Unit 9

• Deoxyribose nucleic acid: genetic material that provides the blueprint to produce an organism’s trait

• All living organisms contain DNA as genetic material

  • for this reason, viruses don’t really count as a living organism

9.1 Properties & Identification of Genetic Information

• In plants and animals, DNA allows for fertilized eggs/embryos

• Genetic information must meet 4 criteria

  • Information: Genetic Material must contain information necessary to construct an entire organism

  • Replication: Genetical material must be accurately copied in process known as DNA replication

  • Transmission: After replication, genetic material must be passed from parent to offspring (cell to cell during cell division)

  • Variation: Differences in genetic material must account for the known variation within each species and among different species

• August Weismann and Karl Nageli believed that chemical substances exist in living cells that is responsible for transmission of traits from parents to offspring

  • experimentation centered on behavior of chromosomes

• Researchers believe that chromosomes carry determinants that control outcome of traits

Griffith’s Bacterial Transformation indicates existence of genetic material

• Strains of S. Pneumoniae could either be smooth and rough

  • In mammals, smooth strain could cause pneumonia and other symptoms

    • in mice, often fatal

  • Rough strain can be killed by immune system

• Transformation: genetic transfer between bacteria, segment of DNA from environment is taken by competent cell

9.2 Nucleic Acid Structure

• Nucleic Acid: DNA and RNA; polymers consisting of nucleotides responsible for storage, expression, and transmission of genetic material

• DNA has 5 levels of complexity

  • nucleotides are building blocks

  • strand of DNA is formed by covalent linkage of nucleotides in linear manner

  • Double Helix: two strands of hydrogen bonded together, twisting around each other

  • DNA is associated with different proteins to form chromosomes, association of proteins with DNA organizes long strands into compact structure

  • Genome is complement of an organism’s genetic material

Nucleotides contain a phosphate sugar and a base

• A nucleotide within a DNA and RNA has 3 components

  • phosphate group, pentose sugar, and nitrogen-containing base

• Nucleotides contain different sugar

  • Deoxyribose: found in DNA

  • Ribose: found in RNA

• 5 different bases are found in nucleotides, which are subdivided into 2 categories

  • Purine bases: adenine (A) and Guanine (G)

    • have a double ring structure

  • Pyrimidine bases: Thymine (T) and Cytosine (C)

    • Uracil instead of Thymine in RNA

A strand is a linear linkage of nucleotides with directionality

• Key features of DNA strand are as follows

  • nucleotides are linked together by covalent bonds called phosphodiester bonds

    • occurs between phosphorous and oxygen

  • Phosphate and sugar molecules form the back bone of a DNA and RNA strand, bases project the backbone

  • A strand has directionality based on orientation of sugar molecules

DNA is double stranded, antiparallel, and helical structure

• Has several distinguishing features

  • double helix is stabilized by hydrogen bonding with opposite strands, forming base pairs

  • Adenine and Thymine pair together via two hydrogen bonds, Guanine and Cytosine pair together

    • known as AT/GC Rule

  • DNA sequences are complementary

  • 5’ and 3’ directionality, two strands of a DNA double helix are antiparallel

  • two grooves are created

    • Major groove: occurs where DNA backbones are farther apart

    • Minor groove: is where the strands come closer together

9.3 Discovery of Double Helix in DNA

• X-Ray diffraction studies provide into DNA structures

  • researchers found diffraction patterns of DNA’s helical structure

Analysis of Base composition

• Chargaff analyzed frequency of bases, realized that pairs occurred in similar frequencies

9.4 Overview of DNA Replication

• DNA Replication: original strands of DNA used as templates for synthesis of new DNA strands

Meselson and Stahl considered 3 proposed mechanisms

• Three proposed models for DNA replication; they all have daughter and parental strands

  • Semiconservative Mechanism: double stranded DNA is half conserved

    • new double stranded DNA has one parental and one daughter strand

  • Conservative Mechanism: Only daughter strands are bonded together

  • Dispersive Mechanism: segments of parental DNA and daughter DNA are mixed together in both strands

DNA replication process occurs due to AT/CG rule

• Template Strand: two complementary strands as templates for daughter strands

9.5 Molecular Mechanism of DNA Replication

• DNA replication begins at the origin of replication

  • Origin of replication: a site within a chromosome that is starting point of replication

    • At origin, two DNA strands unwind to form replication bubble

    • In this bubble, two replication forks are formed

    • DNA replication proceeds toward two replication process called bidirectional replication

DNA replication requires different proteins

• DNA helicase and topoisomerase are responsible for fork formation and movement

  • DNA helicase: at each fork, DNA helicase binds to one DNA strand and travels in 5’ to 3’ direction

    • uses ATP to break apart hydrogen bonds

  • DNA topoisomerase: removes knots/coils caused by helicase unwinding

  • Single-strand binding proteins: coats the now single strands to prevent them from reforming double helix

• Two enzymes needed for DNA synthesis

  • DNA Polymerase: responsible for covalently linking nucleotides to form DNA strands

  • DNA Primase: DNA polymerase is unable to begin DNA on bare DNA strand, Primase acts as a primer

    • Primer is a short segment of RNA

  • Deoxynucleotide Triphosphate: Hydrogen bonds to exposed bases according to AT/CG rule

• At catalytic site, DNA polymerase breaks a bond between first and second phosphate

  • attaches resulting nucleotide with one phosphate group to 3’ via phosphodiester bond

• 2 enzymatic features that affect how DNA strands are made

  • DNA polymerase is unable to begin DNA synthesis on a bare strand

  • DNA polymerase can synthesize only in 5’ to 3’ direction

Leading and Lagging strands are made differently

• Synthesis of daughter strands are different from each other

• Leading strand: made in direction of fork movement; synthesis as one long, continuous strand

• Lagging strand: made as a series of small fragments, primer is needed to start the synthesis

  • small fragments are known as Okazaki fragments

  • Replication occurs opposite direction of fork movement, but is still in 5’ to 3’ direction

• DNA ligase: catalyzes formation of covalent bond between two DNA fragments to complete lagging strand

DNA Replication is very accurate

• Errors could occur, but permanent mistakes are rare

• Three factors explain high fidelity for DNA replication

  • Hydrogen bonding between A/T and C/G is more stable than mismatched pairs

  • Active site of DNA polymerase is unlikely to catalyze bond formation between adjacent nucleotides if mismatched base pair is formed

  • DNA polymerase can identify a mismatched nucleotide and remove it from daughter strand

    • called proofreading

9.6 Molecular Structure of Eukaryotic Chromosomes

• DNA is folded and compacted to fit inside nucleus

• Chromatin: Composition of chromosomes

DNA wraps around Histone proteins to form nucleosomes

• DNA is first compacted by wrapping around a group of proteins called histones

• Repeating structural unit of chromatin is called nucleosome

• negative charges in phosphate DNA attracted to positive charge on histone proteins

Nucleosomes form 30nm fiber

• nucleosome units are organized into more compact structure known as 30-nm fiber

Chromosomes are further compacted by formation of loop domains

• 30-nm fiber needs to be folded into loops to fit in cell nucleus

  • called loop domains

• Involves protein CCCRC binding factor

Non dividing cells

• Compaction of chromosomes aren’t completely uniform

  • Heterochromatin: highly compacted regions of chromosomes during interphase

  • Euchromatin: less condensed regions