Chapter 7 Flashcards
(136 cards)
1
Q
the building blocks of proteins are _____ amino acids
A
20
- Some are acquired from your diet, while others are synthesized in your cells.
- The # of amino acids and their sequence differentiate proteins from each other.
2
Q
The human genome contains more than _____________ genes
A
20 000
- these 20 000 genes code for 100 000 different
proteins
- genes are diff combo of the 4 nucleotide bases along the length of the DNA strands.
- Messages from the genes, in the form of RNA molecules, travel to the ribosomes to direct the
assembly of the proteins.
- Variations in the copying & editing of the messages
culminate in the assembly of the many diff proteins by the ribosomes
3
Q
2 key pieces of research, involving defects in metabolism, led scientists to the discovery of how genes encode for proteins
A
1) Archibald Garrod’s Research (1896-1908)
- Studied alkaptonuria, a human disease causing urine to turn black in air.
- Observed that alkaptonuria is an inherited trait.
- Concluded by 1908 that alkaptonuria is an “inborn error of metabolism”, caused by a defective enzyme encoded by a mutated gene.
- Later research found that affected individuals excrete alkapton, a chemical that accumulates due to an inability to fully break down tyrosine.
- Established the first link between genes and metabolism.
2) George Beadle & Edward Tatum’s Research (1940s)
- Worked with Neurospora crassa (orange bread mold)
- Normal Neurospora grows readily on a minimal medium (MM): a medium that contains several salts, sucrose, and a vitamin, but none of the other, more complex chemicals required by cells.
- Hypothesized that Neurospora suses the simple chemicals in the medium to synthesize all
of the more complex molecules it needs for growth and reproduction.
- Exposed its spores to X-rays, causing random genetic mutations.
- Found some mutated spores could not grow on MM without added nutrients like amino acids or vitamins.
- Demonstrated a direct relationship between genes & enzymes, supporting the gene-protein connection.
4
Q
Beadle & Tatum’s Conclusion
A
- they hypothesized that each mutated strain had a defect in a gene that coded for one of the enzymes needed to synthesize a particular nutrient that was not in the MM. –> Ex, Mutants requiring added arginine had a defective gene coding for an enzyme in the arginine synthesis pathway. –> assembly of arginine from raw materials is a multistep process, with diff enzymes responsible for each step.–> thus, diff “arg” mutants might differ in the particular enzyme that is defective & thus in which step of the synthesis of arginine is blocked.
- they deduced that the biosynthesis of arginine required a # of steps, and each step was controlled by a gene that coded for the enzyme for this step
–> Beadle &Tatum had shown the direct relationship between genes & enzymes, which they put forward as the one gene–one enzyme hypothesis. - Impact laid the foundation for molecular biology., Earned them the 1958 Nobel Prize.
- Later scientists recognized not all proteins are enzymes & many proteins consist of more than
one subunit. –> Since this subunit is called a polypeptide, Beadle and Tatum’s hypothesis was restated as the one gene–one polypeptide hypothesis.
5
Q
one gene–one enzyme hypothesis is
A
the hypothesis, proposed by Beadle and Tatum, that each gene is unique and codes for the synthesis of a single enzyme
6
Q
one gene–one polypeptide hypothesis is
A
the hypothesis that each gene is unique and codes for the synthesis of a single polypeptide; the restated version of the one gene–one enzyme hypothesis
7
Q
central dogma is
A
the fundamental principle of molecular genetics, which states that genetic info flows from DNA to RNA to proteins
- In 1956, Francis Crick gave the name central dogma to the flow of information from DNA to RNA to protein
8
Q
The Central Dogma idea has 2 major processes: List them
A
1) transcription
2) translation.
9
Q
Transcription is
A
the mechanism by which the information encoded in DNA is transcribed into a complementary RNA copy.
-essentially the info in one type of nucleic acid, DNA, is copied onto another type of nucleic acid, RNA.
- occurs in the nucleus of a eukaryotic cell.
- Unlike DNA, RNA is able to exit the nucleus and enter the cytosol
10
Q
Translation is
A
the mechanism by which the information coded in the nucleic acids of RNA is copied into the amino acids of proteins
- It takes place on the ribosomes in the cytosol.-
- RNA contains the information for a polypeptide in the language of bases, but this information must be translated into the language of amino acids.
11
Q
Differences between DNA & RNA
A
Both are carriers of genetic info but differ in many ways
1) RNA contains a ribose sugar rather than a deoxyribose sugar. –> A ribose sugar has a hydroxyl
group on its 2’ carbon.
2) instead of thymine, RNA contains the base uracil. –> similar in structure to thymine, except thymine has a methyl group on its 1’ carbon. –> Uracil in the RNA pairs with adenine in the DNA strand.
3) DNA is double stranded, whereas RNA is single stranded. –> When a gene is transcribed into RNA, only a single-stranded complementary copy is made. –> In the complementary copy, uracil is substituted for thymine.
4) DNA is longer than RNA (Ms. Akhtar)
12
Q
3 major types of RNA molecules are involved in protein synthesis: List them
A
messenger RNA (mRNA)
transfer RNA (tRNA)
ribosomal RNA (rRNA)
13
Q
Messenger RNA (mRNA) is
A
the end product of the transcription of a gene; mRNA is translated by ribosomes into a protein
- acts as the intermediary between DNA and the ribosome
- mRNA is the RNA version of the gene encoded by DNA.
- It varies in length, depending on the gene that has been transcribed; the longer the gene, the longer the mRNA is.
14
Q
Transfer RNA (tRNA) is
A
a carrier molecule that binds to a specific amino acid & adds the amino acid to the growing polypeptide chain
- role: to transfer the appropriate amino acid to the ribosome to build a protein, as dictated by the mRNA template.
-relatively short in length, averaging 70 to 90 ribonucleotides
- The single-stranded RNA molecule loops in on itself, forming antiparallel double strands, which r
complementary to each other (SEE PAGE 315 FOR DIRAGRAM)
15
Q
Ribosomal RNA (rRNA) is
A
an RNA molecule within the ribosome that bonds the correct amino acid to the polypeptide chain
- Along with proteins, it’s a structural component that forms the ribosome, which is the construction site for the assembly of polypeptides
16
Q
An Overview of Transcription & Translation
A
Transcription (Step 1 of Protein Synthesis):
- Enzyme RNA polymerase makes an RNA molecule complementary to the DNA sequence of a given gene.
- Since DNA template strand is read in the 3’ to 5’ direction, RNA is formed in the 5’ to 3’ direction.
- Initially formed RNA is a precursor mRNA molecule cuz it can’t produce a protein directly and undergoes modifications to become functional mRNA.
- The mRNA can now exit the nucleus and enters the cytosol, where ribosomes are located.
Translation (Step 2 of Protein Synthesis):
- The mRNA associates with a ribosome in the cytosol.
