MCAT BIO CH. 4 PART 1 Flashcards
What are DNA and RNA?
Nucleic acids
What is the building block of DNA?
What is dATP?
Deoxyadenosine 5’ triphosphate
What are nucleotides built from?
What are purines and pyrimidines?
What is a nucleoside? What is a nucleotide?
- A ribose or deoxyribose with a purine or pyrimidine linked to the 1’ carbon
What is a nucleotide?
- Phosphate esters of nucleosides with phosphate groups joined to the ribose ring by the 5’ hydroxy group
What is a NTP?
Nucleoside triphosphate, NTP: nucleotide contain three phosphate residues
What is the backbone of the DNA? Why?
The sugar and phosphate portion of the nucleotide
What are polynucleotide?
Nucleotides covalently linked in a chain by phosphodiester bonds
Where is the phosphodiester bond based on nucleotides?
3’ hyroxy group of one of the deoxyribose and the 5’ phosphate group of the next deoxyribose
What if the nucleotide contains the phosphate residues?
dNTP
What is an oglionucleotide?
What is a polynucleotide?
What is the written first in the polynucleotide chain?
What is the Watson-Crick Model of DNA Structure?
How is the orientation of the double stranded DNA?
Antiparallel orientation
What does antiparellel orientation mean?
The 5’ end of one chain is paired with the 3’ nd of the other
Where are the hydrogen bonds located based on the double stranded DNA?
H-bonds in ds-DNA are between the bases on adjacent chains
How do the H-bonds pair up in the double stranded DNA? What does this symbolize?
How many H bonds between A-T? What about G-C?
The GC base pair takes up more room in the DNA double helix. T/F
Two chains of DNA are said to be complimentary based on what…?
If the bases in each strand can hydrogen bond when the strands are orientedin an antiparallel fashion
What is annealing or hybridization?
What is melting or denaturation?
What is a right-handed double helix?
What are the interior and exterior components of the right-handed double helix?
Interior: The bases
Exterior: Ribose/Phosphate backbone
What is the double helix stabilized by?
What is a genome?
The sum total of an organism’s genetic information
What do prokarytoric genomes have based on chromosomes?
The size difference in higher eukaryotic genomes is the result of what…?
What enzyme do prokaryotes use to compact the DNA?
What does DNA Gyrase do?
How does DNA Gyrase function?
What is the resulting strucure caused by DNA Gyrase?
What are the twists created by Gyrase called?
How do eukaryotic cells use to compact the genome even more than prokaryotic cells?
What do histone proteins do?
DNA is wrapped around those globular proteins (histones)
What are nucleosomes?
What are linker DNA?
What is a DNA linker bound by?
What is chromatin?
What are usually used to look for patterns and morphology based on chromosomes and why?
What happens when the chromosomes are treated with stained chemicals?
What are the darker regions of the chromosomes called once stained?
Heterochromatin
What are the lighter regions of the chromosomes called once stained?
Which areas are more dense; heterochromatin or euchromatin?
What do the lighter regions of the chromsomes have?
What is a centromere?
What are kinetochores?
What do other protein complexes do, based on centromere activity?
What are centromeres made from?
What are the names for the arms of the chromsomes?
What defines the ratio between the long and short arms of the chromsomes?
What is a metacentric position?
What is a submetacentric length of arms?
What is an acrocentric centromere position?
What is a telocentric centromere position?
What are telomeres?
How are telemores distinctive?
What are factors of the repeated sequences in the telomeres?
Many verteberates have what repeat in telomeres?
T/F Telomeres are only composed of double stranded DNA.
Where are the single stranded DNA found based on telomeres?
What is the physical appearance of the single strand at the end of the telomere?
Forms a knot and held together by many telomere-associated proteins
What is the function of the telomeres?
Prevent chromosomes deterioration and prevent fusion with other chromsomes; function as disposable buffers by blocking the ends of chromsomes
Prokaryotes also have telomeres. T/F
False: Since mos prokaryotes have a circular genomes, their DNA does not contain telomeres.
