The carbohydrate structures.

The structure of nucleic acids.

Department of Medical Chemistry and Clinical Biochemistry

Charles University in Prague – 2nd Faculty of Medicine and

University Hospital in Motol

Matej Kohutiar, Bruno Sopko

Content

I. Structure of saccharides 1. Monosaccharides

Saccharides reactions

2. Oligosaccharides

3. Polysaccharides

4. Complex saccharides

II. Structure of nucleic acids 1.Basic components of nucleic acids

2.Nucleosides and nucleotides

3.DNA chain structures

4.RNA

I. Structure of saccharides

Saccharides

• Polyhydroxaldehydes and polyhydroxyketons with, at

minimum 3 carbon chain

• Division according to the number os saccharide units:

Monosaccharides

Oligosascharides (2-10)

Polysaccharides

Complex saccharides

Monosaccharide structure CH=O

OHH

CH2OH

C O

CH2OH

OHH

CH2OH

Monosaccharide structure CH=O

OHH

CH2OH

C O

CH2OH

OHH

CH2OH

Monosaccharide structure CH=O

OHH

CH2OH

C O

CH2OH

OHH

CH2OH

Monosaccharide structure CH=O

OHH

CH2OH

C O

CH2OH

OHH

CH2OH

CH=O

OHH

CH2OH

C O

CH2OH

HOH

CH2OH

CH=O

OHH

CH2OH

Monosaccharide structure CH=O

OHH

CH2OH

C O

CH2OH

OHH

CH2OH

C O

CH2OH

HOH

CH2OH

Chiral carbons

H

F

Cl Br

Chiral carbons

H

F

Cl Br

H

F

Cl Br

Chiral carbons

CH2OH

H OHOH HH OHH

H OHCH=O

OH

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

2

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

2

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

2

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

2

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

4

CH2OH

H OHOH HH OHH

H OHCH=O

OH

2

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

4

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

4

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

4

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

4

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

4

CH2OH

H OHOH HH OHH

H OHCH=O

OH

Chiral carbons

Monosaccharide structure

CH=O

CH2OH

H OH

D-glyceraldehyde

Monosaccharide structure

CH=O

CH2OH

H OH

CH=O

CH2OH

OH

H OH

H

D-glyceraldehyde

D-erythrose

Monosaccharide structure

CH=O

CH2OH

H OH

CH=O

CH2OH

OH

H OH

H

CH=O

CH2OH

H

H OH

OH

D-glyceraldehyde

D-erythrose D-threose

Monosaccharide structure CH=O

CH2OH

OH

H OH

H

D-erythrose

Monosaccharide structure CH=O

CH2OH

OH

H OH

H

CH=O

CH2OH

H OH

H OH

H OH

D-erythrose

D-ribose

Monosaccharide structure CH=O

CH2OH

OH

H OH

H

CH=O

CH2OH

H OH

H OH

H OH

CH=O

CH2OH

OH H

H OH

H OH

D-ribose D-arabinose

D-erythrose

Monosaccharide structure CH=O

CH2OH

H

H OH

OH

D-threose

Monosaccharide structure CH=O

CH2OH

H

H OH

OH

CH=O

CH2OH

H OH

OH H

H OH

D-threose

D-xylose

Monosaccharide structure CH=O

CH2OH

H

H OH

OH

CH=O

CH2OH

H OH

OH H

H OH

CH=O

CH2OH

OH H

OH H

H OH

D-threose

D-xylose D-lyxose

Monosaccharide structure

CH=O

CH2OH

H OH

H OH

H OH

CH=O

CH2OH

OH H

OH H

H OH

CH=O

CH2OH

OH H

H OH

H OH

CH=O

CH2OH

H OH

OH H

H OH

D-xylose

D-lyxose D-ribose

D-arabinose

Monosaccharide structure

CH=O

CH2OH

H OH

H OH

H OH

H OH

CH=O

CH2OH

OH H

OH H

OH H

H OH

CH=O

CH2OH

