The nucleic acid bases are of two types – pyrimidines and

purines. Three pyrimidine bases (single-ring aromatic compounds)

– cytosine, thymine, and uracil – commonly occur. Cytosine is

found both in RNA and in DNA. Uracil occurs only in RNA. In

DNA, thymine is substituted for uracil. The common purine bases

are adenine and guanine, both of which are found in RNA and in

DNA.

A nucleoside is a compound that consists of a base and a sugar

covalently linked together. When the sugar is β-D-ribose, the

resulting compound is a ribonucleoside; when the sugar is β-D-

deoxyribose, the resulting compound is a deoxyribonucleoside.

When phosphoric acid is

esterified to one of the hydroxyl

groups of the sugar portion of a

nucleoside, a nucleotide is formed. A

nucleotide is named for the parent

nucleoside, with the suffix

“monophosphate” added. The 5’

nucleotides are most commonly

encountered in nature. If additional

phosphate groups form anhydride

linkages to the first phosphate, the

corresponding nucleoside

diphosphates and triphosphates are

formed.

The polymerization of

nucleotides gives rise to nucleic

acids. The linkage between

monomers in nucleic acids

involves formation of two ester

bonds by phosphoric acid. The

hydroxyl groups to which the

phosphoric acid is esterified are

those bonded to the 3’ and 5’

carbons on adjacent residues. The

resulting repeated linkage is a

3’,5’-phosphodiester bond. The

nucleotide residues of nucleic

acids are numbered from the 5’

end, which normally carries a

phosphate group, to the 3’end,

which normally has a free

hydroxyl group.

Double helix In the double helix, the two chains are coiled around

a common axis called the axis of symmetry. The chains

are paired in an antiparallel manner, that is, the 5’-end

of one strand is paired with the 3’-end of the other

strand. In the DNA helix, the hydrophilic deoxyribose-

phosphate backbone of each chain is on the outside of the

molecule, whereas the hydrophobic bases are stacked

inside.

Watson and Crick model of DNA

As originally presented by Watson and Crick, DNA is composed of two strands, wound

around each other in a right-handed, helical structure with the base pairs in the middle

and the deoxyribosylphosphate chains on the outside. The orientation of the DNA strands

is anti-parallel (i.e. the strands run in opposite directions). The nucleotide bases on each

strand interact with the nucleotide bases on the other strand to form base pairs.

Watson-Crick base pairing of nucleotides in DNA.

The base pairs are planar and are oriented nearly perpendicular to the axis

of the helix. Each base pair is formed by hydrogen bonding between a purine

and a pyrimidine. Guanine forms three hydrogen bonds with cytosine, and

adenine forms two with thymine. Because of the specificity of this interaction

between purines and pyrimidines on the opposite strands, the opposing

strands of DNA are said to have complementary structures.

General classes of RNA

RNA Size and length Percent of total

cellular RNA

Function

rRNA 28s, 18s, 5.8s, 5s

(26s, 16s, 5s)8

80 interact to form

ribosomes

tRNA 65-110 nt 15 adapter

mRNA 0.5-6 kb 5 direct synthesis of

cellular proteins

- ribosomal RNA (rRNA) from prokaryotes consists of three different sizes of RNA, while

rRNA from eukaryotes - four different sizes of RNA. These RNAs interact with each other, and

with proteins, to form a ribosome that provides the basic machinery on which protein synthesis

takes place;

- transfer RNAs (tRNAs) consist of one size class of RNA that are 65-110 nucleotides in

length; they function as adapter molecules that translate the information stored in the mRNA

nucleotide sequence to the amino acid sequence of proteins;

- messenger RNAs (mRNAs) represent the most heterogeneous class of RNAs found in cells,

ranging in size from 500 nt to>6 kb; they are carriers of genetic-information, defining the sequence

of all proteins in the cell

The roles of different kinds of RNA

RNA type Size Function

Transfer RNA Small Transports amino acids to site of protein

synthesis

Ribosomal RNA Several-kinds –

variable in size

Combines with proteins to form

ribosomes, the site of protein synthesis

Messenger RNA Variable Directs amino acid sequence of proteins

Small nuclear RNA Small Processes initial mRNA to its mature form

in eukaryotes

Small interfering

RNA

Small Affects gene expression; used by scientists

to knock out a gene being studied

Micro RNA Small Affects gene expression; important in

growth and development

Transfer RNA

The smallest of the three important kinds of

RNA is tRNA. Different types of tRNA molecules

can be found in every living cell because at least

on tRNA bonds specifically to each of the amino

acids that commonly occur in proteins.

