Chapter 22 Nucleic acids and Protein Synthesis Chemistry 203.

Chapter 22

Nucleic acids and Protein Synthesis

Chemistry 203

Introduction

– Each cell of our bodies contains thousands of different proteins.

– How do cells know which proteins to synthesize out of the extremely large number of possible amino acid sequences?

– the transmission of hereditary information took place in the nucleus, more specifically in structures called chromosomes.

– The hereditary information was thought to reside in genes within the chromosomes.

– Chemical analysis of nuclei showed chromosomes are made up largely of proteins called histones and nucleic acids.

Nucleic acids

Backbones of chromosomes

Ribonucleic acids (RNA)

Deoxyribonucleic acids (DNA)

Nucleic acids

Nucleic acids

DNA stores the genetic information of an organism and transmits that information from one generation to another.

RNA translates the genetic information contained in DNA into proteins needed for all cellular function.

RNA and DNA are unbranched polymers (monomers: nucleotides).

A nucleotide is composed of:

• Nitrogen-containing bases (amines)

• Sugars (monosaccharides)

• Phosphate

Nucleotide

Phosphate

Bases

HN

NO

H

N

N

NH2

H

HN

N

H

CH3

Uracil (U)(in RNA only)

Thymine (T)(DNA only)

Cytosine (C)(DNA andsome RNA)

N

N

Pyrimidine

1

2

3

4

5

6

HN

N N

NO

HH2N

Guanine (G)(DNA and RNA)

N

N N

N

NH2

HAdenine (A)

(DNA and RNA)

N

N N

N

HPurine

1

2

3

4

56 7

8

9

O O

O O

Sugars (monosaccharide)

RNA contains: • D-Ribose sugar

DNA contains: • 2-Deoxy-D-Ribose sugar (without O on carbon 2)

When a N atom of the base forms a glycosidic bond to C1’ (anomeric C) of a sugar.

Nucleoside

Base + Sugar Nucleoside

HH

HH

OHOCH2

HO OH

O

O

HN

N

anomericcarbon

a -N-glycosidicbond

Uridine

-D-riboside

uracil

1'

2'3'

4'

5'1

HN

NO

H

N

N

NH2

H

HN

N

H

CH3

Uracil (U)(in RNA only)

Thymine (T)(DNA only)

Cytosine (C)(DNA andsome RNA)

N

N

Pyrimidine

1

2

3

4

5

6

HN

N N

NO

HH2N

Guanine (G)(DNA and RNA)

N

N N

N

NH2

HAdenine (A)

(DNA and RNA)

N

N N

N

HPurine

1

2

3

4

56 7

8

9

O O

O O

ß-N-glycosidic bond

Nucleoside

To name a nucleoside derived from a pyrimidine base, use the suffix “-idine”.

To name a nucleoside derived from a purine base, use the suffix “-osine”.

For deoxyribonucleosides, add the prefix “deoxy-”.

Nucleotide

A nucleotide forms with the −OH on C5’ of a sugar bonds to

phosphoric acid.

O-

O-

O

P OH +

deoxycytidine and phosphate

HO CH2

O

NH2

N

N

OH

O

5’ 5’

A nucleotide

1’

Phosphate ester bond

The name cytidine 5′-monophosphate is abbreviated as CMP.

Nucleotide

The name deoxyadenosine 5’-monophosphate is abbreviated as dAMP.

Primary structure of DNA and RNA

Sequence of nucleotides.

Each phosphate is linked to C3’ and C5’ of two sugars.

Carry all information for protein synthesis.

Phosphodiesterbond

Polynucleotide

A nucleoside = Base + Sugar

A nucleotide = Base + Sugar + Phosphate

A nucleic acid = A chain of nucleotides

Base sequence is read from the C5’ (free phosphate) end to the C3’ (free hydroxyl) end.

Like amino acids (C-terminal and N-terminal):

-ACGU-

Primary structure of DNA and RNA

• The DNA model is proposed by Watson and Crick in 1953.

• Two strands of polynucleotide form a double helix structure like a spiral.