H OH

H OH

OH H

H OH

CH=O

CH2OH

OH H

OH H

H OH

H OH

CH=O

CH2OH

H OH

OH H

H OH

H OH

D-allose D-talose D-glucose D-idose

D-gulose D-mannose D-altrose D-galactose

CH=O

CH2OH

OH H

H OH

OH H

H OH

CH=O

CH2OH

OH H

H OH

H OH

H OH

CH=O

CH2OH

H OH

OH H

OH H

H OH

Monosaccharide structure

CH=O

CH2OH

H OH

H OH

H OH

H OH

Monosaccharide structure

H OH

H OH

H OH

CH=O

CH2OH

H OH

H OH

H OH

H OH

Monosaccharide structure

H OH

H OH

H OH

CH=O

CH2OH

H OH

H OH

H OH

H OH

Monosaccharide structure

Monosaccharide structure

Monosaccharide structure

D-glucose

D-mannose

D-galactose

Monosaccharide structure

ketoses

CH2OH

CH2OH

O

OH

H OH

H OH

O

OH

OH

OH H

H OH

O

OH

OH

OH H

H OH

H OH

O

OH

dihydroxyacetone

D-ribulose D-xylulose D-fructose

Monosaccharide structure

CH=O

CH2OH

H OH

H OH

H OH

H

OH

CH2OH

H OH

H OH

H OH

H

H OH

O

D-allose D-allose

O

OHH

HH

OHH

OH OH

H

OH

Monosaccharide structure

CH=O

CH2OH

H OH

H OH

H OH

H

OH

CH2OH

H OH

H OH

H OH

H

H OH

O

D-allose D-allose α-D-allopyranose

Monosaccharide structure

CH=O

CH2OH

H OH

H OH

H OH

H

OH

CH2OH

H OH

H OH

H OH

H

H OH

O

O

OHH

HH

OHH

OH OH

H

OH

D-allose D-allose α-D-allopyranose

Monosaccharide structure

• In crystals only cyclic forms (α-, β-anomers)

acyclic form

pyranose -pyranose

-furanose -furanose

Saccharides reactions

• Redox reactions

• Esterification

• Glycosides formation

Redox reactions of saccharides

OH

O

H OH

OH H

H OH

H OH

OH

OH H

H OH

H OH

O

OH

OH

OH

H OH

OH H

H OH

H OH

D-glucose D-fructose D-glucitol

Redox reactions of saccharides

CH=O

CH2OH

H OHOH HH OHH OH

D-glucose

Redox reactions of saccharides

CH=O

CH2OH

H OHOH HH OHH OH

COOH

CH2OH

H OHOH HH OHH OH

D-glucose

D-gluconic acid

CH=O

CH2OH

H OHOH HH OHH OH

Redox reactions of saccharides

COOH

CH2OH

H OHOH HH OHH OH

CH=O

COOH

H OHOH HH OHH OH

D-glucose

D-gluconic acid D-glucuronic acid

CH=O

CH2OH

H OHOH HH OHH OH

Redox reactions of saccharides

COOH

CH2OH

H OHOH HH OHH OH

CH=O

COOH

H OHOH HH OHH OH

COOH

COOH

H OHOH HH OHH OH

D-glucose

D-gluconic acid D-glucuronic acid D-glucaric acid

Redox reactions of saccharides

O

OHOHOH

OH

H

OH

D-glucose

Redox reactions of saccharides

O

OHOHOH

OH

H

OH

O

OHOHOH

OH

H

COOH

D-glucose

D-glucuronic acid

Redox reactions of saccharides

O

OHOHOH

OH

H

OH

O

OHOHOH

OH

H

COOH

O

OHOH

OH

OH

O

D-glucose

D-glucuronic acid δ-gluconolactone

Esterification

O

OHOHOH

OH

H

OH

D-glucose

Esterification

O

OHOHOH

OH

H

OH

O

OHOHOH

OH

H

O

PO

O-

O-

D-glucose D-glucose-6-phosphate

Glycosides formation

O

OHOHOH

OH

H

OH

D-glucose

Glycosides formation

O

OHOHOH

OH

H

OH

O

OOHOH

OH

H

OH

CH3

D-glucose α-methyl-D-glucopyranoside

Monosaccharides derivates deoxysaccharides and aminosaccharides

O

OHOHOH

NH

H

OH

O

CH3

O H

OH

HOH

OH

N-acetylglucosamine 2-deoxy-D-ribose

Oligosaccharides

• Contain 2-10 monosaccharide units bound by glycosidic bond

• Homo/heteroglycosides

• Reducing/nonreducing

O

1

OH

OH

OH

O

OH

O4

OH

OH

OH

OH

Oligosaccharides

maltose Sucrose (saccharose)

