CHEM 161 2nd Exam Reviewer

Carbohydrates, Lipids, Nucleic Acids,

And Central Dogma of Molecular Biology

CARBOHYDRATES O-linked and N-Linked Carbohydrate–

- A class of Polyhydroxy aldehydes and ketones Protein Linkages

Classes of Carbohydrates Protein: Linkage:

1. Monosaccharides Asn N-Linked
2. Disaccharides
3. Oligosaccharides Ser O-linked
4. Polysaccharides Thr

Characteristics of sugars:
1. Predominantly exist in cyclic forms
2. Can be Oxidized or Reduced
3. Joined to Alcohols and Amines by Glycoproteins vs. Proteoglycans
Glycosidic Bonds
Glycoprotein Proteoglycan
Glycosaminoglycans - High Protein Content - High CHO Content
- A type of mucopolysaccharide - Low CHO Content - Tissue organization
- Slimy, mucus-like - Signaling Processes
- High viscosity, High elasticity - Cartilage resilience
- Usually found in connective tissues - Interacts w/ Collagen
- Highly polar and attract water
Glycosyltransferases
Examples: - Connects carbohydrates and oligosaccharides
Chondroitin Sulfate, Hyaluronic Sulfate, - Forms glycosidic bonds that connect
Keratan Sulfate, Dermatan Sulfate monosaccharides

Glycoproteins Monosaccharide + Glycosyltransferase

- Carbohydrate + Protein - Disaccharide Coupling
- Covalent bonding - Protein Glycosylation
- Product of Post-Translational Modification - Glycolipid Formation
in the Golgi Body
- Functions as mode for cell-cell recognition
- Agglomeration of tissues and organs
- Infection by bacteria and viruses
 CHEM 161 2nd Exam Reviewer
Carbohydrates, Lipids, Nucleic Acids,
And Central Dogma of Molecular Biology

Blood Groups are based on Glycosylation Lipids

Patterns - Consist of a heteroatom group of compounds
that are in water and polar solvents

Functions:
1. Storage of energy
2. Insulate vital organs
3. Cover nerve fibers
4. Component of Cell Membrane
5. Chemical Messengers

Mnemonics: SI-Triple C (SICCC)

Classification of Lipids
1. Saponifiable lipids: reacts w/ NaOH
a. Triacylglycerols (TAG)
b. Waxes
Analysis of Carbohydrates c. Phospholipid
1. Purification of Carbohydrates d. Glycerophospholipid
- Chromatography, Electrophoresis e. Glycolipid
- Affinity Chromatography: uses immobilized,
sugar-binding proteins called lectins 2. Non-saponifiable lipids
a. Steroids
Examples of Lectins: b. Terpenes
Concanavalin A (Jackbean)
- Specific for a-D-Glucose, a-D-Mannose Mnemonics: S-TWPGG , NS-ST

Agglutinin (Wheat germ) 3 Platforms for Building Phospholipids

- Specific for b-N-Acetylmuramic Acid
(bAMA) and a-N-Acetylneuraminic Acid 1. Glycerol 2. 3C-Alcohol
(aANA)

2. Characterization of Carbohydrates
- Identity, Anomer, Linkages, Order
3. Sphingosine
For Linkages:
- Exhaustive Methylation
- Hydrolysis of glycosidic linkages
- Identification of Methylated Monosaccharides
- GC Chromatography
- Mass Spectrometry

For Sequences:
- Exoglycosidase
- Endoglycosidase
- N-glycosidase
 CHEM 161 2nd Exam Reviewer
Carbohydrates, Lipids, Nucleic Acids,
And Central Dogma of Molecular Biology