• Hydrogen bonds link paired bases:

Adenine-Thymine (A–T)

Guanine-Cytosine (G-C)

• Sugar-Phosphate backbone is hydrophilic and stays on the outside (bases are hydrophobic).

Secondary structure of DNA

5’

5’

3’

3’

Sugar phosphate backbone

3D structure

Secondary structure of DNA

A Purine base always hydrogen bonds with a pyrimidine.

Complementary base pairs

2 H bonds

3 H bonds

A-T base pair

G-C base pair

Higher structure of DNA

• DNA is coiled around proteins called histones.

• Histones are rich in the basic amino acids

• Acidic DNA basic histones attract each other and form a chain of nucleosomes.

Core of eight histones


Chromatin:Condensed nucleosomes

Chromatin fibers are organized into loops, and the loops into the bands that provide the superstructure of chromosomes.


- DNA molecules contain several million nucleotides, while RNA molecules have only a few thousand.

- DNA is contained in the chromosomes of the nucleus, each chromosome having a different type of DNA.

- Humans have 46 chromosomes (23 pairs), each made up of many genes.

- A gene is the portion of the DNA molecule responsible for the synthesis of a single protein (1000 to 2000 nucleotides).

Chromosome & Gene

Difference between DNA & RNA

1. DNA has four bases: A, G, C, and T. RNA has four bases: A, G, C, and U.

2. In DNA: Sugar is 2-deoxy-D-ribose. In RNA: Sugar is D-ribose.

3. DNA is almost always double-stranded (helical structure). RNA is single strand.

4. RNA is much smaller than DNA.

RNA molecules

Transmits the genetic information needed to operate the cell.

2. Messenger RNA (mRNA)

1. Ribosomal RNA (rRNA)

3. Transfer RNA (tRNA)

Most abundant RNA – is found in ribosomes: sites for protein synthesis.

Carries genetic information from DNA (in nucleus) to ribosomes (in cytoplasm)for protein synthesis. They are produced in “Transcription” from DNA.

The smallest RNA. Translates the genetic information in mRNA and brings specific Amino acids to the ribosome for protein synthesis.

Functions of DNA

1. It reproduces itself when a cell divides (Replication).

2. It supplied the information to make up RNA, proteins, and enzymes.

Replication

Separation of the two original strands and synthesis

of two new daughter strands using the original strands as templates.

By breaking H-bonds

Replication

Replication is bidirectional: takes place at the same speed in both directions.

Replication is semiconservative: each daughter molecule has one parental strand

and one newly synthesized one.

Origin of replication: specific point of DNA where replication begins.

Replication fork: specific point of DNA where replication is proceeding.

Replication occurs at many places simultaneously along the helix.

Replication

Leading strand: is synthesized continuously in the 5’ 3’ direction toward the replication fork.

Lagging strand: is synthesized discontinuously in the 5’ 3’ direction away from the replication fork.

Replication

Replisomes: assemblies of “enzyme factories”.

Component Function

HelicasePrimaseClamp proteinDNA polymeraseLigase

Unwinds the DNA double helixSynthesizes primersThreads leading strandJoins assembled nucleotidesJoins Okazaki fragments in lagging strand

Unwinds the DNA double helix.

- Replication of DNA starts with unwinding of the double helix.

- Unwinding can occur at either end or in the middle.

- Attach themselves to one DNA strand and cause separation of the double helix.

Helicases

Catalyze the synthesis of primers.

Primers: are short nucleotides (4 to 15).

- They are required to start the synthesis of both daughter strands.

- Primases are placed at about every 50 nucleotides in the lagging strand synthesis.

Primases

It catalyzes the formation of the new strands.

- It joins the nucleoside triphosphates found in the nucleus.

DNA Polymerase

- A new phosphodiester bond is formed between the 5’-phosphate of the nucleoside triphosphate and the 3’-OH group of the new DNA strand.

Ligase

In formation of lagging strand, small fragments (Okazaki) are join together by ligase enzyme.

Gene expression: activation of a gene to produce a specific protein.