lactose

O14

OHOH

OH

OH

O

O

14

OHOH

OH

OH

O14

OHOH

OH

OH

O

O2

OH

OH

OH

OH

OH

Polysaccharides

• Contain more than 10 monosaccharide units

• Homo/heteropolysaccharides

• Linear and cyclic polysaccharides

• Branched and non-branched polysaccharides

• Pentosans, hexosans…

Plant polysaccharides starch

• Amylose structure

Non-reducing end Reducing end

O14

OHOH

OH

OH

O14

OH

OH

OH

O

O

O14

OH

OH

OH

O

O4

OHOH

OH

OH

http://bioanalyse.wikispaces.com/Homopolysaccharider

OH

O1

OH

OH

OH

O

O

14

OH

OH

OH

O1

OH

OH

OH

OH

O

O14

OH

OH

6 O

O

O4

OHOH

OH

OH

Plant polysaccharides starch

• Amylopektin

Main chain

branch

http://bioanalyse.wikispaces.com/Homopolysaccharider

Animal polysaccharides

• glycogen

http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/

http://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.html

http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://www.namrata.co/glycogen-metabolism-subjective-questions-solved-set-1/http://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.htmlhttp://dstgroupproject.weebly.com/periodic-acid-schiffdiastase.html

Complex polysaccharides

O

COO-

OH

OH

OH

NH

O

CH3

OH

Hyaluronic acid Chondroitin-4-sulphate

Sialic acid https://wikispaces.psu.edu/display/230/The+Organization+of+Cells+in+Tissue

-+The+Extracellular+Matrix,+Cell+Junctions+and+Cell+Adhesion

II. Structure of nucleic acids

Saccharides present in nucleic acids

O

H

OH

H

OH

H

OH

H

OH

O

H

OH

HH

OH

H

OH

β-D-ribofuranose 2-deoxy-β-D-ribofuranose

Heterocyclic compounds present in

nucleic acids

8

4

9

N3

N1

2 NH5

6

N7

N3

2

4

N1

5

6

pyrimidine purine

Heterocyclic compounds present in

nucleic acids

8

4

9

N3

N1

2 NH5

6

N7

N3

2

4

N1

5

6

N

NH

NH2

O NH

NH

O

O

NH

NH

O

O

CH3

pyrimidine purine

cytosine uracil

thymine

Heterocyclic compounds present in

nucleic acids

8

4

9

N3

N1

2 NH5

6

N7

N3

2

4

N1

5

6

N

N

NH

N

NH2

N

NH

NH

N

NH2

O

N

NH

NH2

O NH

NH

O

O

NH

NH

O

O

CH3

purine pyrimidine

cytosine uracil

thymine

adenine guanine

Keto-enol, and amin-imin

tautomerism

CH3

CH3

NH2

CH3

CH3

NH

CH3

CH3

OH

CH3

CH3

O

Nucleosides

O

OHOH

OH

N

N

N9

N

NH2

O

OHOH

OH

N1

NH

O

O

CH3

adenosine thymidine

Conformation of β-N-glycosidic bond

O

OHOH

OH

N

N

N9

N

NH2

O

OHOH

OH

N

N

N9

N

NH2

adenosine guanosine

Nucleotides

PO-

O

O- O

OHOH

O

N

N

N9

N

NH2

Adenosine monophosphate

Nukleotides

Phosphoanhydride bond

PO-

O

O-

PO

O

O-

PO

O

O- O

OHOH

O

N

N

N9

N

NH2

adenosintriphosphate

Physiologically important nucleotides (NAD+/NADH, FAD/FADH2)