- tRNA delivers amino acids to the ribosome as it moves along the mRNA.
- Amino acids are joined one by one to form the polypeptide encoded by the gene
17
Q
The Genetic Code
A
- The specific amino acid coded for by particular DNA (or complementary RNA) bases is determined by the genetic code.
- while there r only 4 RNA bases, there r 20 amino acids. How is nucleotide info in an mRNA molecule translated into the amino acid sequence of a polypeptide?
- Scientists realized that the 4 bases in an mRNA must be used in combos of at least 3 to provide the capacity to code for 20 amino acids –> if the code used 3-letter combos, 64 different amino acids could be specified (AAA, AAT, AAC, . . . , or 4^3)—more than enough to code for 20 amino acids.
18
Q
genetic code is
A
the specific coding relationship between bases & the amino acids they specify; the genetic code can be expressed in terms of either DNA or RNA bases
19
Q
The Genetic Code: Codons
A
- Each 3-letter combo is= a codon.
-The codons are in the 59 to 39 order in the mRNA. - Of the 64 codons, 61 specify amino acids = “sense codons.”
–> ex, 1 of these codons, AUG, specifies the amino acid methionine. It is usually the first codon translated in any mRNA in prokaryotes & eukaryotes. Thus, AUG = a start codon, or initiator codon. - The 3 codons that don’t specify amino acids—UAA, UAG, & UGA= stop codons (AKA “nonsense codons” or “termination codons”). –> They act as “periods,” indicating the end of a polypeptide-encoding sentence.
–> When a ribosome reaches a stop codon, polypeptide synthesis stops & the newly synthesized polypeptide chain is released from the ribosome.
20
Q
A codon is
A
a group of three base pairs that code for an individual amino acid
21
Q
A start codon is
A
AKA initiator codon
- the codon that signals the start of a polypeptide
chain and initiates translation
22
Q
A stop codon is
A
a codon that signals the end of a polypeptide chain and causes the ribosome to terminate translation
23
Q
Redundancy & wobble hypothesis
A
- there are many synonyms in the genetic code
- Ex, UGU &UGC both specify cysteine, whereas CCU, CCC, CCA, &CCG all specify proline.
–> This feature is known as redundancy & is called the wobble hypothesis. - The presence of this redundancy allows the third base in a codon to change (wobble), while still allowing the codon to code for the same amino acid. –> Notice how both cysteine codons follow the pattern UG_ & all proline codons follow the pattern CC_.
24
Q
The genetic code is ________________.
A
universal
- With few exceptions, the same codons specify the
same amino acids in all living organisms, & also in all viruses.
- The universality of the genetic code indicates that it was established, very early in the evolution of life & has remained virtually unchanged through billions of years of evolutionary history.
- Minor exceptions to the universality of the genetic code have been found in a few organisms, including yeast, some protozoans, and a prokaryote, & in DNA of mitochondria &chloroplasts
25
Transcription is divided into three sequential processes: List Them
1) initiation
2) elongation
3) termination
26
TRANSCRIPTION: Initiation
1st step of Transcription
- transcription begins when the enzyme RNA polymerase binds to the DNA & unwinds it near the beginning of a gene. --> The binding occurs at a promoter
- Since less E is needed to break 2H-bonds as opposed to 3, the RNA polymerase expends less E opening up the DNA helix if it possesses a high conc of A & T base pairs.
- The part of the gene that is to be transcribed into
RNA = the transcription unit.
27
A promoter is
a nucleotide sequence that lies just before a gene and allows for the binding of RNA polymerase
28
TATA box
- A key element of the promoter in eukaryotes is the TATA box --> a section of DNA with a high percentage
of T & A bases, which is recognized by RNA polymerase & enables the binding of RNA polymerase
- Prokaryotes have a TATAAT sequence instead of a TATA box for this purpose
- rmr since less E is needed to break 2H-bonds as opposed to 3, the RNA polymerase expends less E opening up the DNA helix if it possesses a high conc of A & T base pairs.
29
TRANSCRIPTION: Elongation
2nd step of Transcription
- when RNA polymerase binds to the promoter & opens the DNA double helix, it starts to build the single-stranded RNA molecule
- Unlike DNA polymerase, RNA polymerase does not need a primer to start synthesizing RNA. --> RNA is synthesized in the 5'→3' direction, using the 3'→5' DNA strand as the template strand.
- rmr that the template strand contains the sequence that is complementary to the sequence that is going to be transcribed.
- As RNA pol moves along the DNA, it unwinds the DNA at the forward end of the enzyme.
- RNA polymerase adds nucleotides one at a time to elongate the RNA strand.
- The newly formed RNA pairs temporarily with the template strand, creating a hybrid RNA-DNA double helix.
- Beyond the hybrid region, the RNA detaches from the DNA, and the DNA reforms its double helix.
- when an RNA pol has started transcription & progressed past the beginning of a gene, another one may start producing another RNA molecule if there is room at the promoter.
--> Most genes undergoing transcription have many RNA polymerase molecules spaced closely along them, and each molecule makes an RNA transcription cuz of high demand. --> ex, single red blood cell contains 375 million hemoglobin molecules. The process of making hemoglobin would be very slow if the gene had only one RNA polymerase enzyme
making one mRNA molecule at a time.
30
The coding strand is
The opposite strand of DNA—the strand that is not being copied in RNA transcription = coding strand, since it contains the same base-pair sequence as the new RNA molecule, except uracil replaces thymine
31
TRANSCRIPTION: Termination
3rd step of transcription
- Transcription ends when RNA polymerase encounters a termination sequence.
2 TERMINATION MECHANISMS IN PROKARYOTES
1) termination mechanism involves a protein binding to the mRNA and stopping transcription.
2) the mRNA binding with itself in a hairpin loop and stopping transcription
EUKARYOTE TERMINATION
- 1 termination sequence is a string of As, which r transcribed as a string of Us on the RNA.
- Nuclear proteins bind to the polyuracil site & stop transcription.
- The newly made RNA then dissociates from the DNA template strand. --> Transcription stops, & the RNA
polymerase is free to bind to another promoter region & transcribe another gene
32
Post-transcriptional Modifications: Capping & Tailing
newly transcribed eukaryotic RNA, AKA primary transcript or precursor mRNA (pre-mRNA), is vulnerable to the enzymes & conditions outside the cell nucleus.
- The pre-mRNA must undergo additional modifications before it can exit the nucleus & reach the ribosome.
- 1 modification is A poly(A) tail (50–250 adenine nucleotides) is added to the 3' end by poly-A polymerase one nucleotide at a time. --> This tail improves mRNA stability & efficiency of translation while protecting it from cytosolic RNA-digesting enzymes.
- Another modification is at the beginning of the pre-mRNA transcript, where a 5' cap, consisting of 7 Gs, is added by a different enzyme complex. The 5' cap functions as the initial attachment site for mRNAs to ribosomes, to allow for translation.
