Download 1 Protein Synthesis DNA protein (nucleus) (ribosome) 1

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Protein Synthesis
DNA
protein
(nucleus)
(ribosome)
1. Transcription
-DNA
mRNA
-in the nucleus
*mRNA processing
-“splicing”
-in the nucleus
2. Translation
-mRNA
amino acids
(tRNA and
rRNA
are also
involved)
polypeptide (primary structure)
protein
-in the cytoplasm on ribosomes
DNA vs. RNA
DNA
RNA
-double helix
-polymer of nucleotides
-deoxyribose (sugar)
-phosphate group
-4 nitrogen bases:
-A, C, G, T
-single strand
-polymer of nucleotides
-ribose (sugar)
-phosphate group
-4 nitrogen bases:
-A, C, G, U (uracil)
Roles of DNA and RNA
-DNA:
-master plan and remains in the nucleus
-RNA: blueprint and goes to ribosomes in the cytoplasm
Genetic Material
-genetic material consists of two types of biomolecules- DNA and RNA
-both are nucleic acids and both store genetic information
-nucleic acids consist of a long strand of repeating subunits that act as letters in a code
-the subunit bases on one strand pair with the bases of another strand
-base pairing is essential for sending genetic messages
-one strand is the template and the new molecule is built according to the original strand
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genetic code
-a system of symbols used to store information
-remember, proteins are made by joining amino acids into long chains call polypeptides
-living cells store genetic information in DNA
-DNA determines the primary structures of proteins, BUT it needs RNA in the process
-genes are the keys to almost everything that living cells do
-describes how a sequence of bases in DNA or RNA translates into the sequence of amino acids in a
protein -written in nucleotide triplets, or codons
-there 64 different possible codons
-only four bases in RNA carry instructions for 20 different amino acids because they can form 64
different codons
-how and why:
-the nucleotides are the 4 “letters” of the DNA alphabet
-the small size of this alphabet is a problem  protein molecules are built from amino acids, and
there are 20 different amino acids
-so, a genetic code requires at least 20 different code words—one for each amino acid
-when three nucleotides are grouped at a time, 64 triplet combinations are possible
*provides enough code words, and some extra! (so more than one triplet can specify the same
amino acid)
-each nucleotide triplet in DNA specifies a particular triplet for mRNA to be formed during
transcription
-in translation, a second base-pairing step is needed for reading the genetic code
-a triplet in mRNA, called a codon, pairs with a triplet on a tRNA molecule called an anticodon which
carries the correct amino acid
-the start codon is AUG, or the amino acid methionine
-there are 3 possible stop codons: UAA, UGA, UAG
-all amino acids are NOT specified by only one codon
-codon: a sequence of 3 nucleotides in mRNA that encodes an amino acid
-anticodon: 3 nucleotide sequence in tRNA that is complementary to and base pairs with a specific
codon in mRNA
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3 types of RNA
-in addition to these three types of RNA eukaryotic cells have a variety of small nuclear RNA molecules
that interact with specific proteins during RNA processing
-some RNA molecules act as catalysts, like enzymes
-many viruses store genetic information as RNA
mRNA or messenger RNA
-carries copies of the instructions for assembling amino acids from DNA to the rest of the cell
-temporary copy of a gene that encodes a protein
-transcription is the process that makes mRNA
-provides the pattern that determines the sequence of amino acids that are added to the polypeptide
chain in a process known as translation
rRNA or ribosomal RNA
-combine with proteins to make up ribosomes
-80% of the RNA in a cell is rRNA
tRNA or transfer RNA
-transfers each amino acid to the ribosome to help assemble proteins
-each amino acid that will be used in making the protein is attached to this
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Importance of Proteins
-proteins play a very important part in the function of any living system
-they have 8 functions:
-make up structural features
-are enzymes, which catalyze and regulate chemical reactions
-provides ATP
-carry oxygen to the blood (hemoglobins)
-carry chemical messages as hormones like insulin help maintain homeostasis
-cell signaling also involves protein receptor molecules attached to the cell membrane that pass
along signals to a series of regulatory enzymes inside the cell
-a protein’s structure determines its function, and information expressed from the code in DNA
determines the structure of proteins
-many enzymes have cavities or pockets that bind only specific substrate molecules
-ex: the enzyme lysozyme, found in egg white and tears, helps destroy harmful bacteria by cutting a
polysaccharide found in bacterial cell walls
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Protein Synthesis
Transcription
How DNA is converted to RNA
gene
A ---T
G ---C
T ---A
C ---G
goes back
to DNA
A
G
T
C
U
C
A
G
T
C
A
G
nucleus
mRNA leaves through
nuclear pores
-takes place in three stages:
1. initiation
-when the enzyme RNA polymerase attaches to a specific region of DNA