O

OHOH

O N

N

N

N

NH2

P

O

P

O

OHOH

N+

NH2

O

O

OH

OH

OH

O

OHOH

O N

N

N

N

NH2

POPO

N

NNH

NCH3

CH3

O

O

Physiologically important nucleotides

PO-

O

O

OHO

O

N

N

N9

N

NH2

PO-

O

O

OHO

O

N

NH

N9

N

O

NH2

O

OHOH

N

N

N9

N

NH2

O

NH3+

S+

CH3

O-

cAMP cGMP

SAM

Synthetic nucletide analogues

O

HOH

OH

5

N1

NH

O

O

I

O

OHOH

OH

N6N

1

NH

O

O

6

N

N

NH

N

SH

N

N

NH

N

OH

5-iodo-2-deoxyuridine 6-azauridine

6-merkaptopurine allopurinol

DNA chain structure

NO

3´

5´OP N

NHN

NH2

O

OH

NO

3´

5´OP N

NHN

NH2

O

O

NO

3´

5´OP

N

NH2

O

OH

DNA chain structure

NO

3´

5´OP N

NHN

NH2

O

O

NO

3´

5´OP

N

NH2

O

O

NO

3´

5´OP

NH

O

O

CH3

OH

DNA chain structure

NO

3´

5´OP N

NHN

NH2

O

O

NO

3´

5´OP

N

NH2

O

O

NO

3´

5´OP

NH

O

O

CH3

O

NO

3´

5´OP N

NN

NH2

O

P

DNA chain structure

Stabilisation of base pairs

NH NH

O

O

CH3

N

N

NH

N

NH2

Stabilisation of base pairs

NH NH

O

O

CH3

N

N

NH

N

NH2

NNH

NH2

O

N

NH

NH

N

NH2

O

Chargaff’s rule

DNA conformations

http://www.biologyexams4u.com/2012/11/different-forms-of-dna.html#.VDZBrsVdVRo

B-form of DNA

Small cleft

Large cleft

Forces stabilizing the nucleic acids

structures

• Denaturation and renaturation

• Hydrophobic interaction

• Electrostatic interaction

http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html

http://www.atdbio.com/content/53/DNA-duplex-stability

http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html

Forces stabilizing the nucleic acids

structures

• Denaturation and renaturation

• Hydrophobic interaction

• Electrostatic interaction

http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html

http://www.atdbio.com/content/53/DNA-duplex-stability

http://dspace.jorum.ac.uk/xmlui/bitstream/handle/10949/956/Items/S377_1_section5.html

RNA

O

H

OH

H

OH

H

OH

H

OH

NH

NH

O

O

•mRNA

•tRNA

•rRNA

•snRNA

•miRNA

•…

http://www.broadinstitute.org/blog/five-questions-david-root-rna-interference-explained

uracil ribose

RNA stability

O

H

OH

H

OH

H

OH

H

O

P O-

O

O

O OH

OH

OH

OH-

RNA stability

O

H

OH

H

OH

H

OH

H

O

P O-

O

O

O OH

OH

OH

OH-

O

H

OH

H

OH

H

OH

H

OH

O

O OHOH

O

P

O-

O

mRNA

• Highly variable in size

• Transcription starts from 5´-end

• 3´-end: polyA (20-250)

N

NH

N

N

NH2

OCH3

O

H

H

OH

H

OH

H

O NO

3´

5´OP N

NHN

NH2

O

O

NO

3´

5´OP

NH

O

O

O

P

OPOP

O-

OO

OH O-

O

OH

OH

cap

tRNA

• Small molecule (73-95)

• 3´-end: CCA

• Playing also other roles

• At least 1 tRNA for each

aminoacid

http://www.wiley.com/college/boyer/0470003790/structure/tRNA/trna_intro.htm

rRNA

• Majority of cell RNA

• Catalytic activity

http://cronodon.com/BioTech/Ribosomes.html

Other RNAs

• Small interfering RNAs (siRNAs) • mediate the downregulation of gene expression -

binding to specific mRNAs labelled them for destruction by enzymes called endonucleases

• MicroRNAs (miRNAs) • downregulate gene expression - binding to messenger

RNAs (mRNAs) causes preventing mRNAs from being translated into proteins

• Small nucleolar RNAs (snoRNAs) • modify ribosomal RNAs (rRNAs) by organizing the

cleavage of the long pre-rRNA into its functional subunits (18S, 5.8S and 28S molecules)

• Small nuclear RNAs (snRNAs) • are constituents of the cellular machinery

(spliceosome) that helps to produce mRNA

Differences between DNA and RNA

DNA RNA

carbohydrate deoxyribose ribose

pyrimidine base thymine uracil

structure double-helix single helix

stability at high pH resistent cleaved