Frequently there are several tRNA molecules for

each amino acid.

The molecule can be drawn as a cloverleaf

structure, which can be considered the secondary

structure of tRNA because it shows the hydrogen

bonding between certain bases. During protein

synthesis, both tRNA and mRNA are bound to

the ribosome in a definite spatial arrangement

that ultimately ensures the correct order of the

amino acids in the growing polypeptide chain.

A schematic drawing of a

proposed secondary structure for

16S rRNA.

Ribosomal RNA

In contrast with tRNA, rRNA molecules

tend to be quite large, and only a few types of

rRNA exist in a cell. The RNA portion of a

ribosome accounts for 60%-65% of the total

weight.

An E.coli ribosome typically has a

sedimentation coefficient of 70S. When an

intact 70S bacterial ribosome dissociates, it

produces a light 30S subunit and a heavy 50S

subunit. The 30S subunit contains a 16S rRNA

and 21 different proteins. The 50S subunit

contains a 5S rRNA, a 23S rRNA, and 34

different proteins.

The structure of a

typical prokaryotic

ribosome. The

individual components

can be mixed,

producing functional

subunits.

Messenger RNA

The least abundant of the main types of RNA is mRNA. In most

cells, it constitutes no more than 5%-10% of the total cellular RNA.

The sequences of bases in mRNA specify the order of the amino

acids in proteins. In rapidly growing cells, many different proteins

are needed within a short time interval. Consequently, it is logical

that mRNA is formed when it is needed, directs the synthesis of

proteins, and then is degraded so that the nucleotides can be

recycled. Both tRNA and rRNA can be recycled intact for many

rounds of protein synthesis.

The sequence of mRNA bases that directs the synthesis of a

protein reflects the sequence of DNA bases in the gene that codes for

that protein. Messenger RNA molecules are heterogeneous in size, as

are the proteins whose sequences they specify.

Replication

DNA replication yields two DNA molecules identical

to the original one, ensuring transmission of genetic

information to daughter cells with exceptional

fidelity.

Transcription

The sequence of bases in DNA is recorded as a

sequence of complementary bases in a single-

stranded mRNA molecule.

Translation

Three-base codons on the mRNA corresponding to

specific amino acids direct the sequence of building

a protein.

Six kinds of RNA – transfer RNA (tRNA), ribosomal RNA

(rRNA), messenger RNA (mRNA), small nuclear RNA

(snRNA), micro RNA (miRNA), and small interfering

RNA (siRNA) – play an important role in the life process

of cells.

Replication fork - each set of replication machinery together with DNA that it is

replicating

Leading strand - no problems with newly synthesized DNA laid down in a 5’ to 3’

direction

Lagging strand - replicates in a series of short segments, every time the DNA strands

have been peeled apart by 250 nucleotides a polymerase/primase complex initiates DNA

synthesis running back toward the replication origin in a 5’ to 3’ direction

Okazaki fragments - small fragments enabling replication in proper direction

Replication fork - each set of replication machinery together with DNA that it is

replicating

Leading strand - no problems with newly synthesized DNA laid down in a 5’ to 3’

direction

Lagging strand - replicates in a series of short segments, every time the DNA strands

have been peeled apart by 250 nucleotides a polymerase/primase complex initiates DNA

synthesis running back toward the replication origin in a 5’ to 3’ direction

Okazaki fragments - small fragments enabling replication in proper direction

Doubling of Information

Before a cell divides to become two, its DNA must be doubled so that each daughter cell

will receive a perfect copy. This means the strands of DNA must first be separated, then

complementary nucleotides must be linked along each of the separated strands.

