Micro 7

basic subunits of RNA or DNA consisting of purine or pyrimidine covalently bonded to ribose or deoxyribose

• also simply called a base
• 4 different ones for DNA:
• Adenine
• Thymine
• Cytosine
• Guanine
• *Set of 3 nucleotides encodes a specific amino acid, string of amino acids make up protein

• a complete set of genetic info of a cell
• includes plasmids as well as the chromosomes; however genome is often used interchangeably with chromosome
• *The genome of all cells is composed of DNA, but some viruses have an RNA genome

• the functional unit of the genome
• encodes a product, most commonly a protein

the study and analysis of nucleotide sequence of DNA

• 1. the double-stranded DNA must be duplicated 
• 2. info encoded by DNA must be decoded so cell can synthesize necessary gene products

duplication of DNA so encoded information can be passed to next generation

• decoding information which is encoded by DNA so that the cell can synthesize the necessary gene products
• Involves two interrelated events: Transcription and translation

• refers to making the RNA molecule
• Process of copying the info encoded in DNA into RNA
• Involves Initiation, Elongation, and Termination

interprets info carried by mRNA to synthesize the encoded protein

refers to the flow of info from DNA to RNA to protein

• Joined together by covalent bond between the 5'PO₄ (5 prime phosphate) of one nucleotide and the 3'OH (3 prime hydroxyl) of the next
• *5' and 3' refer to numbered carbon atoms on pentose sugar of nucleotide
• *The nucleotides joining in the manner creates the sugar-phosphate backbone

• Because of the chemical structure of nucleotides and how they join together, a single strand of DNA will always have a 5'PO₄  at one end and a 3'OH at the other
• Often referred to as the 5' end (5 prime end) and the 3' (3 prime end)

• The two stands of DNA are complementary and are held together by hydrogen bonds
• Amy marries Tim (with 2 hydrogen bonds)
• Guenevere marries Chris (with 3 hydrogen bonds)

*Because Amy and Tim only have 2 bonds, Amy steps out with Urical with RNA is around. Bond isn't a tight... marriage sucks!

• refers to the characteristic bonding of A to T, and G to C
• Is the fundamental characteristic of DNA

• refers to the double helix in DNA and the two strands being complementary
• They are also antiparallel, meaning they oriented in opposite directions
• One strand is oriented in the 5' to 3' direction, it's complement is oriented in the 3' to 5' direction

Using a region of ONE of the two strands of DNA as a template

• All transcribed from different sets of genes:
• mRNA (messenger RNA) 
• rRNA (ribosomal RNA)
• tRNA (transfer RNA)

• messenger RNA
• info encrypted is deciphered according to genetic code, which correlates each set of 3 nucleotides to a particular amino acid
• *Some genes are never translated into proteins, as the RNAs themselves are final products

• fundamental aspect of gene regulation is instability of mRNA
• Within minutes of being produced, transcript are degraded by enzymes
• If gene if turned on, will continue to be available to translation. 
• If turned off, # of transcripts will rapidly decline

• Process is generally bidirectional, meaning it proceeds in both directions from the starting point.
• This allows a chromosome to be replicated in half the time it would take if the process were unidirectional

• *The progression of bidirectional replication around a circular DNA molecule creates two advancing forks where DNA synthesis is occurring
• The replicating forks ultimately meet at a terminating site when process is complete

• refers to half the original molecule being conserved in each new molecule when DNA is replicated
• The two DNA molecules created through replication each contain one of the original strands

Specific proteins must recognize and bind to origin of replication

• Prokaryotic chromosomes and plasmids typically contain only one of these initiating sites
• Proteins bind to site, cause localized melting of double-stranded DNA, exposing single-stranded regions for templates
• Primases (enzymes) then synthesize short stretches of RNA

distinct region of DNA molecule at which replication is initiated

• Small fragments of nucleic acid to which DNA polymerase can add nucleotides 
• (the enzyme can add nucleotides only to an existing fragment)

The complex of enzymes and other proteins that synthesize DNA

Enzyme that temporarily breaks the strands of DNA, relieving the tension caused by unwinding the two strands of the DNA helix

Enzyme that joins two DNA fragments by forming a covalent bond btwn the sugar and phosphate residues of adjacent nucleotides

Enzyme that synthesizes small fragments of RNA to serve as primers for DNA synthesis

• Enzymes that synthesize DNA
• use one strand of DNA as template to make the complementary strand
• Nucleotides can be added only to the 3' end of an existing fragment - therefore, synthesis always occurs in the 5' to 3' direction
• *Cannot initiate synthesis

Enzymes that unwind the DNA helix ahead of the replication fork

The DNA strand that is synthesized as a continuous fragment, as the DNA polymerase simply adds nucleotides to the 3' end

• The DNA strand that is synthesized in a series of fragments
• More complicated than leading strand as DNA polymerases can't add nucleotides to 5' end, so as additional template is exposed synthesis must be reinitiated
• Each time synthesis is reinitiated, another RNA primer must be made  first.
• This results in the small fragments, each of which has short stretch of RNA at 5' end.

