Protein Synthesis

–DNA specifies the synthesis of proteins in two stages: Transcription, the transfer of genetic information from DNA into an RNA molecule Translation, the transfer of information from RNA into a protein

TRANSLATION Protein RNA TRANSCRIPTION DNA Cytoplasm Nucleus Figure

–The function of a gene is to dictate the production of a polypeptide. –A protein may consist of two or more different polypeptides.

From Nucleotides to Amino Acids: An Overview –Genetic information in DNA is: Transcribed into RNA, then Translated into polypeptides

–What is the language of nucleic acids? In DNA, it is the linear sequence of nucleotide bases. A typical gene consists of thousands of nucleotides. A single DNA molecule may contain thousands of genes.

–When DNA is transcribed, the result is an RNA molecule. –RNA is then translated into a sequence of amino acids in a polypeptide.

–What are the rules for translating the RNA message into a polypeptide? –A codon is a triplet of bases, which codes for one amino acid.

The Genetic Code –The genetic code is: The set of rules relating nucleotide sequence to amino acid sequence Shared by all organisms

–Of the 64 triplets: 61 code for amino acids 3 are stop codons, indicating the end of a polypeptide

TRANSLATION Amino acid RNA TRANSCRIPTION DNA strand Polypeptide Codon Gene 1 Gene 3 Gene 2 DNA molecule Figure 10.10

Second base of RNA codon First base of RNA codon Phenylalanine (Phe) Leucine (Leu) Cysteine (Cys) Leucine (Leu) Isoleucine (Ile) Valine (Val) Met or start Serine (Ser) Proline (Pro) Threonine (Thr) Tyrosine (Tyr) Histidine (His) Glutamine (Gln) Asparagine (Asn) Alanine (Ala) Stop Glutamic acid (Glu) Aspartic acid (Asp) Lysine (Lys) Arginine (Arg) Tryptophan (Trp) Arginine (Arg) Serine (Ser) Glycine (Gly) Third base of RNA codon Figure 10.11

Transcription: From DNA to RNA –Transcription: Makes RNA from a DNA template Uses a process that resembles DNA replication Substitutes uracil (U) for thymine (T) –RNA nucleotides are linked by RNA polymerase.

Initiation of Transcription –The “start transcribing” signal is a nucleotide sequence called a promoter. –The first phase of transcription is initiation, in which: RNA polymerase attaches to the promoter RNA synthesis begins

RNA Elongation –During the second phase of transcription, called elongation: The RNA grows longer The RNA strand peels away from the DNA template

Termination of Transcription –During the third phase of transcription, called termination: RNA polymerase reaches a sequence of DNA bases called a terminator Polymerase detaches from the RNA The DNA strands rejoin

The Processing of Eukaryotic RNA –After transcription: Eukaryotic cells process RNA Prokaryotic cells do not

–RNA processing includes: Adding a cap and tail Removing introns Splicing exons together to form messenger RNA (mRNA) Animation: Transcription

Newly made RNA RNA nucleotides RNA polymerase Template strand of DNA Direction of transcription (a) A close-up view of transcription (b) Transcription of a gene RNA polymerase Completed RNA Growing RNA Termination Elongation Initiation Terminator DNA Area shown in part (a) at left RNA Promoter DNA RNA polymerase DNA of gene Figure 10.13

Translation: The Players –Translation is the conversion from the nucleic acid language to the protein language.

Messenger RNA (mRNA) –Translation requires: mRNA ATP Enzymes Ribosomes Transfer RNA (tRNA)

Transcription Addition of cap and tail Coding sequence mRNA DNA Cytoplasm Nucleus Exons spliced together Introns removed Tail Cap RNA transcript with cap and tail Exon Intron Figure 10.14

Transfer RNA (tRNA) –Transfer RNA (tRNA): Acts as a molecular interpreter Carries amino acids Matches amino acids with codons in mRNA using anticodons

tRNA polynucleotide (ribbon model) RNA polynucleotide chain Anticodon Hydrogen bond Amino acid attachment site tRNA (simplified representation) Figure 10.15

Ribosomes –Ribosomes are organelles that: Coordinate the functions of mRNA and tRNA Are made of two protein subunits Contain ribosomal RNA (rRNA)

Next amino acid to be added to polypeptide Growing polypeptide tRNA mRNA tRNA binding sites Codons Ribosome (b) The “players” of translation (a) A simplified diagram of a ribosome Large subunit Small subunit P site mRNA binding site A site Figure 10.16

Translation: The Process –Translation is divided into three phases: Initiation Elongation Termination

Initiation –Initiation brings together: mRNA The first amino acid, Met, with its attached tRNA Two subunits of the ribosome –The mRNA molecule has a cap and tail that help it bind to the ribosome. Blast Animation: Translation

Start of genetic message Tail End Cap Figure 10.17

–Initiation occurs in two steps: First, an mRNA molecule binds to a small ribosomal subunit, then an initiator tRNA binds to the start codon. Second, a large ribosomal subunit binds, creating a functional ribosome.

