Lecture 18: Nucleic acids monomers / Polynucleotide chains (+ a little of lecture 17)

oligosaccharides

glycoprotein and glycolipids

Glycoproteins

Proteins that have small sugars or short sugar chains attached to themglyco

glycolipids

Lipid molecules that have short oligosaccharide chains attached to them

N-linked glycoproteins

Sugar moieties are attached to a protein through an amino acid with single-letter code N which is asparagine

N-linked glycoproteins occurs

only in the endoplasmic reticulum through asparagine

N-linked glycoproteins Rule

at an Asn which is next to any amino acid (X), followed by Ser or Thr

O-linked glycoproteins

in proteins occur through amino acids with a hydroxyl group

serine, threonine and tyrosine

O-linked glycoproteins occurs in

endoplasmic reticulum

Blood group antigens

are examples of glycolipids

A, O, and B

Nucleotides are made of

base, sugar, and phosphate group

Two types of nitrogenous bases

1. Purines = large bases A, G

2. Pyrimidines = small bases T, U, C

DNA is negatively charged

because of the phosphate backbone

ribose

aldose, beta, and is furanose bc it is a 5 membered ring

Purines

large bases that have 2 aromatic rings A an G

Pyrimidines

small bases that have one aromatic ring U, C, and T

Structural convention for bases

On the top are the purines and the bottom are the pyrimidines

base-pairing edge

the side where most functional groups are present, this is the side involved in hydrogen bonding in DNA double helix formation

Hydrogen bond donors

Functional groups where hydrogen is attached to a more electronegative atom: NH and NH2

Hydrogen bond acceptors

Atoms with lone pairs that can accept a hydrogen bond: nitrogen with lone pair and oxygen with lone pair

Thymine vs uracil

thymine has a methyl group at position 5 but uracil does not

nucleoside

base + sugar

Adenine nucleosides RNA

adenine + ribose = adenosine and abbreviation still tied to A

Adenine nucleosides DNA

adenine + deoxyribose = deoxyadenosine and abbreviated as dA

Guanine nucleosides RNA

guanine + ribose = guanosine

Guanine nucleosides DNA

guanine + deoxyribose = deoxyguanosine

abbreviation dG

Rule for purines as nucleosides

purines get the suffix: -osine

adenosine and guanosine

Cytosine nucleosides RNA

cytosine + ribose = cytidine

Cytosine nucleosides DNA

cytosine + deoxyribose = deoxycytidine

abbreviation dC

Rule for pyrimidines as nucleosides

pyrimidines usually get the suffix: -idine

Uracil nucleosides RNA

uracil + ribose = uridine

Thymine nucleosides DNA

thymine + deoxyribose = deoxythymidine

abbreviation tied to T

nucleotide

base + sugar + phosphate group

Adenine nucleotides RNA

adenosine monophosphate = AMP

adenosine diphosphate = ADP

adenosine triphosphate = ATP

Adenine nucleotides DNA

deoxyadenosine monophosphate = dAMP

deoxyadenosine diphosphate = dADP

deoxyadenosine triphosphate = dATP

Guanine nucleotides RNA

guanosine monophosphate = GMP

guanosine diphosphate = GDP

guanosine triphosphate = GTP

Guanine nucleotides DNA

add deoxy

dGMP, dGDP, dGTP

Cytosine nucleotides RNA

cytidine monophosphate = CMP

cytidine diphosphate = CDP

cytidine triphosphate = CTP

Cytosine nucleotides DNA

add deoxy

dCMP, dCDP, dCTP

Uracil nucleotides RNA

uridine monophosphate = UMP

uridine diphosphate = UDP

uridine triphosphate = UTP

Thymine nucleotides DNA

deoxythymidine monophosphate = dTMP

deoxythymidine diphosphate = dTDP

deoxythymidine triphosphate = dTTP

Acid Anhydride

Acid + Acid =

Ester

Acid + Alcohol

Ether

Alcohol + Alcohol

Large base + acceptor

adenine

Large base + donor

guanine

Small base + acceptor

cytosine

Small base + donor

thymine / uracil

2 hydrogen bonds

A–T

3 hydrogen bonds

C–G

Polynucleotide direction

5′ to 3′

a free 5′ phosphate end and a free 3′ OH end

polynucleotides are formed

condensation reaction phosphodiester linkage

N-glycosidic linkage

between nitrogen of base and sugar

phosphoester bond

between 5′ OH of sugar and phosphate

Why ATP hydrolysis releases a lot of energy

ATP has a lot of (-) charge packed together causing repulsion, hydrolysis happens and less charge repulsion, and then new phosphate containing product is more soluble and stabilized

adenosine

adenine + ribose

Cyclic AMP

Adenosine is part of it and is a secondary messenger

formed from ATP by an enzyme

cyclic AMP contains a

intramolecular phosphodiester bond

Coenzyme A and Acetyl CoA

are coenzymes that help enzymes function adenosine is apart of these enzyme

NAD and NADP

regulates metabolism by acting as electron donors and acceptors

adenosine is apart of these enzymes

FAD

major role with metabolic enzymes and adenosine is also apart of this enzyme

all enzymes mentioned here

all contain ribose sugar