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What functions as the genetic material of all organisms and many viruses
DNA → a sequence of 500-100 nucleotides make up a gene (except for viruses because they can use both DNA and RNA)
What is a genome
Entire genetic complement of an organisms, includes nucleotide sequences and genes → organized into genes that carry instructions for synthesis of RNA and proteins and because RNAs and proteins are workhorses for cells, the genome controls synthesis of all molecules in an organisms
What is a genotype
Complete set of genes in the genome (genetic makeup of an organism)
What is a phenotype
Physical features and functional traits of an organism that result from the expression of genes or set of genes (observable traits of an organisms)
This is environment specific and situation specific
What is replication
Exact duplication of entire DNA genome for purposes of reproduction (cell division)
How many copies of each gene do microbes have
Only 1 copy of each gene called haploid organisms. The geneotype is the same but it gets tricky with phenotypes because for example, with biofilms, it first have flagella but then looses it.
What is central dogma
Going from DNA strand to RNA to Polypeptide/protein in one direction
What is transcription
Copying of a segment of DNA information into RNA nucleotide sequences → RNA can be mRNA, tRNA, or rRNA & 2 different products can be made
(takes certain segments of DNA, known as genes, and reads DNA information, then synthesize/build RNA molecule based on original segment)
What is translation
Synthesis of polypeptides through “interpretation” of mRNA nucleotide sequences
(taking information from mRNA molecules snd putting it with the right amino acid and assembling the protein to allow it to fold correctly to function)
What is nucleotide structure
Phosphate group: gives the molecules a negative charge
Pentose sugar: deoxyribose in DNA/ribose in RNA & lacks OH group at 2’ carbon
Cyclic nitrogenous bases: adenine, guanine, cytosine, thymine, uracil
What are the nitrogenous bases in RNA vs DNA
RNA: adenine - uracil, guanine - cytosine
DNA: adenine - thymine, guanine - cytosine
Where is the nitrogenous base bonded to in a nucleotide structure
1 prime carbon group by a glycosidic bond
Where is the phosphate group bonded to in a nucleotide structure
5 prime carbon group
What can we assume in every place where 2 lines come together
There is a carbon atom and the carbon will make 4 bonds
What does it mean if we do not see a line bonded to make up the 4 bonds in a nucleotide structure
It is assumed that there is a hydrogen bond
What holds the phosphate group and nitrogenous base together
Pentose sugar
Describe the carbon numbering in a nucleotide structure
1’ carbon is where nitrogenous base is attached
2' and 3’ carbons are attached to hydroxyl group (OH)
5’ carbon is where phosphate group is attached
What is on the 2’ carbon for DNA vs RNA
DNA: has H on 2 prime carbon → deoxyribose nucleic acid
RNA: has OH on 2 prime carbon → ribose nucleic acid
Where does the energy comes from to link/bond the monomers in a nucleic acid structure
From the molecule’s tri/diphosphate building blocks
What way/manner are monomers linked and where do the nucleotides get added to in a nucleic acid structure
In an 5’ to 3’ manner → Nucleotides are added to the 3’ end
What do the 2 strands of DNA form
Double helix
What bond forms between C and G/T and A in DNA
Hydrogen bonds (in RNA, T is replaced by U so A is bonded to U)
What are the key features of the double helix
Complementary: meaning nitrogenous bases pair together
Antiparallel: meaning the strands run in opposite directions
5’ to 3’
3’ to 5’
Where are prokaryotic genomes contained
Contained in 2 structures: chromosomes and sometimes plasmids
What are prokaryotic genomes chromosomes
Constitute main portion of DNA and all necessary housekeeping genes
1 chromosome per cell
Circular molecule of DNA fold upon itself to form nucleoid
Associated with proteins and RNA needed for replication and transcription
Necessary for metabolism, genetic processes, binary fission, TCA cycle, ETC…
What are prokaryotic genome plasmids
Small, multiple copies, circular molecules of DNA that replicate independently
Carry information required for replication for 1 or more cellular traits - carries all the non-essential genes that are not needed for day-to-day function
What are plasmids not necessary for and necessary for
Not necessary for normal bacterial metabolism, growth, or reproduction
Necessary for survival advantages: reproductive (fertility), antibiotic resistance, virulence factors
Where are eukaryotic genomes contained
In nuclear chromosomes and extranuclear DNA (in nucleus of eukaryotic cells made up of billions of nucleotides)
