DNA, RNA, and Protein Synthesis

How do our genes work?

• “How do our genes determine our physical characteristics?

• These questions and others led scientists to develop experiments to find answers

• Frederick Griffith, 1928, tried to determine how bacteria make people sick.

• Specifically, he studied bacteria that produce pneumonia, a serious lung disease

Griffith and Transformation

Video

Griffith Experiment• Griffith called this process

transformation because one strain of bacteria (the harmless strain) had changed permanently into another (the disease-causing strain).

• Griffith hypothesized that a factor must contain information that could change harmless bacteria into disease-causing ones.

Avery and DNA• In 1944 Canadian biologist Oswald

Avery repeated Griffith’s experiment

• Made an extract from the heat-killed bacteria

• Treated the extract with an enzyme that destroyed proteins, lipids, carbs, and RNA, leaving only DNA: transformation still occurred

• They destroyed the DNA: transformation ceased

• Concluded that DNA stored the genetic information that is transmitted

Hershey-Chase Experiment• Alfred Hershey and Marsha

Chase studied viruses – nonliving particles smaller than cells

• Viruses contain DNA surrounded by protein coat

• They experiment on bacteriophages – viruses that infect bacteria

• If they could determine which part of the virus infected the bacteria, they could conclude whether genes were made of protein or DNA

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The Hershey-Chase Experiment• If 35S was found in the bacteria, it would mean

that the viruses’ protein had been injected into the bacteria.

Bacteriophage withsulfur-35 in protein coat

Phage infects bacterium

No radioactivity inside bacterium

The Hershey-Chase Experiment• If 32P was found in the bacteria, then it was the DNA that

had been injected.

• Nearly all of the radioactivity in the cell was from phosphorous. Hershey-Chase concluded that DNA was the source of genetic information, not proteins

Bacteriophage withphosphorus-32 in DNA

Phage infects bacterium

Radioactivity inside bacterium

Structure of DNA

• DNA is made up of units called nucleotides• Each nucleotide is made up of three

components:– 5-carbon sugar called deoxyribose– A phosphate group– A nitrogenous base

• Four kinds of nitrogenous base in DNA:– Adenine and Guanine are purines (2 rings)– Cytosine and Thymine are pyrimidines (1 ring)

The Components and Structure of DNA• There are

four kinds of bases in in DNA:– adenine– guanine – cytosine– thymine

DNA structure

• Backbone of DNA strand is formed by sugar and phosphate groups of each nucleotide

• The nucleotides can be joined in any order• Erwin Chargaff discovered that:– The percentages of guanine [G] and cytosine [C]

bases are almost equal in any sample of DNA. – The percentages of adenine [A] and thymine [T]

bases are almost equal in any sample of DNA.

• Therefore, this is called Chargaff’s Rule

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The Components and Structure of DNA

• X-Ray Evidence – Rosalind Franklin used X-ray

diffraction to get information about the structure of DNA.

– She aimed an X-ray beam at concentrated DNA samples and recorded the scattering pattern of the X-rays on film.

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The Double Helix• Using clues from Franklin’s pattern, James Watson

and Francis Crick built a model that explained how DNA carried information and could be copied.

• Watson and Crick's model of DNA was a double helix, in which two strands were wound around each other.

• Watson and Crick discovered that hydrogen bonds can form only between certain base pairs—adenine and thymine, and guanine and cytosine.

• This principle is called base pairing.

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• DNA Double Helix

• Blame it on the DNA• Stanford Video

DNA and Chromosomes

• DNA and Chromosomes• In prokaryotic cells, DNA is located in the cytoplasm.• Most prokaryotes have a single DNA molecule

containing nearly all of the cell’s genetic information.

DNA and Chromosomes

• Many eukaryotes have 1000 times the amount of DNA as prokaryotes.

• Eukaryotic DNA is located in the cell nucleus inside chromosomes.

• The number of chromosomes varies widely from one species to the next.

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DNA and Chromosomes

• Chromosome Structure– Eukaryotic chromosomes contain DNA and

protein, tightly packed together to form chromatin.

– Chromatin consists of DNA tightly coiled around proteins called histones.

– DNA and histone molecules form nucleosomes. – Nucleosomes pack together, forming a thick fiber.

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DNA and Chromosomes– Eukaryotic Chromosome Structure

Chromosome

Supercoils

Nucleosome

DNA double helix

Histones

Coils

DNA Replication• Each strand of the DNA double helix has all the

information needed to reconstruct the other half by the mechanism of base pairing.

• In most prokaryotes, DNA replication begins at a single point and continues in two directions

• In eukaryotic chromosomes, DNA replication occurs at hundreds of places.

• Replication proceeds in both directions until each chromosome is completely copied.

• The sites where separation and replication occur are called replication forks.