- This whole process= capping and tailing
33
A poly(A) tail is
a chain of adenine nucleotides that are added to the 3' end of the pre-mRNA molecule to protect it from
enzymes in the cytosol
34
A 5' cap is
a sequence of 7 Gs that is added to the start of a pre-mRNA molecule; ribosomes recognize this site & use it as the site of initial attachment
35
Post-transcriptional Modifications: Exons & Introns
- The DNA of a eukaryotic gene is composed of coding regions known as exons and non-coding regions known as introns.
- introns r interspersed among exons and are transcribed into pre-mRNAs --> introns do not code
for part of the protein.
--> If left in the mRNA, they would alter the sequence of the amino acids that r used to build the protein.
- This would result in additional amino acids & a protein that would not fold as it should & thus would not function correctly --> thus, introns r deleted & the exons r kept in fully processed mRNA.
- The majority of known eukaryotic genes contain at least one intron, and some contain >60.
- Prokaryote DNA doesn't contain any introns
36
An exon is
a sequence of DNA or RNA that codes for part of a gene
37
An Intron is
a non-coding sequence of DNA or RNA
38
How are introns removed?
- In nucleus, process called mRNA splicing removes introns from pre-mRNAs & joins the exons together.
- mRNA splicing occurs in a spliceosome: a complex formed between pre-mRNA & handful of small ribonucleoproteins called snRNPs.
- snRNPs bind in a particular order to an intron
in the pre-mRNA
- The first snRNPs are those that recognize & form
complementary base pairs with mRNA sequences at the junctions of the intron & adjacent exons.
- Other snRNPs r recruited, causing the intron to loop out & bring the 2 exon ends close together --> At this point, an active spliceosome has been formed, releasing the intron & joining together the 2 exons.
- cutting & splicing r so exact that not a single base of an intron remains in the finished mRNA, & not a single base is removed from the exons.
39
Alternative splicing is
a process that makes diff mRNAs from pre-mRNA
(exons and introns), allowing more than 1 possible polypeptide to be made from a single gene
- Exons can be joined in different combinations, producing various mRNAs from a single gene.
- Alternative splicing mechanism increases the
# & variety of proteins encoded by a single gene.
- 3/4 of all human pre-mRNAs are subjected to alternative splicing.
- In each case, the diff mRNAs that are produced from the parent pre-mRNA are translated to make a family of related proteins with various combos of amino acid sequences.
- Each protein in the family, then, varies in its function. Alternative splicing helps us understand why humans with only about 20 000 genes can make about 100 000 proteins.
- After the final mRNA has been produced, it is ready to leave the nucleus & be translated by a ribosome.
- https://www.youtube.com/watch?v=FAsLzgVHmjQ
- https://docs.google.com/document/d/1fhzDwn1LDRvX5rNqi32z-7VNQDNqxFWYtfkGVp5QY2s/edit?usp=sharing
40
Transcription: Eukaryotes Vs Prokaryotes
LOCATION
Pro: Transcription occurs throughout the cell.
Euk: Transcription takes place in the nucleus.
ENZYMES
Pro: single type of RNA polymerase transcribes all types of genes ( to make all mRNA, rRNA, tRNA)
Euk: Diff RNA polymerases are used to transcribe genes that encode protein (RNA polymerase II) and genes that do not encode protein like rRNA & tRNA (RNA polymerase I, III).
ELONGATION
Pro: Bases are added quickly (15 to 20 nucleotides per second)
Euk: Bases are added slowly (5 to 8 nucleotides
per second)
PROMOTERS
Pro: The promoters are less complex than those in eukaryotes.
Euk: The promoters are immediately upstream of protein-coding genes, & r more complex
TERMINATION
Pro: A protein binds to the mRNA & cleaves it, or the mRNA binds with itself.
Euk: Nuclear proteins bind to the polyuracil site &
terminate transcription.
INTRONS & EXTRONS
Pro: There are no introns.
Euk: There are both introns and exons
PRODUCT
Pro: Transcription results in mRNA ready to be translated into protein by ribosomes.
Euk: Transcription results in pre-mRNA, which
must be modified to protect the final mRNA
from degradation in the cytosol & to remove introns.
41
tRNA
- tRNAs r short RNAs (70–90 nucleotides) with a distinctive cloverleaf structure formed by base-pairing within the molecule. (mRNA is 100s of nucleotides long)
- All tRNAs have regions that base pair with themselves, winding into 4 double-helical segments to form a cloverleaf pattern
- Anticodon: A 3-nucleotide sequence on tRNA that pairs with a codon on mRNA, located at the tip of 1 of the double-helical segments --> Ex, a tRNA that is linked to serine (Ser) pairs with the codon 5'-AGU-3' in mRNA. The anticodon of the tRNA that pairs with this codon is 3'-UCA-5'.
- At other end of the cloverleaf is a region that carries the amino acid that corresponds to the anticodon. (Amino Acid Attachment Site CHATGPT)
42
Recall that 61 of the 64 codons of the genetic code specify an amino acid. Does this mean that we need 61 diff tRNAs to read the different codons?
No
- Francis Crick’s wobble hypothesis proposed that the complete set of 61 codons specify amino acids, but fewer than 61 tRNAs are needed due to the wobble hypothesis:
- Precise pairing occurs at the first two codon nucleotides. --> Ex, UAU & UAC both code for tyrosine. --> If the tRNA’s anticodon is AUA, it can still bind to the codon UAC, despite its complementarity being UAU. Either way, tyrosine is added on.
- Flexibility at the third position allows some tRNAs to recognize multiple codons coding for the same amino acid.
43
Aminoacylation is
AKA “charging” the tRNA
the process by which a tRNA molecule is bound to its
corresponding amino acid
- the amino acid attaches to the 3' end of the tRNA molecule at the amino acid attachment site.
- The finished product, a tRNA linked to its correct amino acid= an aminoacyl–tRNA.
- Aminoacylation is catalyzed by 20 different aminoacyl–tRNA synthetase enzymes, 1 for each of the 20 amino acids.
- The E in the aminoacyl–tRNA eventually drives the formation of the peptide bond that links the amino acids during translation.
44
Ribosomes in protein synthesis
- Ribosomes translate mRNA into polypeptide chains by joining amino acids in a specific sequence dictated by the mRNA.
- A ribosome is made up of 2 diff-sized parts: the large & small ribosomal subunits. Each subunit is made up of a combo of ribosomal RNA (rRNA) & ribosomal proteins
- to fulfill its purpose, it has special binding sites that actively bring together mRNA with aminoacyl-tRNAs
Binding Sites on Ribosomes:
- mRNA Binding Site: is where the mRNA threads through the ribosome.
- A (Aminoacyl) Site: Binds the incoming aminoacyl–tRNA carrying the next amino acid.
- P (Peptidyl) Site: Holds the tRNA carrying the growing polypeptide chain.