Glycerophospholipids Phospholipids
- Glycerol backbone - Forms bimolecular sheets in aqueous media
- Amphipathic nature gives rise to membrane
Fatty Fatty formation
Acid Acid
Formation of Lipid Vesicles from
Phospholipids
Glycerol
1. Prepare Glycine – Water – Phospholipid Sol’n
PO42- 2. Sonicate
3. Prepare the sample for Gel filtration
O–X
Non-Saponifiable Lipids
A. Steroids
Common alcohol moieties of - Cholesterol
phosphoglycerides - Lipoproteins: Transporter of TAGs,
Cholesterol, HDL, LDL
1. Serine - Bile Salts: Synthesized from
2. Ethanolamine cholesterol
3. Choline
4. Glycerol B. Terpenes
5. Inositol - Hydrocarbon derivatives from recurring
isoprene units
Sphingolipids
- Sphingosine backbone Lipid-Soluble Vitamins
1. Vitamin A
Fatty 2. Vitamin D
Acid 3. Vitamin E
4. Vitamin K
Sphingosine Electron Carriers
- Coenzymes Q10, Q
O—X
C. Eicosanoids
- Signaling molecules from arachidonic acid
Sphingomyelin - Hormone-like activities
- Derived from Ceramide - Messengers in Central Nervous System (CNS)
- Examples: Leukotrienes, Prostaglandins,
Fatty Thromboxanes, Pheromones
Acid
Biological Membranes
Sphingosine Functions:
1. Physical Barrier
Phosphoryl 2. Selective Filter
Choline 3. Communication w/ Surroundings
4. Energy Transduction
 CHEM 161 2nd Exam Reviewer
Carbohydrates, Lipids, Nucleic Acids,
And Central Dogma of Molecular Biology

Composition of Biol. Membranes 6. Small Residues

- Gly, Ala, Ser Residues
Proteins 20-80% - Allows interaction optimization adjacent
Lipids 20-80% helices
Carbohydrates ~5%
Proteins in Biol. Membranes
NOTE: Lipid bilayer is ASYMMETRIC in 1. Intrinsic Proteins
biological membranes. 2. Peripheral/ Extrinsic Proteins

Phospholipid Content of the Lipid Bilayer Membrane Transport

1. Passive Transport
Cytoplasmic Outer a. Simple Diffusion/ Osmosis
Leaflet Layer b. Facilitated Diffusion (e.g. Permeases)
Sphingomyelin 2. Active Transport
Phosphatidyl
Choline Nucleic Acids
Phosphatidyl
Ethanolamine
Phosphatidyl
Serine
Phosphatidyl
Inositol

Charge distribution across the Bilayer

Cytoplasmic Outer
Leaflet Layer
Charge Negative Neutral

Lipid Bilayer Movements

1. Flex Purine bases
2. Lateral Shift Adenine: 6-aminopurine
3. Transverse Diffusion Guanine: 2-amino-6-aminopurine

Characteristics of Lipid Bilayer Pyrimidine Bases

1. Polarity Uracil: 2,4-dioxypyrimidine
- Hydrophobic Thymine: 2,4-dioxy-5-methylpyrimidine
- Ile, Leu, Val, Phe Residues Cytosine: 2-oxy-4-aminopyrimidine

2. Basic Residues Charged Nucleic Acids (NTPs)

AMP: Adenosine monophosphate
CDP: Cytidine Diphosphate
dGTP: deoxyguanine triphosphate
dTTP: deoxythymidine triphosphate
CAMP: 3’-5’ cyclic adenosine monophosphate
 CHEM 161 2nd Exam Reviewer
Carbohydrates, Lipids, Nucleic Acids,
And Central Dogma of Molecular Biology

ATP Hydrolysis Types of DNA according to structure

1. B-DNA (Predominant)
2. A-DNA (Wider)
3. Z-DNA (Zigzag DNA)

Central Dogma of Molecular Biology

Functions of Nucleotides: DNA Replication

1. High energy transfer potential Requirements for DNA Replication:
2. Precursors of Nucleic Acids 1. DNA Template
3. Allosteric regulator of enzymes 2. RNA Primer
4. Secondary messengers (cAMP, cGMP) 3. Precursors (dNTPs)
5. Donors 4. Proteins and Enzymes
Energy ATP
Sulfate Donor Adenosine-3’- Characteristics of Replication:
Phosphate-5’- 1. DNA Pols require a template and primer
Phosphosulfate 2. All DNA polymerases have the Klenow
(PAPS) fragement: for Synthesis, Proofreading and
Methyl Donor S-adenosyl Primer Removal.
methionine (SAM)
6. UDP Sugar Derivatives: for Oligosaccharide
Synthesis
7. Cytidine triphosphate (CTP) participates in
the biosynthesis of phosphoglycerides and other
sphingosines.
10. Incorporation in coenzymes 3. Two bound metal ions participate in the
polymerase action:
Coenzymes/ Carriers in Biol. Oxidation Mg2+ 3’ OH end of Primer
dNTP
Active forms of Vitamin B3 (Niacin) 4. DNA replication is semi-discontinuous
1. NAD+: Nicotinamide Adenine Dinucleotide
2. NADP+: Nicotinamide Adenine Dinucleotide

Active forms of Vitamin B2 (Riboflavin)