Protein Synthesis

Only a small fraction (1-2%) of the DNA in a chromosome contains genes.

Base sequence of the gene carries the information to produce one protein molecule.

Change of sequence New protein

Transcription: synthesis of mRNA (messenger RNA)

proteinTranscription Translation

DNAreplication

DNA mRNA

Reverse transcriptase

RNAreplication

Translation

Gene expression

Reverse transcription

Transcription

Genetic information is copied from a gene in DNA to make a mRNA.

Begins when the section of a DNA that contains the gene to be copied unwinds.

Polymerase enzyme identifies a starting point to begin mRNA synthesis.

Transcription

The DNA splits into two strands:

Template strand: it is used to synthesize RNA.

Coding Strand (Informational strand): it is not used to synthesize RNA.

- Transcription proceeds from the 3’ end to the 5’ end of the template.

- When mRNA is released, the double helix of the DNA re-forms.

(informational strand, non-template strand)

Direction of transcription

Transcription

- G – A – A – C – T -

- C – U – U – G – A -

Section of bases on DNA (template strand):

Complementary base sequence in mRNA:

RNA Polymerase

Polymerase enzyme moves along the unwound DNA, forming bonds between the bases.

C is paired with G, T pairs with ABut A pairs with U (not T).

Sample Problem 22.6

From the template strand of DNA below, write out the mRNA and informational strand of DNA sequences:

Template strand: 3’—C T A G G A T A C—5’

mRNA: 5’—G A U C C U A U G—3’

Informational 5’—G A T C C T A T G—3’strand:

Transcription

Translation

mRNA (as a carrier molecule) moves out of the nucleus and goes to ribosomes.

tRNA converts the information into amino acids.

Amino acids are placed in the proper sequence.

Proteins are synthesized.

Gene expression

Overall function of RAN’s in the cell: facilitate the task of synthesizing protein.

Genetic code: language that relates the series of nucletides in mRNAto the amino acids specified.

Genetic code

• The sequence of nucleotides in the mRNA determines the amino acid order for the protein.

• Every three bases (triplet) along the mRNA makes up a codon.

• Each codon specifies a particular amino acid.

• Codons are present for all 20 amino acids.

Genetic code

A

U

U C

C

A

LeuLeuLeuLeu

ValValValVal

SerSerSerSer

ProProProPro

ThrThrThrThr

AlaAlaAlaAla

ArgArgArgArg

GlyGlyGlyGly

UUUUUC

PhePheLeuLeu

IleIleIle

AUUAUCAUA

UAUUAC

TyrTyr

CAUCAC

HisHisGlnGln

AAUAAC

AsnAsnLysLys

AspAspGluGlu

Trp

CysCys

SerSerArgArg

UCUUCCUCAUCG

G

UCAG

CUUCUCCUACUG

CCUCCCCCACCG

CGUCGCCGACGG

UCAG

G

ACUACCACAACG

UCAG

UCAG

GUUGUCGUAGUG

GCUGCCGCAGCG

GGUGGCGGAGGG

Stop

5' 3'

UUAUUG

Met*AUG

UAA UAG

StopStop

CAACAG

AAAAAG

GAUGACGAAGAG

UGAUGG

UGUUGC

AGUAGCAGAAGG

*AUG signals translation initiation as well as coding for Met

Genetic code

• 64 condons are possible from the triplet combination of A, G, C, and U.

• UGA, UAA, and UAG, are stop signals. (code for termination of protein synthesis).

• AUG has two roles:

1. Signals the start of the proteins synthesis (at the beginning of an mRNA).

2. Specifies the amino acid methionine (Met) (in the middle of an mRNA).

•Codons are written from the 5’ end to the 3’ end of the mRNA molecule

tRNA (transfer RNA)

A G U

U C ACodon on mRNA

Anticodon loop

tRNA translates the codons into specific amino acids. Serine

- It contains 70-90 nucleotides.

- The 3’ end, called the acceptor stem andalways has the nucleotide ACC and a freeOH group that binds a specific amino acid.

