Insta-Review�Unit 6
Courtesy of @APBioPenguins
6.1: DNA and RNA Structure
6.1: DNA and RNA Structure
IST-1.K.1
DNA, and in some cases RNA, is the primary source of heritable information.
IST-1.K.2
Genetic information is transmitted from one generation to the next through DNA or RNA—
a. Genetic information is stored in and passed to subsequent generations through
DNA molecules and, in some cases, RNA molecules.
b. Prokaryotic organisms typically have circular chromosomes, while eukaryotic organisms typically have multiple linear chromosomes.
6.1: DNA and RNA Structure
IST-1.K.3
Prokaryotes and eukaryotes can contain plasmids, which are small extra chromosomal, double-stranded, circular DNA molecules.
IST-1.L.1
DNA, and sometimes RNA, exhibits specific nucleotide base pairing that is conserved
through evolution: adenine pairs with thymine or uracil (A-T or A-U) and cytosine pairs with guanine (C-G)—
a. Purines (G and A) have a double ring structure.
b. Pyrimidines (C, T, and U) have a single ring structure.
What is the primary source of genetic information?
What is the primary source of genetic information?
Prokaryotic DNA is...
Prokaryotic DNA is...
Eukaryotic DNA is...
Eukaryotic DNA is...
How do the number of origins of replication differ and why?
How do the number of origins of replication differ and why?
Prokaryotic cells have ONE origin of replication, and Eukaryotic cells have MULTIPLE origins of replication. Prokaryotic cells have single circular DNA strands, so it would be more efficient to start at one location and move around the entire circle to make two DNA strands. Eukaryotic cells have multiple linear DNA strands, so they have multiple origins of replication to increase efficiency and allow for DNA to replicate quickly.
What is a plasmid?
What is a plasmid?
Small, extra chromosomal, double stranded, circular DNA molecule.
All cells have plasmids?
All cells have plasmids?
Plasmids can provide genetic variation to prokaryotes?
Plasmids can provide genetic variation to prokaryotes?
In RNA, adenine pairs with...
In RNA, adenine pairs with...
In DNA, adenine pairs with...
In DNA, adenine pairs with...
In RNA or DNA, cytosine pairs with...
In RNA or DNA, cytosine pairs with...
What is a purine?
What is a purine?
Which bases are purines?
Which bases are purines?
What are pyrimidines?
What are pyrimidines?
Which bases are pyrimidines?
Which bases are pyrimidines?
6.2 Replication
6.2: Replication
IST-1.M.1
DNA replication ensures continuity of hereditary information—
a. DNA is synthesized in the 5’ to 3’ direction.
b. Replication is a semiconservative process—that is, one strand of DNA
serves as the template for a new strand of complementary DNA.
c. Helicase unwinds the DNA strands.
d. Topoisomerase relaxes supercoiling in front of the replication fork.
e. DNA polymerase requires RNA primers to initiate DNA synthesis.
f. DNA polymerase synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand.
g. Ligase joins the fragments on the lagging strand.
Which direction is DNA read for DNA replication?
Which direction is DNA read for DNA replication?
Which direction is DNA synthesized in DNA replication?
Which direction is DNA synthesized in DNA replication?
What is found at the 3' end and 5' ends of DNA?
What is found at the 3' end and 5' ends of DNA?
5' end: phosphate
3' end: hydroxyl
Students a couple years ago would say the DNA is synthesized in the order of "P-OH".
How is DNA replicated?
How is DNA replicated?
What does it mean to say the DNA replicates�semiconservative?
What does it mean to say the DNA replicates�semiconservative?
The parent strand of DNA separates to provide a template strand for base pairing. The two separate strands base pair to synthesize the daughter strand. Each daughter strand has one parent strand (old) and one daughter strand (new) so the original sequence is conserved.
Describe the experiment from Meselson & Stahl that proved semiconservative
Describe the experiment from Meselson & Stahl that proved semiconservative
They grew bacteria in the presence of nitrogen 15 (heavy nitrogen). Then put the bacteria into presence of nitrogen 14 (light nitrogen). After one round of replication, the DNA was a hybrid of heavy and light nitrogen. After two rounds of replication, there was a hybrid of heavy & light and a light strand.
Enzymes responsible for sealing phosphodiester link
Enzymes responsible for sealing phosphodiester link
Enzymes responsible for relieve strand of double helix
Enzymes responsible for relieve strand of double helix
Enzymes responsible for breaking H bonds between strands
Enzymes responsible for breaking H bonds between strands
Enzymes responsible for synthesis of new DNA
Enzymes responsible for synthesis of new DNA
DNA polymerase can start replication independently
DNA polymerase can start replication independently
What does DNA Polymerase require to initiate replication?