- E (Exit) Site: Releases the tRNA after its amino acid has been added to the chain.
45
There are three major stages of translation: List them
1) initiation
2) elongation
3) termination
46
TRANSLATION: Initiating Translation
1st step of Translation
-first stage of protein assembly, where translation begins using mRNA as a template.
- starts when the small & large ribosomal subunits associate with the mRNA.
- A specialized initiator methionine–tRNA (Met–tRNA) pairs with the AUG start codon on the mRNA.
Step 1: The initiator Met–tRNA forms a complex with the small ribosomal subunit.
Step 2: The complex binds to the 5' cap of the mRNA & scans until it finds the first AUG start codon.
Step 3: The large ribosomal subunit binds, completing the ribosome. At the end of initiation, the Met–tRNA is positioned in the P site.
- After the initiator tRNA pairs with the AUG initiator codon, the following stages of translation simply read the nucleotide bases, 3 at a time, on the mRNA.
- cuz each codon consists of 3 bases, a sequence could potentially be read in 3 diff ways, depending on where the ribosome begins. --> The correct pairing of the initiator tRNA with the AUG start codon sets the reading frame, ensuring codons are read in the correct sequence during translation.
47
A reading frame is
a particular system for separating a base pair sequence into readable codons
48
TRANSLATION: Elongating the Polypeptide Chain
- Elongation sequentially adds amino acids to the growing polypeptide chain through a cycle of four steps.
- Step 1: Elongation begins when an initiator tRNA, with its attached methionine, is bound to the P site. The A site is empty.
- Step 2: A second tRNA, with a complementary anticodon and an attached amino acid, binds to the codon in the A site. --> E for this step is provided by GTP hydrolysis.
- the amino acid (Met) is cleaved from the tRNA in the P site and forms a peptide bond with the amino acid on the tRNA in the A site. This bond formation is catalyzed by peptidyl transferase, a ribosomal enzyme. At the end of Step 2, the new polypeptide chain is attached to the tRNA in the A site and an empty tRNA remains at the P site.
- Step 3: the ribosome moves along the mRNA to the next codon. The two tRNAs remain bound to their respective codons, thereby bringing the tRNA with the growing polypeptide to the P site and moving the
empty tRNA to the E site. An appropriate tRNA moves into the A site, and Steps 2 and 3 are repeated. After each repeat, the empty tRNA that was in the P site moves to the E site.
- Step 4: the empty tRNA is released from the ribosome.
49
TRANSLATION: Termination of Protein Synthesis
- Translation switches from the elongation to the termination stage when the A site of a ribosome arrives at one of the stop codons (UAA, UAG, or UGA) on the mRNA.
- A protein release factor will bind to the A site instead of an aminoacyl–tRNA.
- In response, the polypeptide chain is released from
the tRNA at the P site as usual. --> but cuz no amino acid is present at the A site, the freed polypeptide chain is detached from the ribosome
- At the same time, the ribosomal subunits separate & detach from the mRNA. The empty tRNA & the release factor r also released
50
A Polysome is
a complex that is formed when multiple ribosomes attach to the same mRNA molecule in order to facilitate rapid translation
- In both prokaryotes & eukaryotes, multiple ribosomes can translate an mRNA molecule at the same time, thereby increasing the production of crucial proteins --> The complex that is formed is called a polysome
- In eukaryotes, polysomes only form outside the nucleus, in the cytosol.
- In prokaryotes, transcription & translation both occur in the cytosol --> ribosomes have access to mRNA even as it is being made.
--> As a result, protein synthesis can occur at a much higher rate in prokaryotes than in eukaryotes.
--> this also allows prokaryotes to rapidly synthesize proteins in response to changing environmental conditions.
51
Translation in Prokaryotes VS Eukaryotes
LOCATION
Pro: mRNA is translated by ribosomes in the cytosol as it is being transcribed from DNA
Euk: mRNA can only be translated after exiting the nucleus to interact with ribosomes in the cytosol --> some translation occurs in mitochondria & chloroplasts
INITIATION
Pro: mRNA bases pair directly with a ribosomal binding site, just upstream of the start codon --> mRNA 5' cap is involved
Euk: complex of Met–tRNA, with small ribosomal subunits, binds to an mRNA 5' cap and scans until it
encounters the start codon
ELONGATION
Pro: 15 to 20 elongation cycles per second
Euk:1 to 3 elongation cycles per second
TERMINATION
BOTH: stop codon appears & a release factor binds so that the polypeptide is released
POLYSOMES
Pro: mRNA strand can be translated by multiple ribosomes simultaneously, even as it is being transcribed from DNA
Euk: mRNA strand can be translated by multiple ribosomes simultaneously, but only in the cytosol
52
Polypeptide to Protein
- The newly assembled polypeptide is inactive and non-functional immediately after translation.
- The polypeptide chain must fold into the correct three-dimensional shape, which defines its function.
- Multiple processing reactions, carried out by specific enzymes, remove amino acids from the ends or
interior of the chain & may add additional molecules, such as sugars, to the chain.
- These reactions activate the polypeptide, which then folds into its functional shape.
- Also, many proteins are composed of 2 or > polypeptide chains. --> the polypeptides made from a # of diff translation events are processed and then assembled together to form a single functioning protein.
- This process of protein processing, from an inactive to an active state, is one of the many mechanisms that a cell uses to control the expression of its genes
53
Not all proteins are required by all cells at all times. It would be inefficient for a cell to transcribe & translate all its genes at all times. Elaborate
- both prokaryotic & eukaryotic cells regulate gene expression in response to their own life cycles and environmental conditions.
- Ex, human insulin is only required when the glucose
level in the blood is high.
- Similarly, the E. coli enzyme that facilitates the breakdown of lactose is only transcribed & translated when the E. coli bacteria are exposed to lactose.
- The optimal functioning of an organism requires that genes be turned on and off as they are needed. Even though each cell contains the entire genome of an organism, cells know which genes to express & when.
- Intricate systems have evolved to fine-tune gene expression in both prokaryotes & eukaryotes.
54
insulin is
a hormone produced in the pancreas that lowers the blood glucose level by promoting the uptake of glucose by the body cells
55
Housekeeping genes are
proteins that r always needed in a cell, & their genes are continuously transcribed & translated
- these genes regulate processes such as metabolism, growth, & DNA replication & transcription
- The products of other, more specialized genes may be found only in certain types of cells or under
particular environmental conditions.
--> Ex, liver cells require repair enzymes to manage the toxins in the body, & genes that produce hemoglobin molecules r transcribed & translated only in the cells that give rise to red blood cells.
56
Gene expression in prokaryotes is regulated in response to the concentrations of two molecules:
- lactose and tryptophan
- Both of these responses are examples of negative
feedback control
57
Purpose of Lac Operon
- Prokaryotes metabolize lactose, an environmental sugar, as an energy source.