Initiator tRNA mRNA Start codon Met P site Small ribosomal subunit A site Large ribosomal subunit Figure 10.18

Elongation –Elongation occurs in three steps. Step 1, codon recognition: –the anticodon of an incoming tRNA pairs with the mRNA codon at the A site of the ribosome. Step 2, peptide bond formation: –The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site –The ribosome catalyzes the bond formation between the two amino acids

Step 3, translocation: –The P site tRNA leaves the ribosome –The tRNA carrying the polypeptide moves from the A to the P site Animation: Translation

New peptide bond Stop codon mRNA movement mRNA P site Translocation Peptide bond formation Polypeptide ELONGATION Codon recognition A site Codons Anticodon Amino acid Figure

Termination –Elongation continues until: The ribosome reaches a stop codon The completed polypeptide is freed The ribosome splits into its subunits

Review: DNA  RNA  Protein –In a cell, genetic information flows from DNA to RNA in the nucleus and RNA to protein in the cytoplasm.

Transcription RNA polymerase mRNA DNA Intron Nucleus mRNA Intron Tail Cap RNA processing tRNA Amino acid attachment Enzyme ATP Initiation of translation Ribosomal subunits Elongation Anticodon Codon Termination Polypeptide Stop codon Figure

–As it is made, a polypeptide: Coils and folds Assumes a three-dimensional shape, its tertiary structure –Several polypeptides may come together, forming a protein with quaternary structure.

–Transcription and translation are how genes control: The structures The activities of cells

Mutations –A mutation is any change in the nucleotide sequence of DNA. –Mutations can change the amino acids in a protein. –Mutations can involve: Large regions of a chromosome Just a single nucleotide pair, as occurs in sickle cell anemia

Types of Mutations –Mutations within a gene can occur as a result of: Base substitution, the replacement of one base by another Nucleotide deletion, the loss of a nucleotide Nucleotide insertion, the addition of a nucleotide

Normal hemoglobin DNA mRNA Normal hemoglobin Mutant hemoglobin DNA mRNA Sickle-cell hemoglobin Figure 10.21

–Insertions and deletions can: Change the reading frame of the genetic message Lead to disastrous effects

Mutagens –Mutations may result from: Errors in DNA replication Physical or chemical agents called mutagens

–Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection.

mRNA and protein from a normal gene Deleted (a) Base substitution Inserted (b) Nucleotide deletion (c) Nucleotide insertion Figure 10.22

VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS –Viruses exhibit some, but not all, characteristics of living organisms. Viruses: Possess genetic material in the form of nucleic acids Are not cellular and cannot reproduce on their own.

Bacteriophages –Bacteriophages, or phages, are viruses that attack bacteria. Animation: Phage T2 Reproductive Cycle

Protein coat DNA Figure 10.24

Bacterial cell Head Tail fiber DNA of virus Bacteriophage (200 nm tall) Colorized TEM Figure 10.25

Plant Viruses –Viruses that infect plants can: Stunt growth Diminish plant yields Spread throughout the entire plant Animation: Phage T4 Lytic Cycle Animation: Phage Lambda Lysogenic and Lytic Cycles

Phage DNA Phage injects DNA Phage attaches to cell. Bacterial chromosome (DNA) Phage DNA circularizes. LYSOGENIC CYCLE Many cell divisions Prophage Occasionally a prophage may leave the bacterial chromosome. Lysogenic bacterium reproduces normally, replicating the prophage at each cell division. Phage DNA is inserted into the bacterial chromosome. Phage Figure 10.26b

Phage lambda E. coli Figure 10.26c

–Viral plant diseases: Have no cure Are best prevented by producing plants that resist viral infection

Tobacco mosaic virus RNA Protein Figure 10.27

Animal Viruses –Viruses that infect animals are: Common causes of disease May have RNA or DNA genomes –Some animal viruses steal a bit of host cell membrane as a protective envelope.