-this attachment site is called the promoter region because it promotes transcription and is
located just before the segment of the DNA coding strand that will be transcribed
2. elongation
-RNA polymerase partially unwinds the DNA, exposing the coding strand of the gene
-it moves along the DNA away from the promoter site as it builds an RNA molecule
-the sequence of DNA nucleotides determines the sequence of RNA chain
-a single complementary strand of RNA, called a primary transcript, is made
3. termination
-when RNA polymerase reaches the terminator region, or the end of the DNA to be transcribed,
the enzyme and primary transcript are released from the DNA
-DNA never leaves the nucleus, so it’s converted into mRNA which can leave the nucleus
-RNA is like a disposable copy of a DNA segment
-RNA polymerase
-unwinds the DNA double helix
-breaks hydrogen bonds between nitrogen bases in DNA
-adds new RNA nucleotides
*it knows exactly where to bind in the chromosome
-binds only to DNA promoters, which have specific base sequences
-promoters are signals in RNA that indicate to DNA polymerase when to begin translation
-only a section of the chromosome is copied—this section is called a gene
-gene: small section of the chromosome that has genetic information
-only one strand of the DNA directs the synthesis of RNA
-this strand of DNA is called the template, sense strand, or master strand
-prokaryotes have one type of RNA polymerase
-eukaryotes have 3 RNA polymerases in the nuclei and each is responsible for making the 3 types of RNA
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-the nucleolus is the site of RNA synthesis
-the nucleolus is also where rRNA and 70 other proteins are made into ribosomes
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Protein Synthesis
mRNA processing
-takes place in the nucleus
1. MG (methyl guanine) cap is added to the “beginning” of the strand
2. poly A tail (10-25 adenines) is attached to the “end”
-the longer the poly-A tail, the longer the life span of a particular mRNA
-also helps transport mRNA out of the nucleus and helps the mRNA attach to a ribosome and begin
translation
*”beginning” vs. “end”
-provides protection against enzymes that break down nucleic acids
3. “splicing”
-introns are removed
(intervening)
-exons are joined
(expressed)
-protein enzymes catalyze the splicing of tRNA
-there is no correct sequence: it can be put together in many ways
-ex: antibodies are proteins made by the body to protect against antigens like viruses, bacteria,
dander, pollen, etc.
-different bodies make different antibodies  different antibodies due to being differently
spliced
-why?
-only certain information is needed for specific jobs to create different sequences
-there is more information than needed
-processing mRNA before it’s translated makes translation faster and more efficient because
there are less codons to be changed into amino acids
-a primary RNA transcript may contain as many as 200,000 nucleotides (the average for human cells is
5,000)
-mRNA in the cytoplasm averages only 1,000 nucleotides
-enzymes add additional nucleotides and chemically modify or remove others
-if introns are left in RNA, the consequences can be serious
-in addition to splicing, an important step in the processing of tRNA is the chemical modification of
several nucleotides and folding into a cloverleaf shape
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Protein Synthesis
Translation
-steps of translation: initiation, elongation, termination
mRNA binds to the small ribosomal subunit (at the 5’ end)
the smallest ribosomal unit attaches to mRNA at the “start codon” AUG at the P site
the large ribosomal subunit attaches
a charged tRNA brings in an amino acid to the A site
the amino acid released from the tRNA is the P site is transferred to the amino acid (still
elongation
attached) to the tRNA in the A site.
*covalent bond called a peptide bond forms between amino acids
6. The uncharged tRNA in the P site moves to the E site
7. The ribosome shifts down to another mRNA codon
8. tRNA in the A site moves to the P site
9. the site is now open for the next tRNA with an amino acid
10. when the “stop codon” reaches the A site, a special protein (a release factor) binds to the codon
termination
in the A site to stop translation
11. the tRNA releases the polypeptide. The ribosome releases mRNA and tRNA and the ribosome
separates
12. the polypeptide chain moves to the ER (endoplasmic reticulum)
a) folded
b) sugars are added as markers
13. proteins are packaged an shipped in vesicles from the golgi apparatus for use outside the cell
-translocation: when the polypeptide chain moves from the P site to the A site
-the ribosome has 3 parts during this process: the small subunit, the large subunit, and the mRNA strand
-3 stages: initiation, elongation (adding more amino acids), termination
-hydrogen bonds are between tRNA and amino acids  are easily broken
-the mRNA strand is broken down afterwards and recycles
-the start codon is an amino acid (it’s methionine), but the stop codon is NOT an amino acid
-the longer the polypeptide chain, the longer the mRNA stays in the cytoplasm before it’s broken down
initiation
1.