- The lac operon regulates the expression of genes needed for lactose metabolism.
58
The Lac Operon is .... & structure
a cluster of 3 genes that contains the DNA sequences to regulate the metabolism of lactose
- consists of..
- a promoter: the site where DNA transcription begins
- an operator: the sequence of bases that control
transcription,
- & the coding regions for the various enzymes that actually metabolize the lactose. (Structrual Genes CHATGPT)
- Upstream from the operon is a gene that codes for a repressor protein
--> This protein takes cues from the environment (in this case, the conc of lactose within a cell) & regulates the making of lactose-metabolizing proteins. For the lac operon, this protein is = lacI protein/ lac repressor.
- The genes that code for the lac repressor r always transcribed, so the lac repressor is always present within a cell. --> How this protein behaves & the rate of synthesis of the other lac proteins, depends on the conc of lactose in the cell.
59
An operator is
the region in the operon that regulatory factors bind to
60
A repressor protein is
a protein that binds to the operator to repress gene transcription
61
In the absence of lactose...
- lac repressor is active & binds to the operator
- This keeps RNA pol from binding to the promoter region & stops the lactose-metabolizing enzymes from being made
- When lactose is present within a cell, some of it binds to a site on the lac repressor, making it inactive --> inactive lac repressor is unable to bind to the operator & block transcription --> RNA pol is able to bind to the promoter region, and transcription of the lac genes begins.
- The enzymes that metabolize lactose are then made & start to break down the lactose in the cell. --> As the conc of lactose in the cell decreases, the amount of INactivated lac repressor decreases.
- Eventually, the reactivated lac repressor again binds to the operator, stopping transcription.
62
An inducer is
a signal molecule that triggers the expression of an operon’s genes
- Note that the lactose itself acts as an inducer, telling the cell when to make the lactose-metabolizing enzymes
63
The lac operon is known as an inducible operon cuz...
the inducer inactivates the repressor & allows the
gene to be transcribed.
- There is a direct correlation between the amount of lactose in a cell and the rate at which the lac enzymes r made.
- As the conc of lactose in the cell increases or decreases, so too does the transcription of the lac genes.
- This is an important way for the cell to conserve E, by not making proteins when they r not necessary
64
The trp Operon is
- the operon that regulates the production of tryptophan in a cell
- Most prokaryotic cells are able to synthesize tryptophan independently, but they can also take it up
directly if it's available in the environment
- The trp operon has the same structure as the lac operon: a promoter & an operator that precede the genes coding for tryptophan-synthesizing enzymes. There is also a gene that codes for a trp repressor protein.
- This repressor protein is always made (like in the lac operon), but the diff is in how the repressor protein acts to regulate the expression of the tryptophan enzymes.
- Whereas the lac repressor protein is inactivated by a signal molecule, the trp repressor protein is activated in the presence of tryptophan
- When no trytophan available in environment, repressor remains inactive, transcription proceeds, & tryptophan is made. --> RNA pol is able to bind to the promoter region, & the transcription of the genes can proceed.
- When Tryptophan is present in the environment, it acts as a signal molecules & binds to the repressor, activating it. --> the cell can conserve E by using the available tryptophan & stopping the transcription of the genes that code for the enzymes involved in the biosynthesis of tryptophan (amino acid)
- When a signal molecule functions in this way, it= a corepressor: it serves to repress (rather than induce) the expression of a set of genes.
65
A corepressor is
a signal molecule that binds to a regulatory protein to reduce the expression of an operon’s genes
66
Eukaryotic Gene Control Mechanisms Fall into 4 catergories: List Them
- transcriptional (as mRNA is being synthesized)
- post-transcriptional (as mRNA is being processed)
- translational (as the protein is being synthesized)
- post-translational (after the protein has been synthesized)
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Transcriptional Regulation
- Most gene regulation occurs during transcription.
- DNA is wrapped around histone proteins in chromatin, making promoters inaccessible.
- Chromatin must be unwound for transcription to begin.
- 1 type is the promoter is exposed when an activator molecule binds to a sequence that is upstream of the gene’s promoter & signals a protein remodelling complex. --> As a result, the histone core proteins r displaced from the DNA (chromatin remodelling), exposing the promoter.
- In another type, an activator molecule is bound to a regulatory sequence upstream of the gene to be transcribed--> This signals an enzyme that can add an acetyl group (CH3COO–) to histones.
- The addition of the acetyl group to histones loosens their association with DNA, & the promoter is accessible
68
general transcription factors
- To initiate transcription, a series of proteins, called general transcription factors, accumulate on the promoter.
- they bind to the TATA box in the promoter. --> provide a substrate that the RNA pol can bind to & begin transcription
- These proteins & RNA pol to form the transcription initiation complex, establishing a base rate of transcription --> rate can be further altered by adding proteins called activators & repressors, depending on the needs of the cell.
- The activators & repressors (like the regulatory proteins in the lac & trp operons) attach themselves to the promoter to increase or decrease the rate of transcription
69
Methylation
- Another ex of transcriptional regulation
- A methyl group (–CH3) is added to the C bases
in the promoter of a gene, inhibiting transcription.
- This effect is called silencing.
- Methylation is another way to put genes or entire regions of chromosomes “on hold” til required. --> Ex, the genes that code for the production of hemoglobin r in an inactive, methylated state in almost all the body cells. --> but bone marrow cells, which make red blood cells, use specific enzymes to remove the methyl groups & allow transcription
70
An ex of the power of gene methylation is seen in agouti mice.
- Mice whose agouti genes r turned on can look entirely diff in both colour & size, even though they r genetically identical
- On: Mice r yellow, obese, & have a higher risk of cancer & diabetes.
- Off: Mice r small & brown; are in a normal, healthy state (silenced)
71
A # of environmental triggers have been shown to contribute to the agouti gene promoter being methylated or not methylated.
1 suspected trigger= chemical called bisphenol A, which, until recently, was found in many plastic bottles, including baby bottles.
- Researchers exposed pregnant mice to bisphenol A
& watched as more of their offspring developed into yellow, obese mice than would normally be expected.
- These results supported the hypothesis that exposure to bisphenol A results in demethylation, the removal of methyl groups from DNA.
- not all the offspring grew up to be obese. --> Researchers concluded that bisphenol exposure did not guarantee obesity in mice, but simply increased the risk of developing obesity.
- The silencing effect is used by researchers who wish to test the effects of a single gene. Once the coding sequence is located, they can methylate the gene & observe the effect of its absence on the organism they r studying
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Post-transcriptional Regulation
- controls the availability of mRNA molecules to ribosomes
1) ALTERNATIVE SPLICING
- makes diff mRNAs from pre-mRNA by removing diff combos of introns. The remaining exons are spliced together. Depending on which protein is needed by the cell, an intron in one pre-mRNA may be considered an exon in another pre-mRNA & may therefore not be spliced out of the 2nd pre-mRNA transcript. The resulting mRNAs are translated to produce a family of related proteins
2) binding masking proteins to mRNA. When the mRNA is associated with a masking protein, it does not undergo protein synthesis.