1. FAD+: Flavin Adenine Dinucleotide
2. FMN: Flavin Mononucleotide

Nucleic Acid Structures

Chargaff’s Rules in DNA
 CHEM 161 2nd Exam Reviewer
Carbohydrates, Lipids, Nucleic Acids,
And Central Dogma of Molecular Biology
DNA replication enzymes and proteins 7. The pre-mRNA transcript acquires a 5’ cap
Enzyme/ Protein Function and a polyadenylated tail (coupled reaction with
dnaA protein Replication Initiation transcription)
Factor. Opens duplex at Specific sequence for the endonuclease:
OriC AAUAAA
HU (Histone-like Integration host factor. 8. pre-mRNA transcript are spliced by the
protein) Stimulates Initiation spliceosomes
Helicase (dnaB protein) Unwinds the DNA RNA Synthesis enzymes and sites
dnaC protein Loading Factor
Enzyme/ Sites Function
SSB Binds to single- RNA Polymerases
stranded DNA RNA Pol I rRNA production
Primase Catalyzes synthesis of RNA Pol II pre-mRNA transcript
RNA primers RNA Pol III tRNA production
DNA Polymerases TATA Box Promoter region
DNA Pol III Chain Elongation -35 Region Closed Complex
DNA Pol II DNA repair
-10 Region Open Complex
DNA Pol I Excision of Primers
GC rich then AT rich Termination site
Ligase Bridging of Okazaki
region
Fragments
Rho protein Helps in termination
Topoisomerases
AAUAAA Specific sequence for
Topoisomerase I Relax Super Coils
endonuclease
Topoisomerase II Induce (-) Supercoils
termination
Spliceosomes Removal of Intron
RNA Synthesis: Transcription
Steps:
1. Initiation Protein Synthesis: Translation
Steps:
2. Elongation
1. Initiation
3. Termination
2. Elongation
RNA Polymerase:
- Catalyze Transcription Wobble base pairing
- Binds on the promoter sites on the DNA to Anticodon Codon
initiate transcription C G
- Recognizes promoter sites A U
- Unwinds the DNA template U A or G
G U or C
RNA Synthesis I U, C, or A
1. The RNA Pol II recognizes and binds on the
promoter sites situated in the template. Protein Synthesis
Promoter sites: TATA BOX (AT Rich region) 1. The small ribosomal unit (30S) binds to the
2. RNA Pol II forms a closed complex at the -35 mRNA and locates the start codon AUG.
region of the unwound double helix. 2. The initiator tRNA fMet binds to the start
3. RNA migrates to the -10 region to form an codon.
open complex. 3. GTP complexes with several initation factors
4. Elongation proceeds in the transcription to signal the joining of the 2 ribosomal subunits.
bubble. 3. The fMet is placed on the P site of the
5. RNA Pol II approaches GC rich region then ribosome in the formation of the 70s initiation
AT rich region which signals termination. complex.
6. Rho protein help in the termination signaling 4. Elongation factors deliver aminoacyl-tRNAs
to the vacant A site of the 70s complex.
 CHEM 161 2nd Exam Reviewer
Carbohydrates, Lipids, Nucleic Acids,
And Central Dogma of Molecular Biology
5. Peptidyl transferase catalyzes the peptide
bond synthesis.
6. The peptide synthesis is terminated by release
factors that read stop codons: AUG UGA UAA.
7. Ribosome release factor (RRF) dissociates the
70S complex via GTP hydrolysis.

Formation of aminoacyl-tRNA
- Catalyzed by Aminoacyl-tRNA synthethase

AA + ATP ----- Aminoacyl-AMP + PPi

Aminoacyl-AMP + tRNA ----- Aminoacyl-

tRNA + AMP

AA + ATP + tRNA ----- Aminoacyl-tRNA +

AMP + PPi

Protein Synthesis enzymes and sites

Enzyme/ Sites Function
Ribosomal subunits
30S Small subunit
50S Large Subunit
70S Initiation complex
GTP Functions via
hydrolysis to GDP

Signals the creation of

the initiation complex

Hydrolyses to GDP to
displace the tRNA-
peptide complex from
the A site to P site
fMet Peptide counterpart of
the anticodon UAC
Peptidyl Transferase Catalyzes peptide
formation
Codons:
AUG Start codon

UAG Stop codons

UGA
UAA
RF Releases the peptide
from the tRNA
RRF Dissociates the 70s
initiation complex via
GTP hydrolysis