2.
3.
4.
5.
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Transport and Modification of Proteins
-the new protein chain may not be functional
-many proteins must be chemically modified and folded into an active tertiary structure
-helper or “chaperone” proteins often help stabilize the polypeptideas it is folded
-chemical modification often involves adding sugars to specific sites on the protein
-enzymes may cut the polypeptide into smaller segments
-after translation, the protein must be transported to where it will function
-sometimes the protein must move out of the cell, as in the case of hormones such as insulin
-a small membrane vesicle containing the protein fuses with the cell membrane
-the protein is then released outside
-other proteins become part of the cell membrane
-transport can start while the protein is still being translated
-signal sequence is the directions for the transport of proteins to different parts of the cell
-provided by the first few amino acids synthesized on the ribosomes
-the signal sequence binds to a receptor protein in the ER membrane
-as translation continues, the growing chain of amino acids threads through the membrane and into the
space inside the ER
-when translation is complete, the new protein is released from the ribosome into the inner ER
-often a sugar molecule is added to the protein, forming a glycoprotein
-proteins to be released from the cell pass from the ER to the vesicles of the golgi apparatus
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Mutations
-mutations:
-there are 2 type of mutations:
1. chromosome mutations
-when an individual inherits more or less than the normal number of chromosomes
-due to a problem during mitosis or meiosis
-are lethal to the cell most of the time
-ex: down syndrome
-when there is 3 pairs of chromosome 21
-causes similar facial features  not defined, babylike
-serious mental handicaps
2. gene mutations
-results in abnormal protein products
-gene disorders such as sickle cell, cystic fibrosis, and hemophilia are all due to gene mutations
-are due to a change in the cell’s DNA  mRNA  amino acids  polypeptide (protein)
-aren’t as harmful as chromosome mutations
-2 types of gene mutations:
-substitution
-one nucleotide with a nitrogenous base is substituted for another
-ATT GCC may be altered to ATC GCG (in DNA)
-wobble effect: a substitution will often not change an amino acid if the change is in the third
position or base
-deletions and insertions
-cause more serious mutations
-deletion: when at least one nucleotide is left out
-insertion: when a nucleotide is added
-the later the mutation, the less it affects the strand
-both mutations cause a “frame shift”
- a frame shift
-if mRNA is AUG (met) CCC (pro) GCA (ala)
-an insertion might be: AUG (met) ACC (thr) CGC (arg) A
missense: nucleotides
-a deletion might be: AUC (iso) CCG (pro) CA
not in triplets
-both result in the mRNA “read” as a different codon
-the result is a change in amino acids
Do mutations always change the protein?
-mutations in the 3rd base of a codon may not change the amino acid (wobble effect)
-insertions or deletions that occur early in the mRNA change many amino acids
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-insertions or deletions that occur late in the mRNA change fewer amino acids
-mutations that occur in introns (and are cut out) won’t affect the protein produced
Translation Errors
-most errors during translation are caught and corrected
-the most common translation error results from misreading the nucleotide sequence
-initiation determines exactly where translation will begin
-starting from this point, the grouping of bases into codons is called the reading frame
-if the start is shifted by one or two nucleotides in either direction, the frame changes
-a different sequence of codons and amino acids will result
-some errors are due to splicing mistakes or changes in DNA
-if a nucleotide changes so that a codon becomes a stop codon, translation can terminate partway
through the message  the result is a partial polypeptide
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Viruses
Viruses
-viruses: tiny particles that have no cells, yet they replicate and evolve
-called “particles” because they are not living
-Dmitri Ivanovsky: Russian botanist who discovered viruses
-found that the infective agent of tobacco mosaic disease passed through a filter that would have
retained bacteria  the virus was tobacco mosaic virus, TMV
-because they can’t do these things without help, viruses depend on the gene-expression machinery of
the host cells they infect
-Why are viruses not considered living?
-can’t reproduce on their own
-no normal cell structure: no organelles
-no metabolism
- no mitochondria or chloroplasts  no ATP
- are much smaller and simpler than cells
- don’t respond to stimuli, as cells do
-structure of viruses:
-contain a small amount of genetic material: DNA or RNA
-surrounded by a protein coat called a capside
-some contain a few enzyme molecules, like those needed for transcription of their genes
-some viruses that infect animal cells have a membrane envelope
-viruses tend to be very specific
-if you have a virus or a cold, your cat or dog could not get it
-rhinovirus: a virus in the nose or nasal passages
-only in the nose, can’t infect the liver
-HIV infects T cells
-viruses trick cells
-cells are very good at recognizing foreign material, so viruses disguise themselves and attach to cells
-the virus then uses all of the cell’s structures: its ribosomes, its enzymes, etc.
