Molecular Biology of the Gene

Chapter 10

• Gene: a discrete unit of hereditary information consisting of a specific nucleotide sequence in DNA (or RNA, in some viruses). Most of the genes of a eukaryote are located in its chromosomal DNA; a few are carried by the DNA of mitochondria and chloroplasts.

• Gene: portion of a chromosome responsible for the expression of a character

• Bacteriaphages (or phages for short): viruses that infect bacterial cells

• DNA and RNA are nucleic acids

• One of the strands of DNA is a DNA polynucleotide, a nucleotide polymer (chain)

• A Nucleotide is composed

- Nitrogenous Base

- 5-Carbon Sugar

- Phosphate Group

• The nucleotides are joined to one another by a sugar-phosphate backbone

• Each type of DNA nucleotide has a different Nitrogen-containing base

- Adenine (A)

- Cytosine (C)

- Thymine (T)

- Guanine (G)

RNA (Ribonucleic Acid)

- uses sugar ribose (instead of deoxyribose in DNA)

- has a Nitrogenous base Uracil (U) instead of Thymine

10.2 DNA & RNA are Polymers of Nucleotides

10.4

DNA Replication

• DNA replication begins at the origins of replication where• DNA unwinds at the origin to produce a “bubble”

• Replication proceeds in both directions from the origin and

• Replication ends when products from the bubbles merge with each other

• DNA replication occurs in the 5’ to 3’ direction • Replication is continuous on the 3’ to 5’ template

• Replication is discontinuous on the 5’ to 3’ template, forming short segments

10.5 DNA Replication proceeds in 2 directions at many sites simultaneously

• 2 key proteins are involved in DNA replication

• 1. DNA Ligase joins small fragments into a continuous chain

• 2. DNA Polymerase

• Adds nucleotides to a growing chain

• Proofreads and corrects improper base pairings

• DNA polymerases and DNA Ligase also repair DNA damaged by radiation and toxic chemicals

• DNA replication ensures that all the somatic cells (all cells except for sex cells) in a multicellular organism carry the same genetic information

10.5 DNA Replication proceeds in 2 directions at many sites simultaneously

10.5 B

The flow of Genetic info from DNA to RNA to Protein

• DNA specifies traits by dictating protein synthesis

• The molecular chain of command is from • DNA in nucleus to RNA and

• RNA in cytoplasm to protein

• Transcription: synthesis of RNA under the direction of DNA

• Translation: synthesis of proteins under the direction of RNA

10.6 The DNA genotype is expressed as proteins, which provide the molecular basis for genotypic traits

• The sequence of nucleotides in DNA provides a code for constructing a protein

• Protein construction requires a conversion of a nucleotide sequence to an amino acid sequence

• Transcription rewrites the DNA code into RNA, using the same nucleotide ‘language’

• The flow of info from gene to protein is based on a Triplet Code: the genetic instructions for the amino acid sequence of a polypeptide chain are written in DNA and RNA as a series of non-overlapping 3-base “words” called codons

• Translation involves switching from the nucleotide “language” to the amino acid “language”

• Each amino acid is specified by a codon • 64 codons are possible

• Some amino acids have more than one possible codon

10.7 Genetic info written in codons is translated into amino acid sequences

10.7

• Characteristics of the Genetic Code • 3 nucleotides specify one amino acid

• 61 codons correspond to amino acids

• AUG codes for methionine and signals the start of transcription. This is one of the 61 codons above

• The genetic code is • Redundant, with more than one codon for some amino acid

• Unambiguous, in that any codon for one amino acid does not code for any other amino acid

• Nearly universal, the genetic code is shared by organisms from the simplest bacteria to the most complex plants and animals

• Without punctuation in that codons are adjacent to each other, with no gaps in between

10.8 The genetic code dictates how codons are translated into amino acids

• Over view of Transcription:• An RNA molecule is transcribed from a DNA template by a process that resembles

the synthesis of a DNA strand during DNA replication

• RNA nucleotides are linked by the transcription enzyme RNA Polymerase

• Specific sequences of nucleotides along the DNA mark where transcription begins and ends

• The “start transcribing” signal is a nucleotide sequence called a promotor

• Transcription begins with initiation as the RNA Polymerase attaches to promotor

• During 2nd phase, elongation, the RNA grows longer

• As the RNA reels away, the DNA strands rejoin

• Finally the 3rd phase, termination, the RNA polymerase reaches a sequence of bases in the DNA template called a Terminator, which signals the end of the gene

