Topics 5-6 Flashcards
What is a single nucleotide composed of?
The sugar deoxyribose, attached to a phosphate and nitrogenous base
Helicase
unwinds double helix for DNA replication
single strand binding proteins
stabilize unwound template strands in DNA replication
DNA Polymerase
Elongates new DNA at replication fork during DNA replication by adding nucleotides to the growing chain in the 5 to 3 direction
Okazaki fragements/DNA ligase
The lagging strand is synthesized in separate pieces by okazaki fragments, which are then sealed together by DNA ligase
Nucleotide excision repair
incorrectly placed nucleotides are removed by nucleases and filled in with correct ones
Telomeres
Short repetitive nucleotide sequences that do not contain genes. These cap the linear ends of eukaryotic chromosomes to avoid losing genes during mitosis because DNA Polymerase can only add to the 3 end of molecule, it cant complete the 5 end
Bacterial vs Eukaryotic chromosomes
Bacterial: 1, double stranded; circular DNA molecule, small amount of protein
Eukaryotic: Linear DNA molecules, large amounts of protein
transcription location and purpose
Synthesize RNA using DNA as a template, takes place in nucleus
mRNA
Messenger RNA, it carries the message of DNA to the protein making ribosomes
RNA processing
process that make pre-mRNA into mRNA
translation purpose and location
produces polypeptide chain using the mRNA transcript, occurs at ribosomes
Template strand
The one strand of DNA transcribed during transcription, producing mRNA or the complementary strand
Codons
mRNA base triplets, written in the 5 to 3 direction
Promoter/terminator
DNA sequence where RNA polymerase attaches is the promoter, whereas the DNA sequence that signals the end of transcription is called the terminator
3 stages of transcription
- Initiation: In eukaryotes, the transcription initiation complex forms, in bacteria, RNA polymerase binds to the promoter
- Elongation: RNA polymerase moves along DNA, adding nucleotides to the 3 end of the chain. Double helix reforms bands with the RNA molecule hanging off
- Termination
Modifications after transcription
Occurs in Eurkaryotes
5 cap and poly-A tail: facilitate export of mRNA from the nucleus, protect it from degradation and facilitates attachment of mRNA to the ribosome
RNA splicing: Large portions of newly synthesized RNA(introns) are removed/spliced, leaving exons behind.
Ribozymes
RNA that serves a catalytic role
Types of RNA that are important in translation
mRNA: messenger RNA, produced during transcription, carries genetic message of DNA to the ribosome
tRNA: transfer RNA, transfers amino acids from pool of amino acids in cytoplasm to a ribosome. Each type of tRNA is specific to an amino acid. It uses anticodons to pair specifically to a complementary codon on mRNA
rRNA: ribosomal RNA, complexes with proteins to form 2 subunits that form ribosomes. Have P, A, and E sites that bind with tRNA
Codons and anticodons
codons: an mRNA triplet nucleotides. 64 combos possible
anticodons: nucleotide triplet used to pair with a codon by tRNA
P, A and E sites
P: holds tRNA carrying the growing polypeptide chain
A: holds tRNA that carried the amino acid that will be added to the chain next
E: Exit site for tRNA
Steps/substeps of translation
- Initiation, has 3 substeps
a. small ribosomal subunit binds to mRNA so that AUG(start codon) is places in proper position
b. tRNA with matching anticodon bonds to start codon
c. start codon moves to P site, leaving A site open for more codons - Elongation: Codon recognition finds correct codon for open A site. A peptide bonds forms between A site amino group and P site amino group(s). Translocation of codons between sites occurs
- Termination: a stop codons is reached. A release factor(protein) binds to the stop codon and the polypeptide is freed from the ribosome
Point mutations and types
Point mutations are alterations to one base pair of a gene
Types
- Nucleotide-pair substitution: replacement of one nucleotide and its partner with another pair
- Missense mutations: substitutions that enable the codon to still code for an amino acid, it just may or not be the correct one
- Nonsense: change a regular codon into a stop codon - Insertions/deletions
Parts of an operon
- Operator: controls access of RNA polymerase to genes. Found within promoter between promoter and protein coding genes of operon
- Promoter: RNA polymerase attachment site
- Genes of operon
Regulatory gene
Not apart of operon, produce repressor genes that may bond to operator site. When these genes occupy the operator site, RNA Polymerase is blocked off
repressible/inducible operons
Repressible: normally on, can be turned off, anabolic and builds organic molecules. Can produce corepressors
Inducible: Normally off, can be activated, catabolic and breaks stuff down. Can produce inducers
Corepressor: Organic molecule produced by a repressible operon binds to the repressor protein, activating it, shutting down operon
Inducer: binds to and inactivates repressor protein, removing it from the operator site and giving RNA polymerase access to it
DNA Methylation and histone acetylation
These process help controll gene expression
DNA methylation: Addition of methyl groups to DNA, causes DNA to become more tightly packaged, reducing gene expression
Histone acetylation: Acetyl groups are added to amino acids of histone proteins, making chromatin less tightly packed and encouraging transcription
Epigenetic inheritence
inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence. The sequence of DNA isnt changed, just its expression
Zygote transformation processes
- Cell division
- Cell differentiation
- Morphogenesis
- Controlled by Cytoplasmic determinants and cell to cell signals
What controls differentiation and morphogenesis?