- Anticodon: a sequence of threenucleotides at the bottom of tRNA, whichis complementary to three bases in an mRNAand it can identify the needed amino acid.

Transcription

Translation

• mRNA attaches to smaller subunit of a ribosome.

• tRNA molecules bring specific amino acids to the mRNA.

• Peptide bonds form between an amino acid and the end of the growing peptide chain.

• The ribosome moves along mRNA until the end of the codon (translocation).

• The polypeptide chain is released from the ribosome and becomes an active protein.

Protein synthesis

Sometimes several ribosomes (polysome) translate the same strand of mRNA at the same time to produce several peptide chains.

Termination

Ribosome encounters a stop condon.

No tRNA to complement the termination codon.

An enzyme releases the complete polypeptide chain from the ribosome.

A

U

U C

C

A

LeuLeuLeuLeu

ValValValVal

SerSerSerSer

ProProProPro

ThrThrThrThr

AlaAlaAlaAla

ArgArgArgArg

GlyGlyGlyGly

UUUUUC

PhePheLeuLeu

IleIleIle

AUUAUCAUA

UAUUAC

TyrTyr

CAUCAC

HisHisGlnGln

AAUAAC

AsnAsnLysLys

AspAspGluGlu

Trp

CysCys

SerSerArgArg

UCUUCCUCAUCG

G

UCAG

CUUCUCCUACUG

CCUCCCCCACCG

CGUCGCCGACGG

UCAG

G

ACUACCACAACG

UCAG

UCAG

GUUGUCGUAGUG

GCUGCCGCAGCG

GGUGGCGGAGGG

Stop

5' 3'

UUAUUG

Met*AUG

UAA UAG

StopStop

CAACAG

AAAAAG

GAUGACGAAGAG

UGAUGG

UGUUGC

AGUAGCAGAAGG


A

U

U C

C

A

LeuLeuLeuLeu

ValValValVal

SerSerSerSer

ProProProPro

ThrThrThrThr

AlaAlaAlaAla

ArgArgArgArg

GlyGlyGlyGly

UUUUUC

PhePheLeuLeu

IleIleIle

AUUAUCAUA

UAUUAC

TyrTyr

CAUCAC

HisHisGlnGln

AAUAAC

AsnAsnLysLys

AspAspGluGlu

Trp

CysCys

SerSerArgArg

UCUUCCUCAUCG

G

UCAG

CUUCUCCUACUG

CCUCCCCCACCG

CGUCGCCGACGG

UCAG

G

ACUACCACAACG

UCAG

UCAG

GUUGUCGUAGUG

GCUGCCGCAGCG

GGUGGCGGAGGG

Stop

5' 3'

UUAUUG

Met*AUG

UAA UAG

StopStop

CAACAG

AAAAAG

GAUGACGAAGAG

UGAUGG

UGUUGC

AGUAGCAGAAGG


Amino acids form the three-dimensional structure (active protein).

Translation

There are 3 stages in translation:

1. Initiation begins with mRNA binding to the ribosome.

2. Elongation proceeds as the next tRNA molecule delivers the next amino acid, and a peptide bond forms between the two amino acids.

Translation

3. Termination: Translation continues until a stop codon (UAA, UAG, or UGA) is reached and the completed protein is released.

Often the first amino acid (methionine) is not neededand it is removed after protein synthesis is complete.

Mutation

A heritable change in DNA nucleotide sequence.

It changes the sequence of amino acids (structure and function of proteins).

X rays, Overexpose to sun (UV light), Chemicals (mutagens), or Viruses

Enzyme cannot catalyze.

However, some mutations are random events.

CancerAltered DNA will be limited to that cell and its daughter cells.

Effect of Mutation

Somatic cell (nonreproductive cell):

Germ cell (reproductive cell like an egg or sperm):

All new DNA will contain the same defaultand it is passed on to the next generation. Genetic diseases

Type of Mutations

Point (substitution) Mutation

Replacement of one base in the coding strand of DNA with another.

The most common

Different amino acid

Frameshift Mutation

One or more bases is/are added to or deleted from the normal order of bases in DNA.

