Chapter 16 The Molecular Basis of Inheritance and Chapter 17 Gene Expression: From Gene to Protein

Concept 16.1 DNA is the Genetic Material

Concept 16.2 Many Proteins work together in DNA replication & repair

Table 16.1 Bacterial DNA Replication Proteins and Their Functions

The Search for the Genetic Material: Scientific Inquiry

T. H. Morgan's group showed that genes exist as parts of chromosomes: DNA and protein.

Biochemists identified proteins as a class of macromolecules w/ great heterogeneity & hereditary material

Evidence that DNA can Transform Bacteria

In 1928, F. Griffith developed vaccine against pneumonia.

Figure 16.2: Griffith Expt

He used two strains of bacterium, one pathogenic & one nonpathogenic to study streptococcus pneumonia

Two Strains: S (smooth/with capsule) strain caused pneumonia & R (rough/no capsule) strain are nonpathogenic.

Griffith injected mice w/ two strains

Results

Living S cells caused mouse to die

Living R cells caused mouse to stay healthy

Heat-killed S Cells - healthy mouse

Mixture of Heat-killed S cells & icing R cells - dead mouse

In blood sample, living S cells were found

Conclusion: living R bacteria transformed into pathogenic S bacteria by unknown, heritable substance from dead S cells that enabled R cells to make capsules.

Transformation: A change in genotype and phenotype due to the assimilation to external DNA by a cell.

Evidence That Viral DNA can program Cells

Bacteriophage or Phages

Virus DNA/RNA enclosed by a protective coat, that is protein.

DNA is the genetic, material of phage know as T2

T2 typically infects E. Coli

T2 is composed of DNA & protein

Could quickly turn E. Coli cell into a T2 producing factory that released many copies of new phages when cell ruptures.

Hershel & Chase found that the phage DNA entered the host cells but the protein did not.

Results: DNA inside the cells played an ongoing role during injection process.

Concluded that the DNA injected by the phage must be the molecule carrying the gene info that makes the cells produce new viral DNA & proteins.

Is Protein or DNA the genetic material of phage T2?

1) Mixed radioactively labeled phages w/bacteria. The phages infected the bacterial cells.

  1. Agitated the mixture in a blender to free phage parts outside the bacteria from the cells.
  1. Centrifuged the mixture so that bacteria formed a pellet at the bottom of test tube; free phages & phage parts, which are lighter, remained suspended in the liquid.
  1. Measure the radioactivity in the pellet & the liquid.

Additional Evidence that DNA is the Genetic Material

DNA: Nitrogenous Base, Pentose Sugar called deoxyribose & a phosphate group.

Bases can be adenine (A), thymine (T) guanine (G), or cytosine (C)

Chargaff reported that the base composition of DNA varies from one species to another.

EX: Sea urchins = 32.8 % base A, Human DNA = 30.4 % bass A nucleotides, only 24.7% bacterium E. Coli have base A.

In Chargaff's analysis, sea urchin percentages: A = 32.8%; T=32.1%; G = 17.7%; C= 17.3%

Building a Structural Model of DNA: Scientific Inquiry

Figure 16.5

Each DNA nucleotide monomer consists of a nitrogenous base (T, A, G or C, sugar deoxyribose (blue) & a phosphate group (yellow).

Phosphate group of one nucleotide is attached to the sugar of the next by a covalent bond, forming a "backbone" of alternating phosphates & sugars from which base projects.

A polynucleotide strand has directionality from 5' end to 3' (w/the -OH group of the sugar), 5' and 3' refer to the #s assigned to the carbons in the sugar ring.

James Watson & Crick were the first to solve puzzle of DNA structure w/ X-Ray crystallography.

Spots & Smudges in the image were by the X-Rays that were diffracted as they passed thru aligned fibers of purified DNA

Double Helix

The two sugar-phosphate backbones are antiparallel running in opposite directions.

Adenine & Guanine are purine (Nitrogenousbases w/organic rings)

Cytosine & thymine are pyrimidine (Nitrogenous Bases w/a single ring).

The amount of A will equal the amount of T.

The amount of G will equal the of C.

The Basic Principle: Base Pairing a Template Strand

Each Chain acts as a template for the formation on to itself of a new companion chain so the two pairs of chains exist.

When DNA is copied, each strand serves as a template for ordering nucleotides into a new, complementary, strand.

Watson's & Crick's model represents that when a double helix replicates, each of the two daughter molecules will have one old strand, from the parent molecule & one new strand.

The conservative Model: Two parent strands reassociate after acting as templates for new strands, thus restoring the parent double helix.

Semiconservative Model: Two strands of the parental molecule separate & each functions as a template for synthesis of a new complementary strand.

Dispersive Model: Each strand of both daughter molecules contain a mixture of old & synthesized DNA.

DNA Replication Compare/Contrast between Prokaryotes and Eukaryotes

Prokaryotes

Eukaryotes

Proteins that initiate DNA replication recognize this sequence & attach to the DNA, separating the 2 strands & opening up a replication "bubble".

Then Proceeds in both directions until molecule is copied.

Replication bubble has a replication fork at each end (y-shaped region where DNA are being unwound).

Helicases untwist double helix at replication forks, making parental strands as template strands.

single-stranded binding proteins bind to unpaired DNA strands to keep them from repairing

**Okazaki Fragments: 1,000-2,000 nucleotides in E.Coli

DNA polymerase iii & i

The untwisting of double helix causes a tighter twist & strain on Y-Fork.