The “Unzipper”

(helicase)

The “Builders”

(polymerases)

The “Eraser”

(repair nuclease)

The “Untwister”

(topoisomerase)

The “Straighteners”

(single-strand DNA- binding proteins)

The “Stitcher”

(ligase)

The “Initiator”

(initiator protein)

How Enzymes Copy DNA

A Cast of Ingenious Characters

The sequence at the left oversimplifies. DNA doesn't copy itself any more than

a recipe bakes a cake. DNA passively stores information. The team of proteins

shown above does the actual copying, or replication. And they do it with an

accuracy of only one mistake in every hundred thousand or so nucleotides!

DNA Replication — The Details

1. The initiator finds the place to begin

copying and guides the unzipper to the

correct position.

2. The unzipper separates the DNA

strands by breaking the weak bonds

between the nucleotides.

3. Then the builders arrive to assemble a new

DNA strand along each of the exposed strands.

4. They build by joining individual

nucleotides to their matching

complements on the old strand.

How Enzymes Copy DNA (continued)

DNA Replication — The Details

5. Free-floating nucleotides bring their own energy.

Remember ATP? There's also GTP, CTP, and TTP.

6. As each new nucleotide is added to the growing

chain, its phosphate bond energy goes into making

the new bond.

7. The upper builder follows behind the unzipper,

but the lower strand runs the opposite way.

8. Yet the lower builder must build in the same

chemical direction. She solves this by making a

loop...

9. ...and building along the bottom half of it. 10. When she finishes a length, she

lets go of the completed end...

11. ...grabs a new loop, and continues linking

nucleotides along a new stretch.

12. So, while the top new strand is built

continuously, the bottom new strand is

assembled in short lengths...

13. ...which are then spliced together by the stitcher. This reaction requires energy, supplied by ATP.

14. The straighteners keep the single DNA strands

from getting tangled.

15. And the untwister unwinds the double

helix in advance of the unzipper.

DNA Replication –The Details

16. The initiator, the unzipper, the builders, the stitcher, the untwister, and the straighteners work

together in tight coordination, making near-perfect copies at the rate of fifty nucleotides per second!

Despite the elaborate proofreading system employed during

DNA synthesis, errors – including incorrect base-pairing or insertion

of one to a few extra nucleotides – can occur. In addition, DNA is

constantly being subjected to environmental insults that cause the

alteration or removal of nucleotide bases. The damaging agents can be

either chemicals, for example, nitrous acid, or radiation, for example,

ultraviolet light, and high-energy ionizing radiation, which can cause

double-strand breaks. Bases are also altered or lost spontaneously

from mammalian DNA at a rate of many thousands per cell per day. If

the damage is not repaired, a permanent change (mutation) is

introduced that can result in any of a number of deleterious effects,

including loss of control over the proliferation of the mutated cell,

leading to cancer.

DNA REPAIR

Cells are remarkably efficient at repairing damage done to their DNA. Most of the

repair systems involve recognition of the damage (lesion) on the DNA, removal or

excision of the damage, replacement or filling the gap left by excision using the

sister strand as a template for DNA synthesis, and ligation. These repair systems

thus perform excision repair, with the removal of one to tens of nucleotides.

- Methyl-directed mismatch repair

- Repair of damage caused by ultraviolet (UV) light

- Correction of base alterations (base excision repair)

- Repair of double-strand breaks

1860 - chromosomes (chromos - color, soma - body)

Every somatic cell contains normally two copies of each

chromosome

The number of unique chromosomes (N) in such a cell is known as

its haploid number.

