Structure of Nucleic Acids (Reading Assignment)

Nucleic Acids

• chemical repositories of genetic information

• located inside the nucleus (for eukaryotes) or in the nucleoid region (for prokaryotes)

• phosphodiester

  • DNA (2’-deoxyribonucleic acid)

  • RNA (ribonucleic acid)

Nucleic Acids

• biopolymers of nucleotides linked together by __________________ bonds

• two forms:

  • _______________________

  • _______________________

1. nucleic acids

2. ATP and GTP

3. FAD, NADH, NADPH

4. UDP-glucose, UDP-galactose

Functions of Nucleotides

1. As repeating units/precursors of ______________

2. Energy currencies in metabolism

   • ____ and ____

3. Components of co-enzymes and reductants

   • _____, ______, and ______

4. Carriers of activated molecules

   • ____________, ______________

• four

  • ATP (Adenosine Triphosphate)

  • dTDP (Deoxythymidine Diphosphate)

  • dCDP (Deoxycytidine Diphosphate)

  • dGDP (Deoxyguanosine Diphosphate)
    
    

  • 2’-deoxyribonucleotides

  • sugar; phosphate; phosphodiester

Primary Structure of DNA

• polymer of ______ nucleotides

  • Core nucleoide molecules:

    • _____________________

    • _____________________

    • _____________________

    • _____________________

• main structural features:

  • monomer: _____________________

  • backbone: alternating _______ and _________ groups linked together by _________________ bonds

    • 5’-phosphate group of one nucleotide to 3’ ―OH group of another nucleotide

• 5’; 3’

• It is the 5’ end if there is a free phosphate group and it is the 3’ end if thhere is a free hydroxyl group.

Primary Structure of DNA

• by convention, the base sequence is read from the __ to __ direction

• base sequence along a chain carries the genetic information

• What determined which end is which?

• double helix

Secondary Structure of DNA

• The DNA molecule has the form of a _____________:

  • a helical structure consisting of two complementary nucleic acid strands

• Rosalind Franklin; Maurice Wilkins

Elucidation of DNA 3D structure

• _________________ and __________________ obtained the X-ray diffraction photographs of DNA fibers

• James Watson; Francis Crick

Elucidation of DNA 3D structure

• _____________ and ______________ deduced DNA structure in 1953

• helical; polynucleotide

• opposite

  

Watson-Crick DNA Model

• two ________ ________________ chains are coiled around a common axis

• the two chains run in ________ directions

• sugar-phosphate

• purine; pyrimidine

Watson-Crick DNA Model

• the ________________ backbones are on the outside

• __________ and ___________ bases lie on the inside of the helix

• perpendicular

• 3.4 Å

• hydrophobic interactions

Watson-Crick DNA Model

• the bases are nearly _________ to the helix axis

  • bases are stacked on top of the other with distance of _____

  • base stacking maximizes ______________ _____________ to stabilize the DNA structure

• 10; 34

• 36

• 360; 10

• 20

Watson-Crick DNA Model

• each turn of the helix consists of __ stacked base pairs (__ Å /turn)

• rotation per base is __°

• __° per full turn/__ bases per turn

• helix diameter is __ Å

• 
  

  • adenine; thymine

  • cytosine; guanine

• Chargaff’s Rule

  • Erwin Chargaff

Watson-Crick DNA Model

• two strands are complementary due to specific base pairing

  • __________ pairs with ____________

  • __________ pairs with ____________

• ______________ Rule

  • ____________ (1950)

  • A:T and G:C percentages Sare nearly the same in all species

Plasmid DNA

______________

• small DNA molecule which is physically separate from chromosomal DNA and capable of self-replication

Plasmid DNA

_________________

• usually used as vector in genetic engineering

• 
  

  1. ribose

  2. Thymine; uracil

• single

Ribonucleic Acid (RNA)

• primary structure is similar to DNA except for the ff:

  1. Sugar component which is _________

  2. Nucleotide base _________ is replaced with _________

• most cellular RNAs are _______-stranded and exhibit a variety of conformations

• different types of RNA perform different cellular functions

ATP (Adenosine triphosphate)

GTP (Guanosine triphosphate)

CTP (Cytidine triphosphate)

UTP (Uridine triphosphate)

What are the (four mentioned) important ribonucleotides in RNA?

• base pairing; secondary

  • hairpin; stem-loop

• tertiary

2° and 3° Structures of RNA

• in a single-stranded RNA, intramolecular _____ _________ determines the ____________ structure

  • __________ and _____________ are the most common elements of the secondary structure

• __________ structure is formed by joining together the different secondary structures of RNA

1. messenger RNA (mRNA)

2. transfer RNA (tRNA)

3. ribosomal RNA (rRNA)

Types of RNA

1. ____________________

   • serves as template for the synthesis of polypeptide (translation)

2. ____________________

   • carries amino acids in an activated form to the ribosomes for peptide bond formation during polypeptide synthesis

3. ____________________

   • major component of ribosomes