Protein coat RNA Protein spike Membranous envelope Figure 10.28

–The reproductive cycle of an enveloped RNA virus can be broken into seven steps. Animation: Simplified Viral Reproductive Cycle

Protein coat mRNA Protein spike Plasma membrane of host cell Envelope Template New viral genome New viral proteins Exit Virus Viral RNA (genome) Viral RNA (genome) Entry Uncoating Assembly RNA synthesis by viral enzyme RNA synthesis (other strand) Protein synthesis Figure 10.29

Protein spike Envelope Mumps virus Colorized TEM Figure 10.29c

The Process of Science: Do Flu Vaccines Protect the Elderly? –Observation: Vaccination rates among the elderly rose from 15% in 1980 to 65% in –Question: Do flu vaccines decrease the mortality rate among those elderly people who receive them? –Hypothesis: Elderly people who were immunized would have fewer hospital stays and deaths during the winter after vaccination. © 2010 Pearson Education, Inc.

–Experiment: Tens of thousands of people over the age of 65 were followed during the ten flu seasons of the 1990s. –Results: People who were vaccinated had a: 27% less chance of being hospitalized during the next flu season and 48% less chance of dying Blast Animation: HIV Structure

Deaths Hospitalizations Percent reduction in severe illness and death in vaccinated group Winter months (flu season) Summer months (non-flu season) Figure 10.30a

HIV, the AIDS Virus –HIV is a retrovirus, an RNA virus that reproduces by means of a DNA molecule. –Retroviruses use the enzyme reverse transcriptase to synthesize DNA on an RNA template. –HIV steals a bit of host cell membrane as a protective envelope.

Envelope Reverse transcriptase Surface protein Protein coat RNA (two identical strands) Figure 10.31

–The behavior of HIV nucleic acid in an infected cell can be broken into six steps. Animation: HIV Reproductive Cycle Blast Animation: AIDS Treatment Strategies

Reverse transcriptase HIV (red dots) infecting a white blood cell DNA strand Chromosomal DNA Cytoplasm Nucleus Provirus RNA Viral RNA Double stranded DNA Viral RNA and proteins SEM Figure 10.32

–AIDS (acquired immune deficiency syndrome) is: Caused by HIV infection and Treated with drugs that interfere with the reproduction of the virus

Part of a T nucleotide Thymine (T) AZT Figure 10.33

Viroids and Prions –Two classes of pathogens are smaller than viruses: Viroids are small circular RNA molecules that do not encode proteins Prions are misfolded proteins that somehow convert normal proteins to the misfolded prion version

–Prions are responsible for neurodegenerative diseases including: Mad cow disease Scrapie in sheep and goats Chronic wasting disease in deer and elk Creutzfeldt-Jakob disease in humans

EVOLUTION If it weren’t for evolution, we would all be prokaryotic unicellular beings! So how did we evolve from that into a human being?

Here it comes… Viruses and Mutations! These two vectors are the key to evolution. Mutations are generally considered to be in two categories: Nucleotide substitution and Nucleotide insertions or deletions

–Although mutations are often harmful, they are the source of genetic diversity, which is necessary for evolution by natural selection.

mRNA and protein from a normal gene Deleted (a) Base substitution Inserted (b) Nucleotide deletion (c) Nucleotide insertion Figure 10.22

Mutagens (what causes mutations) normally they are spontaneous (no known cause, accidental) Errors during DNA replication or recombination Chemical agents can be mutagens High energy radiation (sun, A-bombs etc.) X-rays carcinogens

Evolution Connection: Emerging Viruses –Emerging viruses are viruses that have: Appeared suddenly or Have only recently come to the attention of science © 2010 Pearson Education, Inc.

Figure 10.35

Figure 10.UN7

VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS –Viruses exhibit some, but not all, characteristics of living organisms. Viruses: Possess genetic material in the form of nucleic acids Are not cellular and cannot reproduce on their own.

Bacteriophages –Bacteriophages, or phages, are viruses that attack bacteria.

Protein coat DNA Figure 10.24

–Phages have two reproductive cycles. (1) In the lytic cycle: –Many copies of the phage are made within the bacterial cell, and then –The bacterium lyses (breaks open)

(2) In the lysogenic cycle: –The phage DNA inserts into the bacterial chromosome and –The bacterium reproduces normally, copying the phage at each cell division

Bacterial cell Head Tail fiber DNA of virus Bacteriophage (200 nm tall) Colorized TEM Figure 10.25

Phage lambda E. coli Figure 10.26c

–Viral plant diseases: Have no cure Are best prevented by producing plants that resist viral infection

Tobacco mosaic virus RNA Protein Figure Plant viruses may use RNA instead of DNA

Animal Viruses –Viruses that infect animals are: Common causes of disease May have RNA or DNA genomes –Some animal viruses steal a bit of host cell membrane as a protective envelope.

Protein coat RNA Protein spike Membranous envelope Figure 10.28

–New viruses can arise by: Mutation of existing viruses Spread to new host species