The total number of chromosomes (2N) is its diploid number Number of chromosomes (2N) in some eukariotes

Organism Chromosomes

Humans 46

Dog 78

Rat 42

Turkey 82

Frog 26

Fruit fly 8

Hermit crab ~254

Garden pea 14

Potato 48

Yeast 34

ORGANIZATION OF EUKARYOTIC DNA

A typical human cell contains 46 chromosomes, whose total DNA is approximately 1m long! Such a

large amount of genetic material can be effectively packaged into a volume the size of a cell nucleus so

that it can be efficiently replicated and its genetic information expressed. To do so requires the

interaction of DNA with a large number of proteins, each of which performs a specific function in the

ordered packaging of these long molecules of DNA. Eukaryotic DNA is associated with tightly bound

basic proteins, called histones. These serve to order the DNA into fundamental structural units, called

nucleosomes, that resemble beads on a string. Nucleosomes are further arranged into increasingly

more complex structures that organize and condense the long DNA molecules into chromosomes that

can be segregated during cell division.

E.coli RNA polymerase (holoenzyme) – ~450 kDa protein α2ββ σ. After

initiation a subunit dissociate from the core enzyme, α2ββ which carries out

the actual polymerization process.

Several function of holoenzyme:

1. template binding

2. RNA chain initiation

3. chain elongation

4. chain termination

The synthesis of a RNA by a polymerase always requires a template.

The copying of DNA by an RNA polymerase to make RNA is called

transcription (two DNA strands are complementary, but not identical -

different protein-coding potentials).

The nucleotide at the terminal 5’ end of a growing RNA strand is

chemically distinct from the nucleotides within the strand in that it retains all

three phosphate groups. When an additional nucleotide is added to the 3’ end of

the growing strand, only the a phosphate is retained; the β and γ are lost.

RNA polymerase

TRANSCRIPTION

The process of transcription can be divided into three phases:

initiation, elongation, and termination. A transcription unit extends

from the promoter to the termination region, and the initial

product of transcription by RNA polymerase is termed the primary

transcript. Initiation: Transcription begins with the binding

of the RNA polymerase holoenzyme to a region of the DNA known

as the promoter, which is not transcribed. The prokaryotic

promoter contains characteristic consensus sequences.

Elongation: Once the promoter region has been recognized and bound by the

holoenzyme, local unwinding of the DNA helix continues, mediated by the polymerase.

RNA polymerase begins to synthesize a transcript of the DNA sequence. The elongation

phase is said to begin when the transcript (typically starting with a purine) exceeds ten

nucleotides in length. The core enzyme is able to leave (“clear”) the promoter and move

along the template strand in a processive manner. During transcription, a short DNA-

RNA hybrid helix is formed. Like DNA polymerase, RNA polymerase uses nucleoside

triphosphates as substrates and releases pyrophosphate each time a nucleoside

monophosphate is added to the growing chain.

Termination: The elongation of the single-stranded RNA chain continues until a

termination signal is reached. Termination can be intrinsic (spontaneous) or dependent

upon the participation of a protein known as the ρ (rho) factor.

Three stages in transcription.

During initiation of transcription,

RNA polymerase forms a

transcription bubble and begins

polymerization of ribonucleotides

(rNTPs) at the start site, which is

located within the promoter region.

Once a DNA region has been

transcribed, the separated strands

reassociate into a double helix,

displacing the nascent RNA except

at its 3’ end 5’ and of the RNA

strand exits the RNA polymerase

through a channel in the enzyme.

Termination occurs when the

polymerase encounters a specific

termination sequence (stop site).

See the text for details.

PROTEIN SYNTHESIS

Genetic information, stored in the chromosomes and

transmitted to daughter cells through DNA replication, is

expressed through transcription to RNA and translation into

proteins (polypeptide chains). The pathway of protein

synthesis is called translation because the “language” of the

nucleotide sequence on the mRNA is translated into the

“language” of an amino acid sequence. The process of

translation requires a genetic code, through which the

information contained in the nucleic acid sequence is

expressed to produce a specific sequence of amino acids.

Any alteration in the nucleic acid sequence may result in an

incorrect amino acid being inserted into the polypeptide

chain, potentially causing disease or even death of the

organism.

Overview

The genetic code

Codons

Codons are presented in the mRNA language of adenine (A), guanine (G), cytosine

(C), and uracil (U). Their nucleotide sequences are always written from the 5'-end to the

3'-end. The four nucleotide bases are used to produce the three-base codons. There are,

therefore, 64 different combinations of bases, taken three at a time.