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DNA Replication

• Before a cell divides, it duplicates its DNA in a process called replication.

• Replication ensures that each resulting cell will have a complete set of DNA.

• During DNA replication, the DNA molecule separates into two strands, then produces two new complementary strands following the rules of base pairing.

• Each strand of the double helix of DNA serves as a template for the new strand.

Nitrogen Bases

Replication Fork

DNA Polymerase

Replication Fork

Original strandNew Strand

Growth

Growth

Active Art

DNA Replication

• DNA replication is carried out by enzymes (Helicase) that “unzip” a molecule of DNA.

• Hydrogen bonds between base pairs are broken and the two strands of DNA unwind.

• The principal enzyme involved in DNA replication is DNA polymerase.

• DNA polymerase joins individual nucleotides to produce a DNA molecule and then “proofreads” each new DNA strand.

• Genes are coded DNA instructions that control the production of proteins.

• Genetic messages can be decoded by copying part of the nucleotide sequence from DNA into RNA.

• RNA contains coded information for making proteins.

Genes

RNA

• RNA consists of a long chain of nucleotides.

• Each nucleotide is made up of a 5-carbon sugar, a phosphate group, and a nitrogenous base.

• There are three main differences between RNA and DNA:– The sugar in RNA is ribose

instead of deoxyribose. – RNA is generally single-stranded.– RNA contains uracil in place of

thymine.

Types of RNA

• There are three main types of RNA:– messenger RNA

– ribosomal RNA

– transfer RNA

• Messenger RNA (mRNA) carries copies of instructions for assembling amino acids into proteins.

• Ribosomes are made up of proteins and ribosomal RNA (rRNA).

Ribosome

Ribosomal RNA

• During protein construction, transfer RNA (tRNA) transfers each amino acid to the ribosome.

Amino acid

Transfer RNA

Transcription

• RNA molecules are produced by copying part of a nucleotide sequence of DNA into a complementary sequence in RNA. This process is called transcription.

• Transcription requires the enzyme RNA polymerase.

• During transcription, RNA polymerase binds to DNA and separates the DNA strands.

Transcription

• RNA polymerase then uses one strand of DNA as a template from which nucleotides are assembled into a strand of RNA.

• RNA polymerase binds only to regions of DNA known as promoters.• Promoters are signals in DNA that indicate to the enzyme where to

bind to make RNAVideo

RNA Editing

• The DNA of eukaryotic genes contains sequences of nucleotides, called introns, that are not involved in coding for proteins.

• The DNA sequences that code for proteins are called exons.

• When RNA molecules are formed, introns and exons are copied from DNA.

RNA Editing• The introns are cut out

of RNA molecules.• The exons are then

spliced together to form mRNA.

• The genetic code is the “language” of mRNA instructions.

• The code is written using four “letters” (the bases: A, U, C, and G).

Exon IntronDNA

Pre-mRNA

mRNA

Cap Tail

The Genetic Code

• A codon consists of three consecutive nucleotides on mRNA that specify a particular amino acid.

The Genetic Code• Each codon specifies a particular amino acid.• Some amino acids can be specified by more

than one codon.• There is one codon AUG that can either specify

the amino acid methionine or serve as a “start” codon for protein synthesis.

• There are three “stop” codons that do not code for any amino acid.

• These “stop” codons signify the end of a polypeptide.

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The Genetic Code

Translation

• Translation is the decoding of an mRNA message into a polypeptide chain (protein).

• Translation takes place on ribosomes.

• During translation, the cell uses information from messenger RNA to produce proteins.

Translation

Nucleus

mRNA

• Messenger RNA is transcribed in the nucleus, and then enters the cytoplasm where it attaches to a ribosome.

Video

Translation

• Translation begins when an mRNA molecule attaches to a ribosome.

• As each codon of the mRNA molecule moves through the ribosome, the proper amino acid is brought into the ribosome by tRNA.

• In the ribosome, the amino acid is transferred to the growing polypeptide chain.

Translation

• Each tRNA molecule carries only one kind of amino acid.

• In addition to an amino acid, each tRNA molecule has three unpaired bases.

• These bases, called the anticodon, are complementary to one mRNA codon.

LysinetRNAPhenylalanine

Methionine

Ribosome

mRNAStart codon

• The ribosome binds new tRNA molecules and amino acids as it moves along the mRNA.

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Translation

• Protein Synthesis tRNA

Ribosome

mRNA

Lysine

Translation direction

Translation• The process continues until the ribosome reaches a stop

codon.

Polypeptide

Ribosome

tRNA

mRNA

Video

The Roles of RNA and DNA• The cell uses the DNA “master plan” to prepare

RNA “blueprints.” The DNA stays in the nucleus.• The RNA molecules go to the protein building

sites in the cytoplasm—the ribosomes.• Genes contain instructions for assembling

proteins.• Many proteins are enzymes, which catalyze and

regulate chemical reactions.• Proteins are each specifically designed to build or

operate a component of a living cell.