How many different chromosomes does the human genome contain?
24 different chromosomes
What are the compositions of the 24 different chrosomomes?
What are intergenic regions?
What are major components of intergenic regions?
What are some factors about intergenic regions, even though they are known not to have any function?
What does a gene include?
What are single nucleotide polymorphism? (SNPs)
Where do SNPs occur more frequently?
What are copy-number variations? (CNVs)
What can happen to regions of the genome, relating to CNVs?
What is a hypothesis as to why large regions of DNA genome is duplicated or deleted?
What is the average for large regions of the genome?
What are tandem repeats?
What can unstable tandem repeats lead to?
What components of the DNA are rich in tandem repeats?
What did Hershey and Chase prove?
What can transcription generate?
What is the central dogma?
How many codons are there in total?
64 codons
How many codons specify for amino acids?
61
If 61 codons specify for an amino acid, what are the three remaining ones?
What are stop codons also known as and why?
What is a synonyms, based on codons?
Two or mroe codons coding for the same amino acid
Because it has such synonyms, the genetic code is said to be what…?
Even thouh an amino acid may be specified by several codons….
What are retroviruses?
What are other ways information can be transferred without using the central dogma?
Many final gene products are not proteins but are…..
What is DNA replication?
What type of process if the DNA replication?
During which phase does DNA replication occur?
What are the three possible ways DNA was thought to replicate?
What is the dispersive replication theory?
Both copies of the genomes were composed of scattered pieces of new and old DNA
What is the replication method of DNA?
What is semi-consevative model?
What is the end result of semi-conservative replication?
What is helicase and what does it do?
The replication of DNA cannot begin unless…..
Where does helicase starts unwinding?
It’s not random; it begins at the origin of replication (ORI)
How is the correct ORI found for helicase to begin?
What finds the ORI in prokaryotes?
A protein called DnaA finds the ORI
What finds the ORI in eukarytoes?
When are the three proteins synthesized, the three proteins that cooperate to find the ORI?
What do the two proteins from the three proteins that cooperate to the ORI, ensure?
What happens when helicase unwinds the DNA?
Why doesn’t the chromsome get tangle or break when helicase unwinds it? It should since it gets even more wound up and downstream, so what happens?
What is the function of topoisomerase?
What is the purpose of single-strand bnding proteins (SSBPs)?
What are the separated DNA strands referred to?
What must be synthesized for each template strand?
What synthesizes the RNA primer?
Why is primer synthesis important in DNA replication?
What is the length of the RNA primer and what happens later?
What does the DNA polymerase do?
How does DNA polymerase elongate the RNA primer?
The template strand is read in what direction and what is the end direction of the daughter strand?
What is at the 3’ end during the addition of dNTPs by DNA poly?
What does the 3’ hydroxyl group do?
What is the DNA polymerase apart of?
What do other accesory proteins help with in regards to DNA poly?
What is the different in components of the prokaryotic replisome and eukayrotic replisome?
Prokaryotic replisome: Contains 13 components
Why is additional complexisty in the eukaryotic system required?
How will the two primers elongate, in what direction?
What do DNA polymerase check during the elongation of the daughter strands?
Checks each nucleotide tomake sure it forms a correct base-pair before it is incorporated in the growing polymer
What is the thermodynamic driving force for the polymerization reaction?
In what direction does polymerization occurs?
Where are the nucleotide added, at which end of the strand?
What does DNA poly require to start its process?
How are both template strands read? How are the daughter strands elongated?
What is the replication fork?
What is the leading strand?
Where are the lagging strands?
Top daughter on the right and bottom
What are lagging strands?
What are okazaki fragments?
Small chunks of DNA comprising the lagging strand
Replication of the leading strand….while the replication of the lagging strand is……
What happens to the RNA primes?
What’s the purpose of DNA ligase?
Why is DNA poly considered to be processive?