All the triplets shift over by one base.Different sequence of amino acids

Point Mutation

In hemoglobin, substitution of just one amino acid can result in the fatal disease sickle cell anemia.

No more amino acids are added. A need protein is not synthesized. The organism may die.

Frameshift Mutation

1. A deletion mutation occurs when one or more nucleotides is/are lost from a DNA molecule.

2. An insertion mutation occurs when one or more nucleotides is/are added to a DNA molecule.

A silent mutation has a negligible effect to the organism, because the resulting amino acid is identical.

The mutation has no effect.

Silent Mutation

Recombinant DNA is synthetic DNA that contains segments from more than one source.

Three key elements are needed to form recombinant DNA:

1. A DNA molecule into which a new DNA segment will be inserted.

2. An enzyme that cleaves DNA at specific locations.

3. A gene from a second organism that will be inserted into the original DNA molecule.

Recombinant DNA

First, bacterial plasmid DNAis cut by the restrictionendonuclease EcoRI, whichcuts in a specific place.

This gives a double strandof linear plasmid DNA withtwo ends ready to bond, called sticky ends.

Recombinant DNA

Then, a second sampleof human DNA is cutwith the same EcoRI.

This forms human DNAsegments with stickyends that arecomplimentary to the plasmid DNA.

Recombinant DNA

Combining the two pieces of DNA (with DNA ligase enzyme) forms DNA containing the new segment.

This DNA chain is slightly larger because of its additional segment.

Recombinant DNA

This new DNA is re-inserted into a bacterial cell. Large amounts of needed proteins can be synthesized by bacteria.

Polymerase chain reaction (PCR) amplifies a specific portion of a DNA molecule, producing millions of exact copies.

Polymerase Chain Reaction (PCR)

Four elements are needed to amplify DNA by PCR:

1. The segment of DNA that must be copied.

2. Two primers—short polynucleotides that are complementary to the two ends of the segment to be amplified.

3. A DNA polymerase enzyme to catalyze the synthesis of a complementary strand.

4. Nucleoside triphosphates—the source of the A, T, C, and G needed to make the new DNA.

HOW TO Use the Polymerase Chain Reaction to Amplify a Sample of DNA

Step [1]Heat the DNA segment to unwind the double helix to form single strands.


Step [2]Add primers that are complementary tothe DNA sequence at either end of theDNA segment.


Step [3]Use a DNA polymerase and addednucleotides to lengthen the DNA segment.

After each cycle the amount of DNA is doubled, so after 20 cycles, 1,000,000 copies have been made.

The DNA of each individual person is unique, so DNA can be used as a method of identification.

•Any type of cell (skin, saliva, semen, blood, etc.) can be used to obtain a DNA fingerprint.

•The DNA is first amplified by PCR, and then cut into fragments by restriction enzymes.

•The DNA fragments are then separated by size by gel electrophoresis.

DNA Fingerprinting

DNA fragments can be visualized on X-ray film after they have been separated:

DNA Fingerprinting

A virus is an infectious agent consisting of a DNA or RNA molecule that is contained within a protein coating.

- It is incapable of replicating alone (no enzyme, no free nucleotide), so it invades a host organism and makes the host replicate the virus.

- Many prevalent diseases like the common cold, influenza, and herpes are viral in origin.

- A vaccine is an inactive form of a virus that causes a person’s immune system to produce antibodies to the virus to ward off infection.

Viruses

proteinTranscription Translation

DNAreplication

DNA mRNA

Reverse transcriptase

RNAreplication

Viruses

A virus with an RNA core is called a retrovirus.

Retroviruses invade a host and then synthesize viral DNA by reverse transcription.

Viruses

The viral DNA can then transcribe RNA, which then directs protein synthesis (new retroviral particles to infect other cells).

AIDS (Acquired Immune Deficiency Syndrome) is caused by the retrovirus HIV (Human Immunodeficiency Virus) .

Chapter 22 Nucleic acids and Protein Synthesis Chemistry 203.

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Transcript of Chapter 22 Nucleic acids and Protein Synthesis Chemistry 203.