What does DNA Polymerase require to initiate replication? �
An open 3' end. To initiate replication, primase will make an RNA primer. This primer has the open 3' end that is required for DNA polymerase for replication. The RNA will be replaced later with DNA by another type of DNA polymerase.
DNA is...
DNA is...
What is meant by leading and lagging strand?
What is meant by leading and lagging strand?
Leading is synthesized continuous with replication fork with the replication fork while lagging strand is synthesized discontinuously. This occurs due to the antiparallel nature of DNA. The two strands when pulled apart only have one strand that can be read 3' to 5'(leading strand's template). Due to this, the lagging strand needs to move away from the replication fork so it can read the template strand in 3' to 5' direction.
Which enzyme connects the Okazaki fragments (lagging)
Which enzyme connects the Okazaki fragments (lagging)
6.3: Transcription and RNA Processing
6.3: Transcription and RNA Processing
IST-1.N.1
The sequence of the RNA bases, together with the structure of the RNA molecule, determines RNA function—
a. mRNA molecules carry information from DNA to the ribosome.
b. Distinct tRNA molecules bind specific amino acids and have anti-codon sequences that base pair with the mRNA. tRNA is recruited to the ribosome during translation to generate the primary peptide sequence based on the mRNA sequence.
c. rRNA molecules are functional building blocks of ribosomes.
6.3: Transcription and RNA Processing
IST-1.N.2
Genetic information flows from a sequence of nucleotides in DNA to a sequence of bases in an mRNA molecule to a sequence of amino acids in a protein.
IST-1.N.3
RNA polymerases use a single template strand of DNA to direct the inclusion of bases in the newly formed RNA molecule. This process is known as transcription.
6.3: Transcription and RNA Processing
IST-1.N.4
The DNA strand acting as the template strand is also referred to as the noncoding strand, minus strand, or antisense strand. Selection of which DNA strand serves as the template strand depends on the gene being transcribed.
IST-1.N.5
The enzyme RNA polymerase synthesizes mRNA molecules in the 5’ to 3’ direction by reading the template DNA strand in the 3’ to 5’ direction.
6.3: Transcription and RNA Processing
IST-1.N.6
In eukaryotic cells the mRNA transcript undergoes a series of enzyme-regulated modifications—
a. Addition of a poly-A tail.
b. Addition of a GTP cap.
c. Excision of introns and splicing and retention of exons.
d. Excision of introns and splicing and retention of exons can generate different versions of the resulting mRNA molecule; this is known as alternative splicing.
Which RNA functions as site of protein synthesis?
Which RNA functions as site of protein synthesis?
Which RNA functions to bring amino acids to the ribosome?
Which RNA functions to bring amino acids to the ribosome?
Which RNA is the transcript from DNA template?
Which RNA is the transcript from DNA template?
Which RNA has an anticodon that pairs with codon?
Which RNA has an anticodon that pairs with codon?
Which RNA has the codons sequence for translation?
Which RNA has the codons sequence for translation?
Big picture, how do the three different RNA molecules work together?
Big picture, how do the three different RNA molecules work together?
mRNA is the product of transcription in the nucleus. It brings the "message" from the nucleus about the order for protein synthesis. mRNA binds to the small subunit of the ribosome. TRNA brings the amino acids The tRNA has an anticodon at one end that base pairs with the codons on the mRNA and an amino acid on the other end. It binds to the large subunit of the ribosome. RRNA is the site of protein synthesis. The rRNA binds with protein to form the ribosome.
How does the location of transcription differ in prokaryotes vs. Eukaryotes?
How does the location of transcription differ in prokaryotes vs. Eukaryotes?
Due to the absence of a nuclear envelope, transcription occurs in the cytosol (nucleoid) of the prokaryote.
Due to the presence of a nuclear envelope, transcription occurs in the nucleus of an eukaryote.
Which enzyme is responsible for transcription?
Which enzyme is responsible for transcription?
What is the name of the strand read for transcription?
What is the name of the strand read for transcription?
(Note: you should know all 4 of these terms as they are directly in the CED and can be used in the prompt.)
In transcription, which direction is DNA read?
In transcription, which direction is DNA read?
In transcription, which direction is RNA made?
In transcription, which direction is RNA made?
Describe the three changes made during post-transcription
Describe the three changes made during post-transcription
Function of 5' Cap...