How many DNA poly does prokaryotes have? Which ones are the most importnat?
- 5
DNA poly III and DNA poly I
What is the purpose of DNA poly III?
What type of activites does DNA poly 3 have?
What does exonuclease mean?
What does endonuclease mean?
What are two important types of endonucleases?
What is the purpose of repair enzymes?
What is the purpose of restriction enzymes?
Destroy the DNA of infecting viruses and restrict the host range of the virus
Where are restriction enzymes found?
What is the proofreading function?
What is the DNA poly III considered based on function?
What does the DNA poly I do?
How is the processitivty of DNA poly I?
What is DNA poly I capable of?
- 3’ to 5’ exonuclease acitivity
2.
What does DNA poly I need to use his 5’ to 3’ exonuclease attribute on?
Which DNA poly is important for excision repair?
What are the activities of DNA poly II?
What is the function of DNA pol II?
Involved in DNA repair and backup for DNA pol III
What is the function of DNA pol IV and DNA pol V?
How many chromosomes do prokayotes have?
How many origins does the prokaryote chromosome have?
What is the physical structure of the chromsome?
Why is the prokaryote replication said to be a theta mechanism and a theta replication?
During replication, the paritially duplicated genome begins to look like the Greek Letter theta
How many origins do chrosomes have in eukaryotic replication?
Each chromsome have several origins
What are replication bubbles?
What happens near the end of a chromosome?
Why is there a roadblock at the end of the chomsome based on the requirements?
After each round o the DNA replication cell cycle, what happens to the telomeres?
What are telomeres?
When the telomeres become too short and reach a critical length where the chromosome may be consumed, what happens?
What is a senescent state?
What is the hayflick limits?
What is the function of telomerase?
Enzyme that adds repetitive nucleotide sequences to the ends of chromosomes and lengthens telomeres
What is telomerase, structural wise?
Rionucleoprotein complex, containing an RNA primer and reverse transciptase enzyme
How does reverse transcriptase reads?
Reads RNA templates and generate DNA
The telomerase complex continuously polymerizes and then….?
Where are telomerase enzymes usually expressed?
Which disease can express telomerase? What does that cause?
Why does telomerase help cancer cells immortalize?
How can genetic mutations occur?
Inherited or acquired throughout life
What are mutations that can be passed onto offsprings?
Why are they called germline mutations?
What are somatic mutations?
What ae the three causes of mutations?
- Physical Mutagens
- Reactive Chemicals
- Biological Agents
What is a type of physical mutagen?
Ionizing radiation
What are types of ionization radiation?
X-ray, alpha particles, gamma rays
What do ionizing radiation do to DNA?
Breaks DNA
What does UV light cause to DNA that is special?
Cause them pyrimidines to become covalently linked
What can reactive chemicals cause to a cell?
Chemicals can covalently alter bases or can cause cross-linking or strand breaks
What arae cross-links?
Abnoral covalent bonds between different parts of DNA
What is the name of a compound that can cause mutations?
Mutagen
What is intercalating compounds, what do they do?
They look like purines and pyrimidines by havng the large flat aromatic ring structure and insert themselves between base pairs
Which chemical is an example of appearing similar to a purine or pyrimidine?
Ethidium bromide
What type of biological agent can cause mutations? Provide an example.
Viruses and transposons exmaple Lysogenic viruses
What do lysogenic viruses do?
Insert into the genome of the host cell and can disrupt genetic function
What are the four common types of mutations?
- Point mutations
- Insertions
- Deletions
- Inversions
What are the three non-common types of mutations?
- Amplifications
- Translocations and rearragements
- Loss of heterozygosity
What are point mutations?
Single base pair substitutions
What are the two versions of point mutations?
- Transitions
- Transversions
What is a transition point mutation?
Substitution of a pyri/puri for another pyri/puri
What is a transversion point mutation?
Substitution of a pyri for a puri or a puri for a pyri
What are the three type of point mutations?
- Missense mutation
- Nonsense mutation
- Silent mutation
What is missense mutation?
