bio Lecture 12: The Structure and Function of DNA Part A

By the 1940s, scientists knew that chromosomes consist of two types of chemicals:

DNA and protein

By the early 1950s, a series of discoveries had convinced the scientific world that

DNA was the molecule that acts as the hereditary material

This breakthrough ushered in the field of

molecular biology (genetics), the study of heredity at the molecular level

Both DNA and RNA are

nucleic acids, which consist of long chains (polymers) of chemical units (monomers) called nucleotides

Polynucleotides can be very long and may have any sequence of the four different types of nucleotides

(abbreviated A, C, T, and G), so a tremendous variety of polynucleotide chains is possible

Nucleotides are joined together by

covalent bonds between the sugar of one nucleotide and the phosphate of the next

a repeating pattern of sugar- phosphate-sugar-phosphate,

which is known as a sugar-phosphate backbone

The nitrogenous bases are arranged like

ribs that project from this backbone

Each nucleotide consists of three components

a nitrogenous base, a sugar (blue), and a phosphate group (gold)

The phosphate group, with a phosphorus atom (P) at its center, is

the source of the acid in nucleic acid

The sugar has five carbon atoms and is called deoxyribose because,

compared with the sugar ribose, it is missing an oxygen atom

The full name for DNA is deoxyribonucleic acid

with nucleic referring to DNA’s location in the nuclei of eukaryotic cells

Nitrogenous bases are

basic (have a high pH)

The four nucleotides found in DNA can be divided into two types

Single ring

Thymine (T) and cytosine (C)

Pyrimidines

The four nucleotides found in DNA can be divided into two types Larger double ring structures

Adenine (A) and guanine (G)

Purines

A pairs with __G pairs with _

t, c

Instead of thymine, RNA has a similar base called

uracil (U)• RNA also contains a slightly different sugar than DNA (ribose instead of deoxyribose)

The celebrated partnership of two scientists (American James Watson and British Francis Crick)

solved the puzzle of DNA structure

puzzle of DNA structure. This was achieved with the help of Rosalind Franklin using a technique called

X-ray crystallography

Watson figured out that the

basic shape of DNA is a helix (spiral) with a uniform diameter

The thickness of the helix suggested that it was made up of two polynucleotide strands

in other words, a double helix

In 1953, Watson and Crick rocked the scientific world with a

succinct paper proposing their molecular model for DNA

In 1962, Watson, Crick, and Wilkins received the

Nobel Prize for their work. Franklin deserved a share of the prize, but she had died from cancer in 1958, and Nobel prizes are never granted posthumously

Watson and Crick’s model of DNA suggests that

each DNA strand serves as a mold, or template, to guide reproduction of the other strand

If you know the sequence of bases in one strand of the double helix, you can very easily determine the sequence of bases in the other strand by

applying the base-pairing rules: A pairs with T (and T with A), and G pairs with C (and C with G)

If one polynucleotide has the sequence AGTC, then the complementary polynucleotide in that DNA molecule

must have the sequence TCAG

The process of DNA replication requires the cooperation of

more than a dozen enzymes and other proteins

The enzymes that make the covalent bonds between the nucleotides of a new DNA strand are called

DNA polymerases

As an incoming nucleotide base-pairs with its complement on the template strand, a

DNA polymerase adds it to the end of the growing daughter strand

In addition to their roles in DNA replication, DNA polymerases can repair DNA

that has been damaged by toxic chemicals or high-energy radiation, such as X-rays and ultraviolet light

DNA replication begins on a

double helix at specific sites, called origins of replication

Replication then proceeds in

both directions, creating what are called replication “bubbles”

The parental DNA strands open up as

daughter strands elongate on both sides of each bubble

The DNA molecule of a typical eukaryotic chromosome has

many origins where replication can start simultaneously, shortening the total time needed for the process

Eventually, all the bubbles merge, yielding two

completed double-stranded daughter DNA molecules

Replication results in two daughter DNA molecules, each

consisting of one old strand and one new strand

The parental DNA untwists as its strands separate,

and the daughter DNA rewinds as it forms

DNA replication ensures that all the body cells in a multicellular organism carry the

same genetic information It is also the means by which genetic information is passed along to offspring

An organism’s genotype, its genetic makeup, is the

heritable information contained in the sequence of nucleotide bases in its DNA

The phenotype, the organism’s physical traits, arises from

the actions of a wide variety of proteins

The molecular “chain of command” is from DNA in the nucleus

to RNA - to protein synthesis in the cytoplasm

the transfer of genetic information from DNA into an RNA molecule,

TRANSCRIPTION

the transfer of the information from RNA into a polypeptide (protein strand)

TRANSLATION

The flow of genetic information in a eukaryotic cell

• A sequence of nucleotides in the DNA is transcribed into a molecule of RNA in the cell’s nucleus

• The RNA travels to the cytoplasm, where it is translated into the specific amino acid sequence of a protein

A typical gene is a few thousand

nucleotides in length

When a segment of DNA is transcribed

the result is an RNA molecule

The process is called transcription because the

nucleic acid language of DNA has simply been rewritten (transcribed) as a sequence of bases of RNA

The nucleotide bases of the RNA molecule are

complementary to those on the DNA strand. This is because the RNA was synthesized using the DNA as a template

the conversion of the nucleic acid language to the polypeptide language

Translation

The sequence of nucleotides of the RNA molecule dictates the sequence of

amino acids of the polypeptide

RNA is only a messenger

The genetic information that dictates the amino acid sequence originates in DNA

Keep in mind that there are only four different kinds of

nucleotides in DNA__. During translation, these four must somehow specify

(A, G, C, T) and RNA (A, G, C, U)