- Common in animal eggs, keeping mRNAs inactive until fertilization & embryonic development.
- Translation resumes when other proteins remove the masking proteins.
3) Changing rate of mRNA degradation
- Regulatory molecules, such as hormones, alter the mRNA lifespan.--> Ex, in rats, prolactin extends the half-life of casein mRNA (from 5 hours to 92 hours) to support milk production. -->When a large amount of
casein is needed for milk production, there is an abundant supply of prolactin and
the lifespan of the casein mRNA is extended.
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Translational Regulation
- Occurs during protein synthesis by a ribosome.
- One vital mechanism changes the length of the poly(A) tail of the mRNA molecules. --> Specific enzymes add or delete repeating sequences of A at the ends of the mRNA molecules. This change in the length of the poly(A) tail may increase or decrease the time that is required to translate the mRNA into a protein
- Scientists don't really understand how this mechanism functions, but believe that cell may take cues from the environment or intracellular molecules to adjust the rate at which certain mRNA molecules are translated
74
Post-translational Regulation & list the 3 methods
- occurs after protein synthesis to control the availability of functional proteins.
3 methods are used: processing, chemical modification, & degradation.
75
Post-translational Regulation: processing
- Proteins are synthesized in inactive forms and activated through specific processing mechanisms--> Ex, Proinsulin is processed into active insulin.
- A processing mechanism removes specific sections of the protein and makes it active.
--> The cell can regulate these types of processing mechanisms to control the availability of activated proteins & thus regulate the end product of
certain genes.
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Post-translational Regulation: chemical modification
During chem modification of a protein, certain chem groups that r attached to the protein r added or deleted, affecting its function. -->presence or absence of these chem groups puts the protein “on hold” until it is needed.
- Once environmental & cellular conditions r sufficient, the groups r added or removed & the protein can carry out its function
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Post-translational Regulation: degradation
- Proteins have varying lifespans, regulated by degradation mechanisms.
- Short-lived proteins are tagged with a small
protein called ubiquitin, which is recognized by the degradation mechanisms of the cell.
--> Adding or removing these tags can either shorten or extend the functional life of a protein.
- Degraded proteins are recycled into amino acids for new protein synthesis.
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Controlling Gene Expression: Cancer
- Cancer cells lack the regulatory mechanisms controlling healthy cell growth.
- Telomere Lengthening: Constant telomere elongation enables uncontrolled growth.
- The unchecked growth & indefinite lifespan of cancer cells r result of changes in gene regulation.
- usual mechanisms & signals that allow healthy cells
to express their genes properly have little to no effect on cancerous cells.
- Healthy cells contain a set of genes that code for various proteins that stimulate cell growth.
- In cancerous cells, these genes are mutated to be oncogenes. --> Oncogenes cause the constant
& undifferentiated cell division that creates tumours.
- Note: Mutations in a cell affect only its daughter cells.
- Changes in gene regulation can arise from mutations in the promoters, mutations in the coding regions that affect the functions of the protein, or the introduction of foreign DNA from viruses
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- The probability that a given sequence of DNA has
experienced a mutation increases...
over the lifespan of an organism. --> due to cumulative exposure to mutagens (e.g., radiation, smoke).
80
A Tumour is
a mass of undifferentiated cells that are produced when a cell begins to deviate from normal cell division
- If this mass of cells grows slowly, remains in place,
& does not return once it has been removed, it's = benign tumour. --> are usually not life-threatening.
- If the cells grow uncontrollably, invade surrounding tissue, & begin to affect the functions of the organism, they r= malignant tumours or cancers.--> r more difficult to remove from the body, & measures such as chemotherapy and radiation are required.
81
Genetic mutations are
changes in the DNA sequence, caused by various mechanisms. --> Ex, synthetic chemicals, radiation, incorrect replication, & random mutations can change the structure and function of the genome.
82
Mutations caused by smoking increase the risk of various forms of cancer. ELABORATE
- A region on chromosome 15 is known to play a part in an individual’s susceptibility to developing lung cancer.
- If mutated, this region increases a smoker’s risk of lung cancer by 30 to 80 %, depending on whether the smoker has 1 or 2 copies of the 15q24 susceptibility locus.
83
A susceptibility locus is
a region on a given chromosome where mutations that affect one or more genes r more likely to be present, based on statistical evidence.
84
Small-scale mutations are
mutations that include mutations of an individual base pair, called point mutations, & of small groups of base pairs
85
A point mutation is
a change in a single nucleotide within a gene
- There r several different types of point mutations, including...
* the substitution of one base for another
* the insertion or deletion of a single base pair
* the inversion of two adjoining base pairs
- Small-scale mutations of a small group of base pairs are categorized similarly: the substitution, insertion, or deletion of the group.
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Mutations: A substitution is
the replacement of one base pair in a DNA sequence by another base pair
87
Mutations: An insertion is
the addition of a base pair (small-scale mutation) or larger coding region (large-scale mutation) to a DNA
sequence
88
Mutations: A deletion is
the removal of a base pair (small-scale mutation) or larger coding region (large-scale mutation) from a DNA sequence
89
Mutations: An inversion is
when two adjacent bases trading places (small-scale mutation) or the reversal of a sequence of DNA (large-scale mutation)
90
β-Thalassemia & Point Mutation:
-Cause: A point mutation (substitution or deletion) creates a stop codon at codon 39 of the β-globin gene: a part of normal hemoglobin,146 amino acids in length
-Impact: β-globin, a component of normal hemoglobin, is not synthesized.
- Symptoms: Small, fragile erythrocytes that rupture easily.--> Often requires blood transfusions.
91
A single nucleotide polymorphism is
- AKA SNP
a diff in the DNA between individuals caused by point mutations
- ", population X may have 120 known SNPs in allele Y"
- cuz SNPs are particularly common in non-coding parts of the genome, they r sometimes used in forensics & paternity testing
-
92
The effects of small-scale mutations can range from...
being positive, through having no effect, to being severe.
93
Functionally, small-scale mutations can be categorized into 4 groups: List Them
- missense mutations
- nonsense mutations
- silent mutations
- frameshift mutations
94
A missense mutation is
- a mutation that changes a single amino acid in the coding sequence
- a change of a single base pair or group of base pairs results in the code for a diff amino acid.
- The protein that is made will have a diff sequence & structure, &it may be non-functional or function
differently.
- can be beneficial IF it creates a new, desirable effect.
95
A nonsense mutation is
a mutation that results in a premature stop codon
- occurs when the change of a single base pair or group of base pairs results in a premature stop code in the gene.
- The polypeptide is cut short &, most likely, will be unable to function
96
A silent mutation is
a mutation that does not alter the resulting sequence of amino acids
- occurs when the change in one or more base pairs does not affect the functioning of the gene.