1. How to translate a codon: This table (or “dictionary”) can be used to translate any

codon and, thus, to determine which amino acids are coded for by an mRNA sequence.

Sixty-one of the 64 codons code for the 20 common amino acids.

2. Termination (“stop” or “nonsense”) codons: Three of the codons, UAG, UGA, and

UAA, do not code for amino acids, but rather are termination codons. When one of

these codons appears in an mRNA sequence, synthesis of the polypeptide coded for by

that mRNA stops.

Usually, only one reading frame (#3) will produce a functional protein since the

other two reading frames will include several Stop codons

READING FRAMES

Reading frame 1 5' 3' UUA UGA GCG CUA AAU

Leu Stop Ala Leu Asn

Reading frame 2

U UAU GAG CGC UAA AU

Tyr Glu Arg Stop

Reading frame 3 UU AUG AGC GCU AAA U

Met Ser Ala Lys

1. Specificity: The genetic code is specific, that is, a particular codon always

codes for the same amino acid.

2. Universality: The genetic code is virtually universal, that is, its specificity

has been conserved from very early stages of evolution, with only slight

differences in the manner in which the code is translated.

3. Degeneracy: The genetic code is degenerate. Although each codon

corresponds to a single amino acid, a given amino acid may have more than

one triplet coding for it. Only Met and Trp have just one coding triplet.

4. Nonoverlapping and commaless: The genetic code is nonover-lapping

and commaless, that is, the code is read from a fixed starting point as a

continuous sequence of bases, taken three at a time. For example,

AGCUGGAUACAU is read as AGC/UGG/AUA/CAU without any “punctuation”

between the codons.

Characteristics of the genetic code

A large number of components are required for the synthesis of a

protein. These include all the amino acids that are found in the finished

product, the mRNA to be translated, transfer RNA (tRNA) for each of

the amino acids, functional ribosomes, energy sources, and enzymes, as

well as protein factors needed for initiation, elongation, and

termination steps of polypeptide chain synthesis.

COMPONENTS REQUIRED FOR TRANSLATION

- Amino acids

All the amino acids that eventually appear in the finished protein must

be present at the time of protein synthesis. If one amino acid is missing,

translation stops at the codon specifying that amino acid.

- Transfer RNA

At least one specific type of tRNA is required for each amino acid. In

humans, there are at least 50 species of tRNA. Because there are only 20

different amino acids commonly carried by tRNA, some amino acids have

more than one specific tRNA molecule. This is particularly true of those

amino acids that are coded for by several codons.

1. Amino acid attachment site: Each

tRNA molecule has an attachment site for

a specific (cognate) amino acid at its 3'-

end. The carboxyl group of the amino acid

is in an ester linkage with the 3'-hydroxyl

of the ribose portion of the adenosine (A)

nucleotide in the – CCA sequence at the

3'-end of the tRNA.

2. Anticodon: Each tRNA molecule also

contains a three-base nucleotide

sequence – the anticodon – that pairs with

a specific codon on the mRNA. This codon

specifies the insertion into the growing

peptide chain of the amino acid carried by

that tRNA.

Is required for attachment of amino

acids to their corresponding tRNAs. Each

member of this family recognizes a

specific amino acid and all the tRNAs that

correspond to that amino acid.

Aminoacyl-tRNA synthetases

catalyze a two-step reaction that results in

the covalent attachment of the carboxyl

group of an amino acid to the 3'-end of its

corresponding tRNA.

Aminoacyl-tRNA synthetases

The extreme specificity of the

synthetase in recognizing both the amino

acid and its cognate tRNA contributes to

the high fidelity of translation of the

genetic message. In addition, the

synthetases have a “proofreading” or

“editing” activity that can remove amino

acids from the enzyme or the tRNA

molecule.