Function of 5' Cap...
Function of Poly A tail...
Function of Poly A tail...
What process allows the synthesis of different proteins from same DNA
What process allows the synthesis of different proteins from same DNA
Alternative RNA splicing
6.4: Translation
6.4: Translation
IST-1.O.1
Translation of the mRNA to generate a polypeptide occurs on ribosomes that are present in the cytoplasm of both prokaryotic and eukaryotic cells and on the rough endoplasmic reticulum of eukaryotic cells.
IST-1.O.2
In prokaryotic organisms, translation of the mRNA molecule occurs while it is being transcribed.
IST-1.O.3
Translation involves energy and many sequential steps, including initiation, elongation, and termination.
6.4: Translation
IST-1.O.4
The salient features of translation include—
a. Translation is initiated when the rRNA in the ribosome interacts with the mRNA at the start codon.
b. The sequence of nucleotides on the mRNA is read in triplets called codons.
c. Each codon encodes a specific amino acid, which can be deduced by using a genetic code chart. Many amino acids are encoded by more than one codon.
d. Nearly all living organisms use the same genetic code, which is evidence for the common ancestry of all living organisms.
6.4: Translation
IST-1.O.4
The salient features of translation include—
e. tRNA brings the correct amino acid to the correct place specified by the codon on the mRNA.
f. The amino acid is transferred to the growing polypeptide chain.
g. The process continues along the mRNA until a stop codon is reached.
h. The process terminates by release of the newly synthesized polypeptide/protein.
6.4: Translation
IST-1.O.5
Genetic information in retroviruses is a special case and has an alternate flow of information: from RNA to DNA, made possible by reverse transcriptase, an enzyme that copies the viral RNA genome into DNA. This DNA integrates into the host genome and becomes transcribed and translated for the assembly of new viral progeny.
What is the function of the ribosomes?
What is the function of the ribosomes?
Identify two locations ribosomes are found in eukaryotic cells
Identify two locations ribosomes are found in eukaryotic cells
Transcription & Translation (T&T) are simultaneously completed in a prokaryote
Transcription & Translation (T&T) are simultaneously completed in a prokaryote
Why does transcription and translation take place simultaneously in prokaryotic cell?
Why does transcription and translation take place simultaneously in prokaryotic cell?
The absence of the nuclear membrane allows the ribosomes to gain access to the mRNA as it is synthesized.
Which describes initiation of translation?
Which describes initiation of translation?
What is the start codon?
What is the start codon?
Describe steps in elongation phase of translation
Describe steps in elongation phase of translation
Polypeptide is attached to tRNA at the P site
THEN REPEAT
One codon codes for multiple amino acids...
One codon codes for multiple amino acids...
One amino acid is coded by multiple codons...
One amino acid is coded by multiple codons...
What does AGU code for?
What does AGU code for?
Prokaryotes can synthesize human insulin...
Prokaryotes can synthesize human insulin...
What does it tell us that prokaryotes are able to synthesize human insulin?
What does it tell us that prokaryotes are able to synthesize human insulin?
Common ancestry of all living things because of common genetic code among all living things.
Which is not a stop codon?
Which is not a stop codon?
What is added when the stop codon is reached
What is added when the stop codon is reached
HIV is a retrovirus. What does that mean?
HIV is a retrovirus. What does that mean?
Retroviruses have an RNA genome. They use the enzyme reverse transcriptase to catalyze the synthesis of DNA from their RNA template for insertion in host DNA.
6.5
6.5: Regulation of Gene Expression
6.5: Regulation of Gene Expression
IST-2.A.1
Regulatory sequences are stretches of DNA that interact with regulatory proteins to control transcription.
IST-2.A.2
Epigenetic changes can affect gene expression through reversible modifications of DNA or histones.
6.5: Regulation of Gene Expression
IST-2.A.3
The phenotype of a cell or organism is determined by the combination of genes that are expressed and the levels at which they are expressed—
a. Observable cell differentiation results from the expression of genes for tissue specific proteins.
b. Induction of transcription factors during development results in sequential gene expression.
6.5: Regulation of Gene Expression
IST-2.B.1
Both prokaryotes and eukaryotes have groups of genes that are coordinately regulated—
a. In prokaryotes, groups of genes called operons are transcribed in a single mRNA
molecule. The lac operon is an example of an inducible system.
b. In eukaryotes, groups of genes may be influenced by the same transcription factors to coordinately regulate expression.