- The mutated DNA sequence codes for the same amino acid as the non-mutated sequence, & the resulting protein is not altered.
97
A frameshift mutation is
a shift in the reading frame resulting in multiple
missense and/or nonsense effects
- occurs when 1 or more nucleotides r inserted into or deleted from a DNA sequence, causing the reading
frame of codons to shift in one direction or the other. - This results in multiple missense and/or nonsense effects.
- The frameshift mutation “shifts” the reading frame by one or more steps, & every amino acid coded for after this mutation is affected.
- Any deletion or insertion of base pairs in multiples of 3 does not cause frameshifts because the reading frame is unaltered.
- Tay-Sachs disease is a result of the insertion of four base pairs
98
Large-Scale Mutations are
mutations that involve multiple nucleotides, genes, or chromosome regions
99
Large-Scale Mutations: Amplification
- AKA gene duplication
-occurs when a gene or group of genes is copied to
multiple regions of chromosomes. --> leads to a larger #of copies of the gene or group of genes, which compounds its effects.
- can create opportunities for new genes with new
functions to evolve. --> The original gene function is retained by one gene, but the copies r subjected to further mutations, which may be selected for by nature.
99
Large-Scale Mutations: Deletions
- Entire coding regions r removed. --> Unless many copies of a gene r available, this large loss of genetic material may negatively affect cell functioning
Examples
- Duchenne Muscular Dystrophy: Deletion of all or part of the dystrophin gene (protein that is vital to skeletal muscle); leads to respiratory muscle weakness and death in early 20s.
- Becker Muscular Dystrophy: Smaller dystrophin gene deletion; results in weaker muscles but near-normal lifespan.
99
Large-Scale Mutations: Chromosomal translocation
- the movement of entire genes or sequences of DNA from one chromosome to another
- Genes or groups of genes move between non-homologous chromosomes --> usually occurs when portions of each chromosome break off & exchange places.
- Can create new genes & polypeptides when coding sequences are translocated adjacent to another
coding sequence.
- some DNA sequences move freely about the genome= transposable elements.
- If transposable elements r inserted near an existing gene sequence, they can enhance, disrupt, or modify the expression of the gene.
100
Large-Scale Mutations: Inversion
- occurs when a portion of a DNA molecule, often containing one or many genes, reverses its direction in the genome.
- does not directly result in the loss of genetic material but if the break occurs in the middle of a coding
sequence, the gene may be compromised.
101
Large-Scale Mutations: trinucleotides & mutations
A trinucleotide= triplet of nucleotides.
-EX of a trinucleotide REPEAT is CAG CAG CAG CAG. --> these repeats r normal.
- Sometimes a mutation occurs, & these repeats become unstable & expand uncontrollably.
- This mutation = trinucleotide repeat expansion --> increases in the # of repeats from one generation to the next.
- Huntington’s disease arises from a trinucleotide repeat.
102
Mutations can be grouped into 2 categories:
- spontaneous mutations
- induced mutations.
- Both spontaneous & induced mutations can take the form of either small-scale or large-scale mutations
- Every subsequent round of cell division can compound the effects of a mutation.
103
A spontaneous mutation is
a mutation that is caused by an error in DNA replication
104
An induced mutation is
a mutation that is caused by an environmental agent, known as a mutagen, that directly alters the DNA within a cell.
- A mutagen can enter the cell nucleus & directly access the genome.
- 2 of the most common forms of mutagens are: chemicals and radiation
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Mutagens: A chemical mutagen is
any chemical agent that can enter the cell nucleus & chemically alter the structure of the DNA
- CO in exhaust fumes & tobacco smoke, acts as a mutagen & is linked to various cancers
- some like nitrous acid, can modify individual nucleotides so that the nucleotides resemble other base pairs. --> This confuses the replication machinery & results in inaccurate copying
- Others cause mutations by mimicking a DNA nucleotide.
---> Ex, individual nucleotides that have bonded with benzene molecules can be added to a replicating DNA strand. --> can alter the shape of the DNA & negatively affect replication.
--> Ex, ethidium bromide, used widely in biotechnology research & is similar in structure to a nitrogenous base. can insert itself between the strands of the double helix & alter the structure of the molecule. --> This may lead to inaccuracies in replication & damage future gens of cells.
106
Mutagens: Radiation
- Electromagnetic radiation can cause mutations
1) Lower-Energy Radiation (e.g., UVB Radiation) causes non-homologous end joining, forming bonds between adjacent nucleotides on DNA strand,
-->Creates kinks in the DNA backbone, disrupting replication & transcription.
--> Associated with certain types of skin cancer.
2) Higher-energy radiation, AKA ionizing radiation, can strip molecules of e-s & break DNA bonds, causing rearrangement or deletion of large portions of chromosomes.
- X-rays: Prolonged exposure linked to tumour development; protective measures like lead vests are used.
- Some of highest-energy radiation= from gamma rays & radioactive decay products of nuclear material.
- Resident children of near the former nuclear reactor at Chernobyl have suffered from various birth defects, & the 2011 tsunami-induced nuclear meltdowns in Japan have raised ongoing public health concerns.
107
it is important to remember that mutations
are ultimately responsible for the variety of _____________ & _____________
Individuals, species
108
he majority of mutations are ___________. Elaborate
neutral
- Ex, silent mutations have no effect on an organism.
- cuz most of our DNA (90 %) is non-coding, changes in the non-coding regions are almost always neutral and unnoticed. --> more likely to be true in eukaryotes, which usually have a lot of non-coding DNA, & less in prokaryotes.
- Prokaryote DNA is mostly coding sequences, so a mutation is much more likely to be harmful than neutral or positive
- A mutation is only beneficial or negative in a given time and situation --> rmr sickle cell anemia gives resistance to malaria
109
mutation in the gene filaggrin
- Recently, researchers discovered that a mutation in the gene filaggrin increases the risk of having a peanut allergy.
- 1in 5 peanut allergy sufferers have the mutation.
- In our current environment, we view the peanut allergy as a disadvantage.
- the key point is not to consider mutations as inherently good or bad, but simply as a change that can lead to the evolution of life.
110
Random animal facts
- The sweat glands of a cow are in its nose.
- Bees can see ultraviolet light.
- Bee-pollinated flowers look different in UV light than they do in the human visual spectrum
111
All diff species r the result of changes
in sequence, length, and organization of a molecule that is composed of four nitrogenous bases.
112
The genetic material of each and every species has the same _______________________________
organizational structure
113
Human DNA is found in the nucleus of human cells in duplicate. ELABORATE
Each nucleus has 2 copies of the 22 autosomal chromosomes &1pair of sex chromosomes (XX or XY). - Each autosomal chromosome is #ed by size from 1 to 22,1 being largest.
- Each gene has 2 copies= alleles, that may be identical or different. --> Each allele of a given gene resides at the same locus on both homologous chromosomes.