• The polymerase molecule now detaches from the RNA molecule and the gene

10.9 Transcription produces genetic messages in the form of DNA

• Messenger RNA (mRNA)• Encodes amino acid sequences

• Conveys genetic messages from DNA to the translation machinery of the cell, which in

• Prokaryotes occurs in the same place that mRNA

• Eukaryotes, mRNA must exit the nucleus via nuclear pores to enter the cytoplasm

• Eukaryotic mRNA has • Introns, interrupting sequences that separate

• Exons, the coding regions

• Eukaryotic mRNA undergoes processing before leaving the nucleus• RNA splicing removes introns and joins exons to produce a continuous

coding sequence

• A cap and tail of extra nucleotides are added to the ends of the mRNA to

• Facilitate the export of the mRNA from the nucleus

• Protect the mRNA from attack by cellular enzymes

• Help ribosomes bind to mRNA

10.10Eukaryotic RNA is processed before leaving the nucleus as mRNA

• Transfer RNA (tRNA) molecules function as a language interpreter

• Converting the genetic message of RNA

• Into the language of proteins

• Transfer RNA molecules perform this task by • Picking up the appropriate amino acid and

• Using a special triplet of bases, called an anticodon, to recognize the appropriate codons in the mRNA

10.11 Transfer RNA molecules serve as interpreters during translation

• Translation occurs on the surface of the ribosome • Ribosomes coordinate the functioning of mRNA and tRNA and,

ultimately, the synthesis of polypeptides

• Ribosomes have 2 subunits: small and large

• Each subunit is composed of ribosomal RNAs and proteins

• Ribosomal subunits come together during translation

• Ribosomes have binding sites for mRNA and tRNAs

10.12 Ribosomes build Polypeptides

• Translation can be divided into the same 3 phases as Transcription

1. Initiation

2. Elongation

3. Termination

• Initiation brings together • mRNA

• A TRNA bearing the first amino acid and

• The 2 subunits of a ribosome

• Initiation establishes where translation will begin

10.13 An initiation codon marks the start of an mRNA message

Initiation occurs in 2 steps

1. An mRNA molecule binds to a small ribosomal subunit and the first tRNA binds to mRNA at the start codon

The start codon reads AUG and codes for Methionine The 1st tRNA has the anticodon UAC

2. A large ribosomal subunit joins the small subunit, allowing the ribosome to function

The 1st tRNA occupies the P Site, which will hold the growing peptide chain

The A Site is available to receive the next tRNA

10.13 An initiation codon marks the start of an mRNA message

• Once initiation is completed, amino acids are added one by one to the 1st amino acid

• Elongation is the addition of amino acids to the polypeptide chain

10.14 Elongation adds amino acids to the polypeptide chain until a stop codon terminates translation

Each cycle of elongation has 3 steps:

1. Codon Recognition: the anticodon of an incoming tRNA molecule; carrying its amino acid, pairs with the mRNA codon in the A site of the ribosome

2. Peptide Bond Formation: the new amino acid is joined to the chain

3. Translocation: tRNA is released from the P site and the ribosome makes tRNA from the A site into the P site

Elongation continues until the termination stage of translation when:

- the ribosome reaches a stop codon

10.14

• Transcription is the synthesis of RNA from a DNA template.

• In Eukaryotic cells:• Transcription occurs in the nucleus

• The mRNA travels from nucleus to cytoplasm

• Translation = 4 steps. It occurs in the Cytoplasm 1. Amino acid attachment

2. Initiation of polypeptide synthesis

3. Elongation

4. Termination

10.15 REVIEW: Flow of genetic info in cell is DNA RNA Protein

• A mutation is any change in the nucleotide sequence of DNA

• A mutation can involve• Large chromosomal regions or

• Just a single nucleotide pair

• Mutations within a gene can be divided into 2 categories

1. Base Substitutions involve the replacement of one nucleotide w/ another. Base substitutions may:

• Have no effect at all, producing a silent mutation

• Change the amino acid coding producing a Missense mutation, which produces a different amino acid

• Lead to a base substitution that produces an improved protein that enhances the success of the mutant organism and its descendent or

• Charge an amino acid into a stop codon, producing a nonsense mutation

10.6 Mutations can change the meaning of jeans

2. Mutations can result in deletions or insertions that may• Alter the reading frame (triplet grouping) of the mRNA, so that

nucleotides are grouped into different codons

• Lead to significant changes in amino acid sequence downstream of the mutation and

• Produce a non-functional polypeptide

10.6 Mutations can change the meaning of jeans