Name of small nucleic acid fragments made during synthesis of lagging strand of DNA

• in transcription, enzyme that synthesizes single-stranded RNA molecules from a single-stranded DNA template
• Like DNA polymerase, RNA polymerase can add nucleotides ONLY to 3' end and therefore ONLY synthesizes RNA in 5' to 3' direction
• UNLIKE DNA polymerase, RNA polymerase can start synthesis w/o a primer

• Nucleotide sequence to which RNA polymerase binds to initiate transcription
• ID's regions that will be transcribed
• Also orient the direction of RNA polymerase on DNA molecule, dictating which strand will be used as template

• Nucleotide sequence at which RNA synthesis stops
• RNA polymerase falls off the DNA template and releases the newly synthesised RNA

• The DNA strand that serves as the template for transcription
• Resulting RNA molecule is complementary to this strand

• Strand of DNA complementary to the one that serves as the template for RNA synthesis
• the nucleotide sequence of the RNA molecule is the same as this strand, except it has uracil rather than thymine

• *In prokaryotes, mRNA can carry info for one or multiple genes
• Monocistronic is a transcript that carries one gene
• Polycistronic carries multiple genes

• Portion of RNA polymerase that recognizes the promoter regions
• A cell can have different types of σ factors that recognize different promoters, allowing the cell to transcribe specialized sets of genes as needed

• RNA polymerase moves along DNA, using minus strand as template to synthesize single-stranded RNA molecule
• Nucleotides are added only to 3' end
• Reactions fueled by hydrolyzing high energy Phosphate bonds of incoming nucleotide
• When RNA polymerase advances, denatures new stretch of DNA & allows previous section of close
• This exposes new region of template so elongation can continue

From mRNA, using the genetic code, which correlates a series of 3 nucleotides, a codon, with one amino acid

• Set of 3 adjacent nucleotides that encode either an amino acid or the termination of the polypeptide
• Because of triplet combination btwn 4 different nucleotides, there are 64 different codons

• ways in which triplets can be grouped
• Each 2 letter group

AUG

• UAA
• UAG
• UGA
• "University of AlabamA"
• "University of Alabama and Georgia"
• "University of Georgia and Alabama"

• Structure that serve as translation machines
• facilitates the joining of amino acids during the process of translation
• does so by aligning two amino acids so ribosomal enzyme can easily create peptide bond btwn them
• composed of protein and ribosomal RNA
• The prokaryotic ribosome (70S) consists of a 30S and 50S subunit

• segments of RNA which act as keys to genetic code
• Recognizes and base-pairs with certain codons and, in the process, delivers the appropriate amino acid to that site
• Recognition is possible cause each tRNA has an anticodon
• Once it's donated it's amino acid during translation, can be recycled

• sequence of 3 nucleotides in a tRNA molecule that is complementary to a particular codon in mRNA
• Allows tRNA to recognize and bind to appropriate codon

• Sequence of nucleotides in mRNA to which a ribosome binds
• the first time the codon for methionine (AUG) appears after that site, translation generally begins

*AUGustus MaCrae gets me going"

• Codon at which translation is initiated
• typically the first AUG after a ribosome-binding site
• *AUG only functions as start codon when preceded by ribosome-binding site

• Codon that terminates translation, signaling the end of the protein
• 3 stop codons

• Elongation is terminated when ribosome reaches a stop codon, which is a codon not recognized by tRNA
• Enzymes free polypeptide by breaking covalent bond that joins it to RNA
• Ribosome falls off mRNA, dissociating into it's 2 subunits (30S & 50S) which can then be reused to initiate translation at other sites

proteins that assists folding polypeptides into specific shapes

• characteristic series of hydrophobic amino acids at their amino terminal end, which "tags" polypeptides destined for transport
• must be removed by proteins in the membrane

• specific to eukaryotes
• must be processed (formed) both during and after transcription to form mature mRNA

• mRNA is NOT processed 
• mRNA does not contain introns
• Translation of mRNA begins as it is being transcribed
• mRNA is often polycistronic; translation usually begins at the first AUG codon that follows a ribosome-binding site