Describe the effect of DNA methylation
Describe the effect of DNA methylation
DNA methylation involves binding methyl groups to the DNA. This causes the strand to condense which will inhibit transcription (so decreases gene expression)
Describe the effect of histone acetylation
Describe the effect of histone acetylation
Firstly, histones are the proteins that DNA wraps around to condense.
The acetylation decreases the binding between DNA and histone which causes the DNA to loosen. This increases transcription or stimulates gene expression.
What are the transcription factors?
What are the transcription factors?
All somatic (body) cells have the same genetic information
All somatic (body) cells have the same genetic information
If all the cells have the same DNA how are your cells so different?
If all the cells have the same DNA how are your cells so different?
Cell differentiation
The cells have different transcription factors/activators which will enhance transcription of certain genes.
What types of cells have operons?
What types of cells have operons?
What are three components of an operon?
What are three components of an operon?
What types of cells have operons?
What types of cells have operons?
6.6: Gene Expression and Cell Specialization
6.6: Gene Expression and Cell Specialization
IST-2.C.1
Promoters are DNA sequences upstream of the transcription start site where RNA polymerase and transcription factors bind to initiate transcription.
IST-2.C.2
Negative regulatory molecules inhibit gene expression by binding to DNA and blocking
transcription.
6.6: Gene Expression and Cell Specialization
IST-2.D.1
Gene regulation results in differential gene expression and influences cell products and
function.
IST-2.D.2
Certain small RNA molecules have roles in regulating gene expression.
What is the function of the promoter?
What is the function of the promoter?
Location for RNA polymerase to bind.
What is the function of RNA Polymerase?
What is the function of RNA Polymerase?
How do transcription factors affect transcription?
How do transcription factors affect transcription?
They regulate transcription/gene expression. They can bind to enhance the binding of RNA polymerase.
I explain it like a baseball/softball glove. When you catch a ball, you would rather catch it in your glove with TWO hands instead of bare handling it. Why? It's more stable. The transcription factors create a "secure" fit for the RNA polymerase to get started
What are siRNA?
What are siRNA?
Describe what is the function of siRNA
Describe what is the function of siRNA
Describe the mechanism involved with miRNA
Describe the mechanism involved with miRNA
6.7: Mutations
6.7: Mutations
IST-2.E.1
Changes in genotype can result in changes in phenotype—
a. The function and amount of gene products determine the phenotype of organisms.
i. The normal function of the genes and gene products collectively comprises the
normal function of organisms.
ii. Disruptions in genes and gene products cause new phenotypes.
6.7: Mutations
IST-2.E.2
Alterations in a DNA sequence can lead to changes in the type or amount of the protein produced and the consequent phenotype. DNA mutations can be positive, negative, or neutral based on the effect or the lack of effect they have on the resulting nucleic acid or protein and the phenotypes that are conferred by the protein.
IST-4.A.1
Errors in DNA replication or DNA repair mechanisms, and external factors, including radiation and reactive chemicals, can cause random mutations in the DNA—
a. Whether a mutation is detrimental, beneficial, or neutral depends on the environmental context.
b. Mutations are the primary source of genetic variation.
6.7: Mutations
IST-4.A.2
Errors in mitosis or meiosis can result in changes in phenotype—
a. Changes in chromosome number often result in new phenotypes, including sterility caused by triploidy, and increased vigor of other polyploids.
b. Changes in chromosome number often result in human disorders with developmental limitations, including Down syndrome/ Trisomy 21 and Turner syndrome.
6.7: Mutations
IST-4.B.1
Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected for by environmental conditions—
a. The horizontal acquisitions of genetic information primarily in prokaryotes via
transformation (uptake of naked DNA), transduction (viral transmission of genetic
information), conjugation (cell-to-cell transfer of DNA), and transposition
(movement of DNA segments within and between DNA molecules) increase variation.
6.7: Mutations
IST-4.B.1
Changes in genotype may affect phenotypes that are subject to natural selection. Genetic changes that enhance survival and reproduction can be selected for by environmental conditions—
b. Related viruses can combine/recombine genetic information if they infect the same host cell.
c. Reproduction processes that increase genetic variation are evolutionarily conserved and are shared by various organisms.
What are mutations?
What are mutations?
Changes in the DNA sequence or the DNA quantity in a cell.
Which mutation results in a change in the amino acid?
Which mutation results in a change in the amino acid?
Which mutation results in no change in the amino acid?
Which mutation results in no change in the amino acid?
Which mutation results from +/- one nucleotide base?