- Cytoplasmic determinants
2. Cell-cell signals and induction
p53 gene and how does it’s protein product supress cancer
p53 is an important tumor suppressor gene and it’s protein product prevents cancer in 4 ways
- Activate p21 gene, whose product halts the cell cycle by binding to cyclin dependent kinases, allowing time for DNA to be repaired before the resumption of cell division
- Activates a group of miRNAs, which inhibit the cell cycle
- turns on genes directly involved in DNA repair
- Activates apoptosis when cell s beyond repair
In what ways do phages reproduce?
- Lytic cycle: Ends in death of the host cell, the phage injects it’s DNA into the host cell and takes over inirder to synthesize viral DNA copies. When the host cell ruptures, it releases new copies of the virus
- Lysogenic cycle: phage’s DNA becomes incorporated into host cell DNA and replicated along the host cell’s genome. Viral DNA is known as a prophage, under certain conditions, prophages can enter the lytic cycle
Recombinant DNA
DNA that has been artificially made using DNA from different sources
Restriction enzymes
used to cut strands of DNA at specific locations called restriciton sites, derived from bacteria
Sticky end
an end of a restriction fragment that can form H bonds with complementary single stranded pieces of DNA, these unions are sealed with the enzyme DNA ligasr
Nucleic acid hybridization
a process that can be used to find a gene of interest among the many colonies present after tranformation by making a probe specialized for the target nucleotides and tracking it
Polymerase chain reaction
aka PCR, this is a method used to amplify a particular piece of DNA without the use of cells when the source is impure
Process
1. Denaturation: Heat to separate DNA strands
- Annealing: cool to allow primers to form H bonds with ends of the target sequence
- Extensions: DNA polymerase adds nucleotides to the 3’ end of each primer
Gel electrophoresis
a lab technique used to separate macromolecules, primarily DNA and proteins
Process
1. An electric current is applied, DNA is negatively charged and migrates to the positive electrode
- Agarose gel is used as a matrix to separate molecules by size, the gel allows smaller molecules to move more easily than larger fragments of DNA
- DNA is stained or tagged for visualization
Transposable elements
Make up much of the repetative DNA present, these are stretches of DNA that can move from one location to another in the genome with the aid of an enzyme called transposase
Transposons/Retroposons
Transposons: Move by means of a DNA intermediate
Retrotransposons: moves by means of an RNA intermediate, and leave a copy at the original sige. This involves reverse transcriptase
Retroviruses
RNA viruses that use reverse transcriptase to transcribe DNA from an RNA template, which then permanently integrates into the nucleus of the host cell. The host then transcribes the viral DNA to RNA that may be used to synthesize viral proteins or may be relased from the cell to infect more cells
Carolis Linnaeus
Grouped similar species into increasingly similar categories. He developed taxonomy and binomial nomenclature
Georges Cuvier
French geologist opposed to evolution
Jean-Baptiste de Lamarck
developed early theory of evolution based on use/disuse and inheritsnce of acquired characteristics
Evidence of evolution
- Direct observations of evolutionary change in insect populations becoming resistant to pesticides and drug resistant bacterial/viruses
- Fossil record
- Homology and convergent evolution: similarites internally and externally. Similar problem, similar solution
- Biogeography: species with similar biogeography tend to be similar
Sources of the most genetic variation in organisms
- crossing over during mitosis
- independent assortment of chromosomes during meiosis
- fertilization
Factors that alter allel frequencies and bring about evolution
- mutations(rarely)
- natural selection: proportions of genes expressed in different generations vary due to certain genes being selected
- Genetic drift: unpredictable fluctuation in allele frequencies from one generation to the next. Smaller population=greater chance of genetic drift
- Gene flow occurring when populations gain or lose alleles from populatiln changes. Tends to make populations more similar
Types of natural selection
- Directionaly selection: Favors variants at one extreme end of the spectrum
- Disruptive selection: Favors variants at both ends of the distribution, but not intermediates
- Stabilizing selection: favors intermediate and not extreme distributions
Biological species concept
defines species as a population or group of population whose members have the potential to interbreed in nature and produce viable, fertile offspring but are unable to do the same with members of other populations
Types of speciation
allopatric: a population forms a new speciesb because it is geographically isolated from the parent population
sympatric: a small part of a population forms a new population without being geographically isolated
autopolyploid
can lead to sympatric speciation in plants, is the formation of plants through nondisjunction in meiosis. If they survive, they can not breed with normal diploid members and produce fertile, viable offspring
Endosymbiotic hypothesis and evidence
proposes that mitochondria and plastids were formerly small prokaryotes that began living within larger cells
Evidence
1. Both organelles have enzymes and transport systems homologous to those found in the plasma membrane of living prokaryotes
- Both replicate through a splitting process similar to prokaryotes
- Contain a single, circular, DNA molecule not associated with histone proteins
- Have their own ribsomes
Heterochrony
an evolutionary change in the rate or timing of developmental events
Hox genes
a class of homeotic genes
