibodies)




Amino acids



~20
Central carbon ( carbon)
Carboxyl group
 Amino group
 H atom
 Side chain (R group)


R group
(different for each amino acid)
Amino
group

H3N+

C
H

BIO 1140 – SLIDE 12

Carboxyl group R
C

OO



R group


Properties of amino acid determined by R group:  Nonpolar
 Polar, uncharged
 Polar, acidic (-ve charge)
 Polar, basic (+ve charge)
 Reactive functional groups

Common functional groups:
Chemical formula
Name
-OH
Hydroxyl group
-C=O
Carbonyl group
-SH
Sulphhydryl group
-COOH
Carboxyl group
-PO32Phosphate group
-NH2
Amino group

Properties
Neutral, polar
Neutral, polar
Neutral, polar
-ve charge at cellular pH
-ve charge at cellular pH
+ve charge at cellular pH

+

Nonpolar

R group


-

See purple pages F18

BIO 1140 – SLIDE 13



-

Properties of amino acid determined by R group:  Nonpolar
 Polar, uncharged
 Polar, acidic (-ve charge)
 Polar, basic (+ve charge)
 Reactive functional groups

Polar, uncharged

Reactive functional groups

Polar, charged

Purple pages F25



BIO 1140 – SLIDE 14

Polypeptide
Peptide bond
N-terminus vs C-terminus
 Average 400-500 aa residues





From polypeptide to protein...


One or more polypeptides folded into native conformation





monomeric (single polypeptide) multimeric  homomeric, homomeric heteromeric

Conformation is dependent on covalent and non-covalent interactions in backbone and/or R groups 


Conformational changes
Denaturation
BIO 1140 – SLIDE 15

Purple pages F26



Polypeptide
Peptide bond
N-terminus vs C-terminus
 Average 400-500 aa residues





From polypeptide to protein...


One or more polypeptides folded into native conformation





monomeric (single polypeptide) multimeric  homomeric, homomeric heteromeric

Conformation is dependent on covalent and non-covalent interactions in backbone and/or R groups 


Conformational changes
Denaturation
BIO 1140 – SLIDE 16



Purple pages F27-28

Protein structure


Primary structure



Secondary structure



aa sequence, 20n possibilities where n = # aa

Hydrogen bonding in backbone
 helix vs ß pleated sheet
 Motifs, e.g. hairpin loop, helix-turn-helix



 helix

ß sheet

Fig. 2.31 Karp 2010

BIO 1140 – SLIDE 17



Purple pages F27-28

Purple pages
F27-28

Tertiary structure
Overall shape or conformation
Interactions between R groups
 Disulphide bridge
 Hydrogen bonds, ionic bonds, hydrophobic interactions, van der
Waals interactions
 Relative contributions of 2° and 3°?
 Fibrous vs globular proteins
 Domains



Ch. 4

Fig. 2.22
Fig. 3-13 Becker et al. 2009

BIO 1140 – SLIDE 18



Tertiary structure
Overall shape or conformation
Interactions between R groups
 Disulphide bridge
 Hydrogen bonds, ionic bonds, hydrophobic interactions, van der
Waals interactions
 Relative contributions of 2° and 3°?
 Fibrous vs globular proteins
 Domains



Autumn et al. 2000 Nature 405: 681-685 http://geckolab.lclark.edu/dept/AutumnLab/ van_der_Waals_mini-presentation.html

BIO 1140 – SLIDE 19



Quaternary structure




Interactions of subunits to form multimeric protein

Multiprotein complexes

Purple pages F27-28

Fig. 3-6 Becker et al. 2009

BIO 1140 – SLIDE 20



Test your recall:


Deduce the chemical nature of the amino acids below by examination of their side chains.

Between what groups does a peptide bond form?
Distinguish between a polypeptide and a protein.
List three functions of proteins.
 Distinguish between a motif and a domain.
 For what level of protein structure is hydrogen bonding in the backbone responsible?  True or false – Monomeric proteins do not exhibit quaternary structure.




BIO 1140 – SLIDE 21

Lipids
 ‘Macromolecules’ not polymers
Insoluble in water, soluble in nonpolar solvents
 energy storage, membrane structure, signalling





Types


6 main classes






Fatty acids
Phospholipids
Steroids

Purple pages F32-F34

Fatty acids


Hydrocarbon chains with carboxyl group



Saturated vs unsaturated




14 - 22 carbon fatty acids very common amphipathic BIO 1140 – SLIDE 22



Phospholipids
Structural component of membranes  Phosphoglycerides

R group



Phosphate

Glycerol
2 fatty acids (16 - 18 C)
 Phosphate
 Hydrophilic R group = serine, ethanolamine, choline, inositol
 amphipathic


glycerol

polar



BIO 1140 – SLIDE 23



Fatty acids nonpolar

Purple pages F33-34

Steroids
Derivatives of 4-ringed hydrocarbon skeleton
Only in eukaryotic cells
 Sterols



Cholesterol (animals)
Phytosterols (plants)
 Ergosterol (fungi)



stigmasterol

cholesterol
BIO 1140 – SLIDE 24

Purple pages F34



Test your recall:
Are lipids polymers?
Distinguish between a fatty acid and a phosphoglyceride.
What lipids play a role in signalling?
 Define amphipathic. Use a sketch of a phosphoglyceride to illustrate your answer.  Would you expect to find sterols in the inner membrane of a mitochondrion or chloroplast? Explain your answer.




BIO 1140 – SLIDE 25