Onw amino acid replaced with a different amino acid; not serious if amino acids are similar
What is a nonsense mutation?
A stop codon replaces a regular codon and prematurely shortens protein
What is a silent mutation?
A codon is changed into a new codon for the same amino acid, no change in the protein’s amino acid sequence
What is an insertion type of mutation?
Addition of one or more extra nucleotides into the DNA sequence
What is a deletion type of mutation?
The removal of nucleotide from the sequence
What are frameshift mutations?
Change in the reading frame
What can framshift lead to?
Premature termination of translation if it results in the presence of an abnormal stop codon (incomplete polypeptide)
What is an inversion mutation?
A segment of a chromosome is reversed end to end
What mutations can cause transposons?
Insertions, deletions and inversions
What is chromsome amplification?
A segment of a chromsome is duplicated
What is translocations mutation?
Recombination occurs between nonhomologous chromosomes
What can traslocation cause?
Gene dusion; a new gene product is made from parts of two genes that were not previously connected
What are two types of translocations mutations and what do they mean?
- Balanced
- Unblanced
What are transposons?
Mobile genetic elements in genomes
What does it mean when we state that transposons have genetic mobility?
These short segments can jump around the genome
What are the three common types of transposons?
- IS element
- Contain additional genes
- Composite transposons
What are IS element composed of?
Composed of tranposase gene flanked by inverted repeated sequences
What is an example of complex tranpossons with additional genes in the center?
Contains gene for antibiotic resistance
What are composite transposons?
Two similar or identical IS elecments with a central region in between?
Whatis a gene that all tranposons have?
Protein called tranposase
What type of activity do transposase have?
“Cut-and-paste”
What is the function of transposase?
Catalyzes mobilization of tranposon and intergration into a new geneti location
Based on tranposons, what is the mobilization of tranposon site considered? What about the intergration into a new genetic locatino, what is it called?
- Excision from the donor site
- The acceptor site
The inverted repeats in transposase are important for what?
For mobilization
What does the transposase gene codes for?
A tranposase enzyme
What can tranposons cause based on structure?
Structural changes to chromosomes when they work in pair
What can happen if a chromsome has two tranposons inthe samedirection?
The transposons can line up beside each other to be parallel and cause the chromsomal segement b/n them to loop around
What happens to the chromsome segment attached to the DNA when the transposons caused a loop around?
Causes deletion of the DNA b/n the to trnsposons and the original chromosome loses the DNA segment between
What can the transposon with the new chunk of DNA cause?
It can jump back into the genome somewhere else, causing rearrangement
What can happen if two transposons with inverted orientations cause to the chromsome and how?
Recombine and seqnce of DNA between the two transposons may be inverted
Why is a mutation in one copy of a diploid organism tolerable?
Because diploid organisms have two copies of a gene
What is a loss of heterozygosity?
If a deletion removes the normal copy of the gene and the only one reaining is the mutated version
What does the loss of heterozygosity cause to the locus?
Makes the locus hemizygous; only one gene copy in the diploid organism
What type of example was provided for loss of heterozygosity?
Hereditary retinoblastoma
What is heriditary blastoma?
A type of retinal cancer commo in young children
What does heriditary retinoblastoma occur?
A child receives a bad copy of tumor suppressor Rb1 from a perent, and a loss of heterozygosity leads to the normal allele lost
Why are mutations on sex chromosomes have greater effects than mutations on autosomes?
Males have only one X chromosome and one Y chromosome with no backup copy either
Haploid expression in a diploid organism is called what?
Hemizygosity
What is gain-of-function muttion?
Increase the activity of a certain gene product, or change it such that it gains a new and abnormal function
What is a loss of function mutation?
Result in the gene product having less or no function
What is haploinsuficiency?
Sometimes having only a single functional copy of the gene is not enough
What are two types of beneficial mutations?
- Sickle-cell anemia
- Missing 32 base pairs in gene called CCR5