What are eukaryotic genome nuclear envelope (95%)
Nuclei have more than 1 chromosome per cell → chromosome number is characteristic of species
Chromosomes are linear and sequestered within a membrane-bound nucleus
What are eukaryotic genome extranuclear DNA (5%)
DNA of mitochondria and chloroplasts is circular and resembles chromosomes of prokaryotes
What is DNA replication and what does it begin with
An anabolic polymerization process that requires nucleotide monomers and energy → Triphosphate deoxyribonucleotides (DNTP’s) serve both functions providing nucleotide monomers and energy to DNA replication
Begins with double-stranded parental DNA helix
What is the key to DNA replication
Complementary nature of the 2 parental strands → each parental strand serves as a template for the synthesis of a new, complementary daughter strand
How is replication in DNA replication
Replication is semiconservative: new helices are composed of 1 original strand and 1 daughter strand (you take 2 strands and break the hydrogen bonds. the old strand is called old/parental/template strand and we synthesize the nucleotides and form a new strand that matches up)
What do we get at the end of DNA replication
An old strand/parental strand paired with a new daughter strand. You always have an old with new which is called semiconservative DNA replication
What are the steps of DNA replication
Remove DNA-associated proteins: clean off DNA template of any proteins that are not involved in DNA replication
Unwind and separate original (template) strands (DNA helicase): the DNA helicase takes the 2 hybridized strands and break the hydrogen bonds to have 2 single stranded molecules (helicase is an enzyme that moves to left & result in 2 strands)
Synthesize RNA primers (primase): primase determines the starting point that will lay down a complementary template and put down the primer to signify the starting location for DNA replication
Extend primers with DNA polymerase III, synthesis of DNA in the 3’ direction: DNA polymerase III is the one doing main replication process. It finds primer since the primer tells use when to start replication. so DNA polymerase III binds and exten the 5’ to 3’ by reading and making more DNA
Degrade RNA primer and fill in the gaps with DNA polymerase I: DNA polymerase I will identify primer and remove it. The primer is about 8 nucleotides so we need to fill in the gaps with DNA which is the role of DNA polymerase I (does 2 things)
Rewind new hybrid strands: last enzyme called DNA ligase create any final possible diester bonds
What is the function of primase in the initial processes of DNA replication
Primase binds to the template strand and synthesizes short RNA primer
What is the function of DNA polymerase III in the initial processes of DNA replication
DNA polymerase III binds to primer and begins adding nucleotides to its 3’ end. It will also extend the new DNA strand by reading the template strand and adding complementary nucleotides
What is the function of DNA polymerase I in the initial processes of DNA replication
DNA polymerase I will remove the primer and extend the new DNA strand by reading the template strand and adding complementary nucleotides
What does DNA polymerase III synthesizes and in how many directions
Synthesizes new DNA strands in only 1 direction, from the 5’ end to the 3’ end
What happens because the two template strands are antiparallel
The two new strands are synthesized differently → leading strand or lagging strand
What is leading strand
Continuous DNA synthesis towards the replication fork
(polymerase and helicases move in the same direction)
What is the lagging strand
Discontinuous DNA synthesis away from the replication fork
(polymerase and helicase move in opposite direction)
What are the steps of leading strand replication
Clean DNA off of any proteins
Helicase: move helicase to left and break hydrogen bonds and leave behind 2 single stranded molecules
Primase: put down RNA primer 5’ to 3’
DNA primase III binds and extends
What does the starting and stopping of lagging strands create
Okazaki fragments
In prokaryotes, where does replication begin and proceed (and ending)
At a specific site on a bacterial chromosome called the origin of replication (ori) It proceeds around both sides of circular chromosome called bidirectional replication (it also has an ending point called termination point)
Does replication of a circular chromosome have to be completed before a cell can start another round of replication
No, it does not have to be completed before the cell can start another round of replication
What does bacteria use to relieve strain as replication places great torsional strain on circular chromosomes
Topoisomerases to relieve strain (it removes the kinks and tangles, allowing DNA strands to unwind and relieve tension)