Which mutation results from +/- one nucleotide base?
Frameshift mutation in what area causes most damage?
Frameshift mutation in what area causes most damage?
How does a heterozygote and homozygous dominant produce same phenotype?
How does a heterozygote and homozygous dominant produce same phenotype?
The single dominant allele produces enough enzyme/protein products to produce the desired phenotypic result.
What is the primary source of genetic variation?
What is the primary source of genetic variation?
Which of the following is the cause of Trisomy 21?
Which of the following is the cause of Trisomy 21?
What phase of meiosis is cause of nondisjunction? Describe nondisjunction.
What phase of meiosis is cause of nondisjunction? Describe nondisjunction.
Anaphase I or II
Nondisjunction involves the chromatids or homologous chromosomes not separating during anaphase. This results in a gamete with an additional chromosome or missing a chromosome.
Triploid organisms are sterile (unable to reproduce)
Triploid organisms are sterile (unable to reproduce)
Why are triploid organisms sterile?
Why are triploid organisms sterile?
Unable for homologous chromosomes to pair up during meiosis.
(Triploid is three sets, how can you get paired off with three)
Which enzyme has proofreading capabilities?
Which enzyme has proofreading capabilities?
Which is responsible for halting DNA replication because of error?
Which is responsible for halting DNA replication because of error?
In disease with too many copies of genes (Huntington's)...
In disease with too many copies of genes (Huntington's)...
Involved in cru de crit where chromosome is shorter
Involved in cru de crit where chromosome is shorter
Involved in down syndrome without nondisjunction
Involved in down syndrome without nondisjunction
What is horizontal transmission of traits?
What is horizontal transmission of traits?
Transmission of traits NOT from parent-progeny
Cell-to-cell transmission?
Cell-to-cell transmission?
Movement of DNA between or within segmented?
Movement of DNA between or within segmented?
Viral transmission of traits
Viral transmission of traits
Uptake naked DNA
Uptake naked DNA
What type of virus is able to insert its genome into host genome?
What type of virus is able to insert its genome into host genome?
Retrovirus
Viruses like HIV have an RNA genome. They can use reverse transcriptase to make a complement DNA strand then inserts in genome to become a pro virus.
6.8: Mutations
6.8: Biotechnology
IST-1.P.1
Genetic engineering techniques can be used to analyze and manipulate DNA and RNA—
a. Electrophoresis separates molecules according to size and charge.
b. During polymerase chain reaction (PCR), DNA fragments are amplified.
c. Bacterial transformation introduces DNA into bacterial cells.
d. DNA sequencing determines the order of nucleotides in a DNA molecule
Which DNA tech separates fragments by size/charge
Which DNA tech separates fragments by size/charge
Why does the DNA move towards positive end?
Why does the DNA move towards positive end?
Which fragments travel farther>
Which fragments travel farther>
What cuts the DNA prior to running gel electrophoresis?
What cuts the DNA prior to running gel electrophoresis?
Minimum restriction sites for ECO on plasmid to get this
Minimum restriction sites for ECO on plasmid to get this
Which suspect was at crime scene?
Which suspect was at crime scene?
Which DNA tech is responsible for multiple copies of a gene?
Which DNA tech is responsible for multiple copies of a gene?
What does PCR stand for?
What does PCR stand for?
Polymerase Chain Reaction
PCR uses a specific type of polymerase, why and where does it come from?
PCR uses a specific type of polymerase, why and where does it come from?
PCR involves a heating up then cooling cycle. Proteins (polymerase) denature in high temperatures so heat resistant polymerase from thermophile prokaryotes is needed to allow the enzymes to remain functional after heating phase.
What is the function of the heating process in PCR?
What is the function of the heating process in PCR?
Which DNA tech involves adding plasmid to prokaryote?
Which DNA tech involves adding plasmid to prokaryote?
Plate has non transformed bacteria& no antibiotics
Plate has non transformed bacteria& no antibiotics
Why no growth on plate II?
Why no growth on plate II?
Bacteria is not transformed and there is antibiotic in the agar which restricts growth.
What is function of plates I and III?
What is function of plates I and III?
Control:
Positive control- you are verifying that the bacteria is viable. You need to be sure that the bacteria would grow in the absence of the antibiotic to know that the antibiotic killed non-resistant bacteria (explains plates II and IV)
If plasmid also had the gene to synthesize insulin...�Which plate has the highest % of insulin producing bacteria?
If plasmid also had the gene to synthesize insulin...�Which plate has the highest % of insulin producing bacteria?