114
the Human Genome Project
- undertaken in 1990 to determine the sequence of the 3 billion base pairs that make up the human genome.
- >200 scientists collaborated to sequence the genetic code.
- Knowing the sequence of the nitrogenous bases for is a monumental achievement.
- Even so, the size of a genome or the total # of genes in the genome reveals little about an organism’s
complexity.
- Scientists are now working toward a comprehensive understanding of the patterns in our genome organization & the way that these patterns produce the proteins required for human life
115
Genome organization refers to...
the sequential organization of the genome.
- Eukaryotic genomes are composed of coding and non-coding regions.
- Composed of coding (<2%) and non-coding regions (~98%).
- Introns (non-coding regions within genes) occupy ~24% of the genome.
- ~75% of the genome is intergenic DNA (between genes), with regulatory sequences and non-functional repetitive DNA.
--> Some of this intergenic DNA is functional & includes regulatory sequences, such as promoters --> However, much of it, more than 50 % of the total genome, consists of repeated sequences that are non-functional
116
variable number tandem repeats (VNTRs) are
- AKA microsatellites
non-coding, repeating DNA sequences that vary in length between homologous chromosomes & between individuals
- The lengths of VNTRs vary, as do their positions in the genome.
- The # of these non-coding regions in an organism’s genome is proportional to the complexity of the organism.
117
Long repetitive non-coding DNA sequences r used as a defence mechanism against the shortfalls of DNA replication
- Telomeres
- Repetitive DNA sequences are also found near the centromeres & play a role during cell division
118
LINEs are
- AKA long interspersed nuclear elements
repetitive DNA sequences, about 6500 bp in length on
average, interspersed throughout the genome
- The origin and function of LINEs and SINEs are not yet clear.
119
SINEs are
- AKA short interspersed nuclear elements
repetitive DNA sequences, about 500 bp in length on
average, interspersed throughout the genome
- The origin and function of LINEs and SINEs are not yet clear.
120
A significant portion of the genomes of many, if not all, species is made up of DNA that originated from ancient viral infections. ELABORATE
- When certain viruses infect cells, they insert copies of their genetic code at random into the host cell genome.
- Often this inserted DNA is not active and behaves as simple non-coding sequences.
--> If these insertions are passed on from gen to gen, they have the potential to spread & become part of the shared genome of entire species.
121
A transposon is
a small segment of DNA that can move to a different position in the genome & insert itself into diff chromosomes.
122
A pseudogene
a sequence of DNA that is similar to an existing gene but does not code for proteins
- differs in certain base pairs, which make it unable to code for proteins
- thought to be mutated versions of older genes, in other words, vestigial genes that have lost their evolutionary adaptive value.
- remain in the genome but serve no function
- Ex, n. Dolphins possess hundreds of pseudogenes that are mutated versions of genes originally associated with the sense of smell
123
The quantity and particular sequence of _____________________________ are responsible for the diversity among organisms.
both coding and non-coding regions
- Ex, the mammalian genome is about 300 times the size of the yeast genome but acc # of genes in each organism differs by only a factor of 4.
-the complexity of a species does not depend on the total number of base pairs or genes within a given genome (its size) but on the organization of the genes & how they are regulated (its content).
124
comparative genomics is
the study of the organization, functions, & relationships of the genomes of different species
- provided us with some surprising results.
---> 70 % of sea urchin genes have a human gene counterpart, whereas only 40 % of fruit fly genes do.
-->section of the sea urchin’s genome that codes for its immune system is more complex than the immune system section of the human genome. --> cuz the sea urchin can live up to 100 years, its immune system could shed some light on our understanding of the evolution of the human immune system
- Comparative genomics also includes the study of individual sequences of DNA.
125
The Government of Ontario invests about _____million each year to develop, promote, and administer the flu shot and ensure the health of Ontarian. Why?
$40
- Most healthy adults= experience mild symptoms, yet respiratory viruses can be a serious threat to children and the elderly.
- The flu is caused by the influenza virus
- Each year, the flu is caused by a different strain of the virus, so a different vaccine must be developed.--> Some strains r more virulent (infectious) than others, & some affect people worldwide (pandemics).
126
Viruses are not technically considered to be alive, due to ...
their inability to replicate on their own as other living organisms do.
-but cuz they can replicate themselves, they r classified in the same way as living organisms.
127
In addition to the capsid, some viruses r surrounded by an____________.
envelope.
- The envelope is created when a virus leaves a host cell & part of the host cell membrane wraps around the virus.
128
Over ______species of viruses have been classified, and they vary widely in their size, genomic structure (RNA or DNA), the way that they replicate their genome, and
their preferred host
4000
129
Why does influenza have so many strains?
only 8 genes, which code for 11 proteins.
- The virus’s polymerase enzymes show a very high rate of replication error.
- This accounts for the large number of mutations that occur, and therefore the large number of strains. As a result, the virus changes from one flu season to the next.
130
Usually, a virus infects only...
a single species or a few closely related species.
- A virus may even infect only one organ system or a single tissue or cell type in its host.
131
A retrovirus is
a virus that uses reverse transcriptase for replication
- basically a virus that has RNA instead of DNA as its hereditary material
- One of the most widely studied retroviruses is the human immunodeficiency virus (HIV), which has killed about 25 million people worldwide.
132
reverse transcriptase is
a viral enzyme that uses RNA as a template strand to
synthesize complementary DNA
- When a retrovirus infects a host cell, it injects its RNA
genome along with the reverse transcriptase.
- Using the cell’s supply of materials, the reverse transcriptase copies the viral RNA to make a complementary molecule of single-stranded DNA
- the reverse transcriptase directs the synthesis
of a second DNA strand that is complementary to the first strand.
- The enzyme integrase, which is put to the host cell along with the RNA, incorporates the reverse-transcribed double-stranded DNA into the host cell genome.
- Transcription of the viral DNA results in the production of viral RNA.
- This RNA can serve as the genome for new viruses & can also be translated to produce viral proteins.
- The manipulation of the host’s own cellular machinery is what allows the virus to have such a simple structure & yet be so effective at infection.
133
A viral vector is
a virus that is used to transfer the DNA from a donor to a host
- The ability of a virus to enter a cell and use the cell’s replication enzymes provides scientists with a method for inserting new genetic material into an existing cell’s genome --> Ex, the human gene for insulin has been inserted into the nucleus of safflower seeds
134
Transduction is
the process of inserting genetic material into a cell or bacterium using a viral vector
- used since 1960s
- It is now being developed for therapeutic purposes
- Researchers remove the harmful genetic material from the virus & replace it with the desired genetic material.
- Retroviruses, adenoviruses, & herpes viruses are widely used for transduction.
- The original viral genome and the new genetic material must be engineered so they do not damage the host cell.
- The modified virus must be highly stable to ensure the successful uptake of the new genes.