Ribosomes are large complexes of protein and ribosomal RNA. They consist of two subunits – one large and one small – whose relative sizes are given in terms of their sedimentation coefficients, or S (Svedberg) values. 1. Ribosomal RNA 2. Ribosomal proteins 3. A, P, and E sites on the ribosome: Together, they cover three neighboring codons. During translation, the A site binds an incoming aminoacyl-tRNA as directed by the codon currently occupying this site. This codon specifies the next amino acid to be added to the growing peptide chain. The P-site codon carries the chain of amino acids that has already been synthesized. The E site is occupied by the empty tRNA as it is about to exit the ribosome. 4. In eukaryotic cells, the ribosomes are either “free” in the cytosol or are in close association with the endoplasmic reticulum.

STEPS IN PROTEIN SYNTHESIS

Initiation of protein synthesis involves the assembly of the components of the translation system before peptide bond formation occurs. These components include the two ribosomal subunits, the mRNA to be translated, the aminoacyl-tRNA specified by the first codon in the message, GTP, and initiation factors that facilitate the assembly of this initiation complex. The initiating AUG is recognized by a special initiator tRNA. Recognition is facilitated by IF-2-GTP in prokaryotes and eIF-2-GTP in eukaryotes. In bacteria and in mitochondria, the initiator tRNA carries an N-formylated methionine. After methionine is attached to the initiator tRNA, the formyl group is added by the enzyme transformylase, which uses N10-formyl tetrahydrofolate. In eukaryotes, the initiator tRNA carries a methionine that is not formylated.

Initiation

Elongation of the polypeptide chain

involves the addition of amino acids to

the carboxyl end of the growing chain.

During elongation, the ribosome moves

from the 5'-end to the 3'-end of the mRNA

that is being translated.

Elongation

The formation of the peptide bond is catalyzed

by peptidyltransferase, an activity intrinsic to the

23S rRNA found in the large ribosomal subunit. After

the peptide bond has been formed, what was

attached to the tRNA at the P site is now linked to

the amino acid on the tRNA at the A site.

Translocation causes movement of the uncharged

tRNA from the P to the E site (before being

released), and movement of the peptidyl-tRNA from

the A to the P site. The process is repeated until a

termination codon is encountered.

Termination occurs when one of the three termination codons moves into the A site.

The newly synthesized polypeptide may undergo further modification and the ribosomal

subunits, mRNA, tRNA, and protein factors can be recycled and used to synthesize another

polypeptide.

Termination

Translation begins at the 5'-end of the mRNA, with the ribosome proceeding along the

RNA molecule. Because of the length of most mRNAs, more than one ribosome at a time

can translate a message. Such a complex of one mRNA and a number of ribosomes is

called a polysome or polyribosome.

Polysomes

Many polypeptide chains are covalently modified,

either while they are still attached to the ribosome

(cotranslational) or after their synthesis has been

completed (posttranslational). These modifications may

include removal of part of translated sequence, or the

covalent addition of one more chemical groups required for

protein activity.

Trimming

Many proteins destined for secretion from the cell are

initially made as large, precursor molecules that are not

functionally active. Portions of the protein chain must be

removed by specialized endoproteases, resulting in the

release of an active molecule. Zymogens are inactive

precursors of secreted enzymes.

CO- AND POSTTRANSLATIONAL MODIFICATION OF POLYPEPTIDE CHAINS

1. Phosphorylation: Phosphorylation occurs on the

hydroxyl groups of serine, threonine, or, less frequently,

tyrosine residues in a protein. The phosphorylation may

increase or decrease the functional activity of the protein.

2. Glycosylation: Many of the proteins that are destined

to become part of a plasma membrane or to be secreted

from the cell, have carbohydrate chains attached to the

amide nitrogen of asparagine or the hydroxyl groups of

serine, threonine, or hydroxylysine. Glycosylation is also

used to target proteins to the matrix of lysosomes.

Covalent attachment

- Hydroxylation: Proline and lysine residues of the α

chains of collagen are extensively hydroxylated by

vitamin C-dependent hydroxylases in the endoplasmic

reticulum.