• A cap is added to the 5' end of mRNA, and a poly A tail is added to the 3' end
• mRNA contains introns, which are removed by splicing
• the mRNA transcript is transported out of the nucleus to that it can be translated in the cytoplasm
• mRNA is monocistronic, translation begins at the first AUG

• transmits info from outside a cell to the inside
• allows cells to monitor and react to environmental conditions

• a phenomenon in which some organisms can "sense" the density of cells within their own population
• Allows cells to activate genes that are only useful when expressed by a critical mass
• Involves the bacteria "talking" to each other
• Only when a signaling molecule reaches a critical level does it induce the expression of specific genes

• an important mechanism cells use to detect and react to changes in the external environment
• consist of 2 different proteins - a sensor and a response regulator
• Sensor spans cytoplasmic membrane. In response to enviro variation, sensor chemically modifies a region on it's internal portion.  This alerts the response regulator which can turn genes on or off, depending on the system

• an alteration in the characteristic of certain surface proteins
• Pathogens that do this can stay one step ahead of body's defenses by altering the very molecules our immune systems learn to recognize

• another mechanism of randomly altering gene expression
• the routine switching on and off of certain genes

a set of regulated genes transcribed as a single polycistronic message

• separate operons controlled by a single regulatory mechanism
• two component regulatory systems often control regulons

simultaneous regulation of numerous genes

• According to the type of regulation that governs their synthesis:
• Constitutive
• Inducible
• Repressible

• Enzymes are synthesized constantly
• genes that encode these are always active
• Usually play indispensable roles in central metabolic pathways

• enzymes that are not routinely produced at significant levels; instead, their synthesis can be turned on when needed
• Often involved in the transport and breakdown of specific energy sources

• Enzymes are produced routinely, but their synthesis can be turned off when they are not required
• Generally involved in biosynthetic (anabolic) pathways

• Alternative sigma factors
• DNA-binding proteins

Recognize different sets of promoters, thereby controlling the expression of specific groups of genes

• *transcription is often controlled by proteins that bind to specific DNA sequences
• When a regulatory protein attaches to DNA, it can act either as a repressor, which blocks transcription, or an activator, which facilitates transcription

• a regulatory protein that blocks transcription (negative regulation)
• Does this by binding to operator, a specific DNA sequence located immed downstream of a promoter
• Makes it so RNA polymerase cannot progress past

• Induction
• Repression

• The repressor is synthesized as a form that binds to operator, blocking transcription.
• A molecule called an inducer attaches to repressor, changes shape of repressor so it no longer grasp operator
• With repressor unable to bind DNA, RNA polymerase may transcribe the gene

• The repressor is synthesized as form that cannot bind to operator
• When a molecule termed a corepressor attaches to repressor, the corepressor-repressor complex can then bind to operator, blocking transcription

• A regulatory protein that facilitates transcription (pos regulation)
• Genes controlled by activators have ineffective promoter preceded by an activator-binding site
• Binding of activator to DNA enhances ability of RNA polymerase to initiate transcription at that promoter

Nucleotide sequence that precedes an ineffective promoter

• Encodes proteins involved with the tranport and degradation of lactose, and is only turned on when lactose in in the cell but glucose is not available
• Uses a repressor that prevents transcription when lactose is not available; the repressor binds to operator, blocking RNA polymerase

• CCR
• The phenomenon that when glucose is available, the lac operon is not expressed
• Global control system that allows glucose to regulate expression of the lac operon as well as other sets of genes

• the characteristic 2-phase growth pattern that can be seen when cells are using glucose for fuel
• When glucose is used up, growth stops for short period as cells gear up to begin metabolizing lactose, then cells begin multiplying again using lactose to fuel growth

• catabolite activator protein
• one mechanism of carbon catabolite repression
• required for transcription
• must be bound by an inducer to work - an ATP derivative called cAMP
• inducer only made when extracellular glucose levels are low, as enzyme required for it's synthesis is activated by idle form of glucose transporter component

• another mechanism of regulation 
• When glucose is being moved into the cell, a glucose transport component binds to the lactose transporter, locking it in a non-functional position
• Can't move lactose into cell, so lac operon will not be induced

• (RNAi)
• Cells use this routinely to destroy specific RNA transcripts
• Cell synthesizes short single-stranded RNA pieces to locate specific RNA transcripts destined for destruction

a new field which creates the computer technology to store, retrieve, and analyze nucleotide sequence data

• ORF's
• protein-encoding regions in DNA which computers help locate
• stretches of nucleotide sequences generally longer than 300 bp that bein with a start codon and end with a stop codon

• the analysis of total microbial genomes in an environment
• By examining, researchers can study all microorganisms and viruses in a community, instead of just the relatively few that grow in a culture
• Also being used to study microbial life in the open oceans and in soils