Topoisomerase:enzyme helps relieve strain by breaking swiveling & rejoin strands.

Multiple replication bubbles form & fuse. Speeding up the copying of the very long DNA molecules.

Eukaryotic DNa replication proceeds in both directions of each origin.

Replication Fork at each end (Yshaped region where DNA are being unwound).

Helicases untwist double helix at the replication forks, making parental strands as template strands.

single-stranded binding proteins bind to unpair DNA strands to keep them from repairing.

Okakzaki Fragments 100-200 nucloeotideslong.

The untwisting of the double helix causes tighter twist & strain on Y-Fork

Topoisomerase: enzyme helps relieve strain by breaking, swiveling, and rejoin strands

Synthesizing a New DNA Strand

Initial Nucleotide Chains: RNA chain called a primer & synthesized by primase

Primase begin w/a single nucleotide & adds RNA nucleotide one at a time using parental DNA strand as template.

The new DNA will start from 3' end of RNA primer.

DNA polymerases catalyze synthesis of new DNA by adding nucleotides to 3' end of a preexisting chain.

Antiparallel Elongation

Antiparallel: opposite direction of each other

New strands must be antiparallel to template strands

New DNA strands elongate in 5 --> 3 direction.

leading strand: only one primer is required for DNA pol iii to synthesize the entire leading strands.

DNA pol III must work along template strand in direction "away" from Y-fork.

lagging strand: strand elongating in direction; okazaki fragments are segments of the lagging strands.

Figure 16.14

Addition of a nucleotide to a DNA strand.

DNA polymerase catalyzes the addition of a nucleotide to the 3' end of a growing DNA strand, with release of two phosphates

Figure

Figure 16.15

Synthesis of the leading strand during DNA replication

Figure 16.15

  1. After RNA primer is made, DNA pol III starts to synthesize the leading strand.
  1. The leading strand is elongated continuously in the 5 ---> 3 direction as the fork progresses.

Figure 16.16

Synthesis of the lagging strand

Figure 16.16

Figure 16.17

16.17

Protein: Helicase

Function: Unwinds parental double helix at replication forks

Protein: single-stranded binding protein

Function: Binds to and stabilizes single-stranded DNA until it is used as a template

Protein: Topoisomerase

F: Relieves overwinding strain ahead of Y-Forks by breaking, swiveling, and rejoining DNA strands

P: Primase

F: Synthesizes an RNA primer at 5' end of leading strand and at 5' end of each Okazaki fragment of lagging strand

P: DNA pol III

F: Using parental DNA as a template, synthesizes new DNA strand by adding nucleotides to an RNA primer or a pre-existing DNA strand

P: DNA pol I

F: Removes RNA nucleotides of primer from 5' end and replaces them with DNA nucleotides added to 3' end of adjacent fragment.

P: DNA ligase

F: Joins Okazaki fragments of lagging strand; on leading strand, joins 3' end of DNA that replaces primer to rest of leading strand DNA.

Telomeres

Nucleotide sequences in Eukaryotic chromosomal DNA

Contain NO genes

consists of multiple repetitions of one short nucleotide sequence

EX: 6-nucleotide sequence TTAGGG is repeated b/w 100 and 1,000times

Two protective functions

telomeric DNA prevent the staggered ends of the daughter molecule from activating the cell's systems for monitoring DNA damage.

telomeric DNA acts as a buffer zone to protect against the organism's genes shortening.

Telomere

Concept 17.5 Mutations of one or a few nucleotides can affect protein structure and function

Concept 17.4 Translation is the RNA-directed synthesis of a polypeptide: a closer look

Concept 17.1 Genes specify proteins via transcription and translation

Concept 17.2 Transcription is the DNA-directed synthesis of RNA: a closer look

Concept 17.3 Eukaryotic Cels modify RNA after transcription

17.8

The Stages of transcription: initiation, elongation, and termination

Figur179

Figure 17.9 The initiation of transcription at a eukaryotic promoter.

Figure 17.8

Figure 17.10 Transcription Elongation

figure 17.10

Figure 17.19 The initiation of translation

Figure 17.19

Figure 17.20 The Elongation Cycle of Translation

Figure 17.20

Figure 17.21 The Termination of Translation

F 17.21

Structure of tRNA tRNA

Alteration of mRNA Ends

Split Genes and RNA Splicing

RNA Splicing

large portions of RNA molecules are removed & the remaining portions are reconnected.

similar to editing a movie

Introns

intervening sequences

Exons

are eventually expressed usually by being translated into amino acid sequences.

spliceosome

the removal of intron is accomplished by a large complex made of proteins and small RNAs

Figure 17.22 The signal mechanism for targeting proteins to the ER

17.22

Figure 17.23 Polyribosomes

Polyribosomes

may either be free or bound

seen with electron microscope

transcribe multiple mRNAs from the same gene.

Transcription

synthesis of RNA using info in the DNA

mRNA

carries genetic message from DNA to protein-synthesizing machinery in the cell.

Translation

synthesis of a polypeptide using info in the mRNA

ribosomes

site of translation

molecular complexes that facilitate the orderly linking of amino acids into polypeptide chains.

Mutations

are the ultimate source of new genes

huge diversity of genes

Point Mutations

changes in a single nucleotide pair of a gene

Types of Small-scale Mutations

Substitutions

Insertions and Deletions

nucleotide pair substitution is the replacement of one nucleotide and its partner with another pair of nucleotides.

silent

missense mutation