- Other covalent modifications: For example, additional

carboxyl groups can be added to glutamate residues by

vitamin K-dependent carboxylation. The resulting γ-

carboxyglutamate (Gla) residues are essential for the

activity of several of the blood-clotting proteins. Biotin is

covalently bound to the ε-amino groups of lysine

residues of biotin-dependent enzymes that catalyze

carboxylation reactions, such as pyruvate carboxylase.

Attachment of lipids, such as farnesyl groups, can help

anchor proteins to membranes. Histone proteins can be

reversibly acetylated.

Protein processing by proteolysis and self-splicing, (a) Three successive enzyme-catalyzed cleavages produce insulin from preproinsulin. The first cleavage occurs immediately after synthesis of preproinsulin, a single chain of 108 amino acids. This cleavage removes the 25-aa signal sequence from the amino end of the molecule. The remaining 84 amino acids constitute proinsuiin, a molecule in which all the correct disulfide bridges are present While the hormone is being packaged for secretion, the 33-residue C segment is removed via two proteolytic cleavages, yielding the A and B chains of insulin.

- Protein folding

Folding can be spontaneous (as a result of the

primary structure), or facilitated by proteins known

as “chaperones”.

- Protein degradation

Proteins that are defective, for example,

misfolded, or destined for rapid turnover are often

marked for destruction by ubiquitination – the

attachment of chains of a small, highly conserved

protein, called ubiquitin. Proteins marked in this way

are rapidly degraded by a cellular component known

as the proteasome, which is a macromolecular, ATP-

dependent, proteolytic system located in the

cytosol.

Action of chaperones during translation Chaperones bind to the amino (N) terminus of the growing polypeptide chain, stabilizing it in an unfolded configuration until synthesis of the polypeptide is completed. The completed protein is then released from the ribosome and is able to fold into its correct three-dimensional conformation.

Action of chaperones during protein transport A partially unfolded polypeptide is transported from the cytosol to a mitochondrion. Mitochondrial chaperones facilitate transport and subsequent folding of the polypeptide chain within the organelle.

1. RNA polymerase I, located in the nucleoli (dense granular bodies with ribosomal genes in nucleus).

2. RNA polymerase II, occurs in nucleoplasm, synthesized mRNA precursors.

3. RNA polymerase III, occurs in nucleoplasm, synthesizes the precursors of 5S ribosomal RNA, tRNA,

and variety of other small nuclear and cytosolic RNAs

4. Mitochondrial RNA polymerase

Amanita phalloides (death cap)

Tight 1:1 complex with RNA polymerase II (K=10-8M) and RNA polymerase III (K=10-6M) block of elongation step. Despite the amatoxins’ high toxicity (5-6 mg, which occur in ~40 g of fresh mushrooms, are sufficient to kill a human adult), they act slowly (liver dysfunction ~7th day). This, in part, reflects the slow turnover rate of eukaryotic mRNA and proteins.

Antibiotics are bacterially or fungally produces substances that inhibit the growth of other organisms. DNA replication - novobicin, transcription - rifamycin, bacterial cell wall synthesis - penicillin, translation - majority.

SOME RIBOSOMAL INHIBITORS

Inhibitor Action

Chloramphenicol Inhibits peptidyl transferase on the prokaryotic large subunit

Cycloheximide Inhibits peptidyl transferase on the eukaryotic large subunit

Erythromycin Inhibits translocation by the prokaryotic large subunit

Fusidic acid Inhibits elongation in prokaryotes by binding to EF-G-GDP in a way that

prvents its dissociation from the large subunit

Puromycin An aminoacyl-tRNA analog that causes premature chain termination in

all cells

Streptomycin Causes mRNA misreading and inhibits chain initiation in prokaryotes

Tetracycline Inhibits the binding of aminoacyl-tRNAs to the prokaryotic small

subunit

Diphteria toxin Catalytically inactivates eEF-2 by ADP-ribosylation

Ricin/abrin Poisonous plant proteins that catalytically inactivate the eukaryotic large

subunit

A selection on of antibiotics that act as translational inhibitors