-it turns the cell from a protein factory to a genetic material and protein (for viruses) factory
-the virus parts then assemble inside the cell and the cell explodes, or lyses
-2 types of viruses:
-bacteriophage
-infects the cells of bacteria
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-ex: T2 is a bacteriophage that is a DNA virus-contains DNA surrounded by a protein
-the elongated structure attaches to bacterial cells and injects DNA
-retrovirus
-only virus particles with RNA
-goes from RNA which is read to DNA
-when retroviruses infect a cell, they produce a DNA copy of their RNA  this DNA is inserted
into the DNA of the host cell
-an enzyme called reverse transcriptase does the copying of RNA to DNA
-ex: HIV, which infects human cells, is surrounded by a protein and lipid membrane envelope
-the genetic material is RNA
-HIV also carries two molecules of the enzyme reverse transcriptase, ready to copy the RNA
after entry into a host cells
-how do viruses replicate?
-the process varies among types of viruses, but the general principle of copying stored ggenetic
information is the same as for cells
-there are two patterns of replication:
-lytic infections
-the host cell’s enzymes replicate the viral DNA
-viral genes are transcribed and translated on the host’s ribosomes to make proteins for the out
capsule
-new viral particles assemble
-when there are many new viruses, the cell lyses (breaks open) and releases them to infect
other cells
-lysogenic infections
-the viral DNA (or a DNA copy of it) inserts into the cellular DNA
-it is copied as the cell replicates
-there is little or no production of new viruses
-instead the genetic information for the virus is passes along to new cells
-sometimes an external stress, like starvation, of the host cell activates a lytic cycle of replication
-in animal cells, a few viral particles may be given off from time to time without lysing the cell
-when the viral particle emerges, it can pick up part of the cell membrane
-the membrane makes it difficult for the host to recognize the viral particle as an invader
-in tumor viruses, the cell may lose control of normal growth and become cancerous
The Impact of Viruses
-viruses live at the expense of the host organism
-they pose a serious threat to cell life because they replicate quickly, evolve rapidly, and can remain
hidden inside host cells
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-antibiotics on bacteria vs. viruses:
-antibiotics are effective against bacterial infections because they interfere with aspects of bacterial
metabolism that are different from their hosts’ metabolism
-they are useless again viruses because viruses do not have their own metabolism
-moving geographic locations
-modern technologies have made the treat of viral diseases much greater
-ex: increased air travel may…
- discontinue the geographic isolation of the Ebola virus which causes a highly contagious,
usually lethal respiratory disease
-led to the spread of severe acute respiratory syndrome (SARS) which was first reported in asia
and spread to more than 24 countries in just a few months
-mechanical harvesting
-international shipping of seeds, foods, and other agricultural products also can spread viruses that
infect valuable crops and animals
-viruses are beneficial for scientific research:
-scientists can disarm viruses by removing the genes that cause disease
-disarmed viruses are useful tools for delivering DNA in cloning experiments
-researchers are developing a vaccine for West Nile virus using components of the West Nile virus
and other similar viruses
Vaccines
-Edward Jenner was an English physician who developed the 1st vaccine
-Louis Pasteur developed vaccination procedures for rabies and other diseases
Immune Systems
-B cells: trigger antibodies that are specific to antigens
-T cells: look for cells that are infected with viruses but haven’t exploded yet
-inject poison into the cell, killing the cell which prevents the virus from reproducing
-doctors give a sample of protein coat or virus that has the potential to make you sick but actually helps
you build immunity to the virus
-stimulates B and T cells as memory cells: they remember the virus and are ready to recognize and
fight the virus if it ever comes
Terms to Know
-translation: process of converting mRNA into a polypeptide chain
-peptide bond: type of covalent bonds that forms between two amino acids
-tRNA: molecule that brings specific amino acids to the ribosome
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-nucleus: site of transcription and mRNA processing
-DNA, sense, or master strand: serves as a template for DNA
-codon: three-nucleotide code on mRNA
-transcription: process of converting DNA into mRNA
-AUG: this specific triplet is the start codon
-introns: these sections are cut out of mRNA during processing
-gene mutations, substitution: usually the least harmful
-anitcodon: the name given to the three nucleotide code of tRNA
-ribosome: the specific organelle at which translation occurs
-substitution: a genetic disorder due to a single nucleotide mutation
-wobble effect: both CCC and CCG code for proline
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