•20 amino acids

If each nucleotide base coded for one amino acid,

only 4 of the 20 amino acids could be accounted for

Triplets of bases are how amino acids are coded for:

there can be 64 (that is, 43) possible code words of this type — more than enough to specify the 20 amino acids

There are enough triplets to allow more than one coding for each amino acid

example, the base triplets AAA and AAG both code for the same amino acid

The flow of information 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 three-base words called

one DNA codon (three nucleotides) → one RNA codon (three nucleotides) → one amino acid

The genetic code is the

set of rules that convert a nucleotide sequence in RNA to an amino acid sequence

61 of the 64 triplets code for

amino acids

The triplet AUG has a dual function:

It codes for the amino acid methionine (Met) and also provides a signal for the start of a polypeptide chain

Three codons (UAA, UAG, and UGA) do not designate amino acids:

they are the stop codons that instruct the ribosomes to end the polypeptide

A given RNA triplet always specifies a given amino acid: although codons UUU and UUC both specify phenylalanine (Phe), neither of them ever represents any other amino acid

The codons in the figure are the triplets found in RNA. They have a straightforward, complementary relationship to the codons in DNA The nucleotides making up the codons occur in a linear order along the DNA and RNA, with no gaps separating the codons

The genetic code is

nearly universal, shared by organisms from the simplest bacteria to the most complex plants and animals

The universality of the genetic vocabulary suggests that

it arose very early in evolution and was passed on over the eons to all the organisms living on Earth today

Because diverse organisms share a common genetic code, it is possible to

program one species to produce a protein from another species by transplanting DNA

Transcription

the transfer of genetic information from DNA to RNA

Only one of the DNA strands serves as a template for the newly forming

RNA molecule; the other strand is unused

The nucleotides that make up the new RNA molecule take their place one at a time along the

DNA template strand by forming hydrogen bonds with the nucleotide bases there

The RNA nucleotides are linked by

the transcription enzyme RNA polymerase

Transcription has 3 phases

1. Initiation

2. Elongation

3. Termination

1: Initiation of Transcription: The “start transcribing” signal is a nucleotide sequence called

a promoter, which is located in the DNA at the beginning of the gene

A promoter is a

specific place where RNA polymerase attaches

The first phase of transcription, called initiation, is the

attachment of RNA polymerase to the promoter and the start of RNA synthesis

For any gene, the promoter dictates which of the two DNA strands is to be

transcribed (the particular strand varies from gene to gene)

2: RNA Elongation: During the second phase of transcription, elongation, the

RNA grows longer

As RNA synthesis continues, the RNA strand peels away from its DNA template,

allowing the two separated DNA strands to come back together in the region already transcribed

3: Termination of Transcription: In the third phase, termination,

the RNA polymerase reaches a special sequence of bases in the DNA template called a

This sequence signals the end of the gene

terminator:

At this point, the polymerase molecule detaches from the

RNA molecule and the gene, and the DNA strands rejoin

In addition to producing RNA that encodes amino acid sequences,

transcription makes two other kinds of RNA that are involved in building polypeptides

In the cells of prokaryotes, which lack nuclei, the RNA

transcribed from a gene immediately functions as messenger RNA (mRNA), the molecule that is translated into protein

But this is not the case in eukaryotic cells

The eukaryotic cell not only localizes transcription in the nucleus but also

modifies, or processes, the RNA transcripts there before they move to the cytoplasm for translation by the ribosomes

In eukaryotes there are noncoding stretches of nucleotides that

interrupt the nucleotides that actually code for amino acids

Most genes include such internal noncoding regions

which are called introns

The coding regions — the parts of a gene that are expressed

are called exons

Both exons and introns are

transcribed from DNA into RNA

Before the RNA leaves the nucleus, the introns are removed, This process is called

and the exons are joined to produce an mRNA molecule with a continuous coding sequence RNA splicing

The production of messenger RNA (mRNA) in a eukaryotic cell With capping, tailing, and splicing completed, the “final draft” of eukaryotic mRNA is ready for

translation: Note that the molecule of mRNA that leaves the nucleus is substantially different from the molecule of RNA that was first transcribed from the gene

Translation conversion between different languages — from the

from the nucleic acid language to the protein language and it involves more elaborate machinery than transcription

The first important ingredient required for translation is the

mRNA produced by transcription

The first important ingredient required for translation is the mRNA produced by transcription. Once it is present,

the machinery used to translate mRNA requires enzymes and sources of chemical energy, such as ATP

in addition, translation requires two other important components:

ribosomes and a kind of RNA called transfer RNA

Translation of the genetic message carried in mRNA into the amino acid language of proteins also requires

an interpreter

acids to the amino acid words of proteins

a cell uses a molecular interpreter, a type of RNA called transfer RNA (tRNA)

tRNA molecules must carry out two distinct functions:

– (1) pick up the appropriate amino acids

– (2) recognize the appropriate codons in the mRNA

• The unique structure of tRNA molecules enables them to perform both tasks

At one end of the folded molecule is a special triplet of bases

called an anticodon

The anticodon triplet is

complementary to a codon triplet on mRNA

During translation, the anticodon on the tRNA

recognizes a particular codon on the mRNA by using base-pairing rules

At the other end of the tRNA molecule is a site where

one specific kind of amino acid attaches

Although all tRNA molecules are similar,

there are slightly different versions of tRNA for each amino acid