• The sequence of bases in DNA is used as a template for mRNA.

• The codons of mRNA specify the sequence of amino acids in a protein.

CodonCodon Codon

Codon Codon Codon

mRNA

Alanine Arginine Leucine

Amino acids within a polypeptide

Single strand of DNA

Central Dogma

•DNA RNA Protein

12-4 Mutations

• Mutations – changes in the genetic material

Kinds of Mutations

• Mutations that produce changes in a single gene are known as gene mutations.

• Mutations that produce changes in whole chromosomes are known as chromosomal mutations.

• Gene mutations involving a change in one or a few nucleotides are known as point mutations because they occur at a single point in the DNA sequence.

• Point mutations include substitutions, insertions, and deletions.

• Substitutions usually affect no more than a single amino acid.

Kinds of Mutations

• The effects of insertions or deletions are more dramatic.

• The addition or deletion of a nucleotide causes a shift in the grouping of codons.

• Changes like these are called frameshift mutations.

• Frameshift mutations may change every amino acid that follows the point of the mutation.

• Frameshift mutations can alter a protein so much that it is unable to perform its normal functions.

• In an insertion, an extra base is inserted into a base sequence.

• Video

• In a deletion, the loss of a single base is deleted and the reading frame is shifted.

ChromosomalMutations

• Chromosomal mutations involve changes in the number or structure of chromosomes.

• Chromosomal mutations include deletions, duplications, inversions, and translocations.

• Deletions involve the loss of all or part of a chromosome.

• Duplications produce extra copies of parts of a chromosome.

Video

• Inversions reverse the direction of parts of chromosomes.

• Translocations occurs when part of one chromosome breaks off and attaches to another.

Video

Significance of Mutations

• Many mutations have little or no effect on gene expression.

• Some mutations are the cause of genetic disorders.• Beneficial mutations may produce proteins with new

or altered activities that can be useful.• Polyploidy is the condition in which an organism has

extra sets of chromosomes.• Example: Durum wheat is 3N (3 times N, where N equals

number of chromosomes; we are 2N)• Mutations Video• Abby & Brittany Hensel Video

Gene Regulation

Gene Regulation: An Example

• E. coli provides an example of how gene expression can be regulated.

• An operon is a group of genes that operate together.

• In E. coli, these genes must be turned on so the bacterium can use lactose as food.

• Therefore, they are called the lac operon.

Operons

• The lac genes are turned off by repressors and turned on by the presence of lactose.

• On one side of the operon's three genes are two regulatory regions. – In the promoter (P) region, RNA polymerase binds

and then begins transcription.

• The other region is the operator (O).

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• When the lac repressor binds to the O region, transcription is not possible.

• When lactose is added, sugar binds to the repressor proteins.

• The repressor protein changes shape and falls off the operator and transcription is made possible.

Gene Regulation: An Example

• Many genes are regulated by repressor proteins.

• Some genes use proteins that speed transcription.

• Sometimes regulation occurs at the level of protein synthesis.

Eukaryotic Gene Regulation• Operons are generally not found in

eukaryotes.

• Most eukaryotic genes are controlled individually and have regulatory sequences that are much more complex than those of the lac operon.

Eukaryotic Gene Regulation

• Many eukaryotic genes have a sequence called the TATA box.

Promotersequences

Upstreamenhancer

TATAbox Introns

Exons

Direction of transcription

Eukaryotic Gene Regulation• The TATA box seems to help position RNA

polymerase.

Promotersequences

Upstreamenhancer

TATAbox

Introns

Exons

Direction of transcription

Eukaryotic Gene Regulation• Eukaryotic promoters are usually found just before the

TATA box, and consist of short DNA sequences.

Promotersequences

Upstreamenhancer

TATAbox

Introns

Exons

Direction of transcription

Eukaryotic Gene Regulation• Genes are regulated in a variety of ways by

enhancer sequences.• Many proteins can bind to different enhancer

sequences.• Some DNA-binding proteins enhance

transcription by:• opening up tightly packed chromatin • helping to attract RNA polymerase • blocking access to genes

Development and Differentiation

• As cells grow and divide, they undergo differentiation, meaning they become specialized in structure and function.

• Hox genes control the differentiation of cells and tissues in the embryo.

• Careful control of expression in hox genes is essential for normal development.

• All hox genes are descended from the genes of common ancestors.

Hox Genes• In fruit flies, a series of hox genes determines the basic structure of the fly’s body. •Mice have very similar genes on four different chromosomes. •The color bars along the mouse’s back show the approximate body area affected by genes of the corresponding colors.