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104 Cards in this Set
- Front
- Back
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Genome |
A cell's total genetic material, for bacterium it would mean both the chromosome and the plasmids |
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Chromosomes |
DNA containing structures within a cell that carry genetic information |
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Note to self |
Bacteria have one chromosome. You have 46 |
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Genetics |
The study of heredity |
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Nucleotide |
Composed of a: nitrogenous base -(A,T or U,C,G) a pentose sugar (deoxyribose or ribose) phosphate group |
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DNA backbone |
Composed of an alternating chain of sugar and phosphate groups |
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Two strands of DNA are held together by... |
Hydrogen bonding between the bases |
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The two strand twist to form a... |
Double helix |
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Complimentary |
Means that the base pairing occurs in a specific manner A always pairs w/ T (or U in RNA) C always pairs with G So if you know the sequence of one strand You can predict the sequence of the complementary strand |
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Gene |
A specific segment of DNA which codes for a functional product
Final product maybe tRNA, rRNA or protein |
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Transcription |
The copying of a specific mRNA from a DNA template |
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Translation |
The reading of the mRNA message and production of a protein product |
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Expressed |
When a message has been produced from a gene |
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Genotype |
A description of the genes which an organism has |
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Phenotype |
Refers to the actual physical properties which are visible or measurable |
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Bacteria have... |
A single circular chromosome which is looped folded and attached to the cytoplasmic membrane They may also contain plasmid DNA |
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Plasmid DNA |
Extra chromosome elements meaning they're not part of the chromosome but are considered accessory and may Supply additional genes such as virulence genes are toxic genes that the cell would normally not have |
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DNA replication |
Involves the separation of a small region of two strands of DNA exposing the nitrogenous bases to free bases in the cytoplasm |
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DNA polymerase |
Joins the free bases in matches them up with their respective partners in the growing DNA strand |
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Replication fork |
Region where DNA replication is occurring |
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Daughter strand |
The new DNA strand which is being formed from the parent template |
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Semi conservative |
As each daughter strand is formed it twist into a double helix with the parent strand which was its blueprint
Parent strand is conserved and joined with a new daughter strand |
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All the carbons making up the deoxyribose suga |
numbered 1' - 5' |
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each PHOSPHATE group in the phosphate sugar backbone... |
attached to the 5' carbon of its own nucleotide and the 3' carbon of the adjacent nucleotide in the chain.
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if a DNA molecule is linearized (in a straight line), you will only find a OH (hydroxyl) group attached to... |
the 3' carbon therefore the end w/ the OH group is called the 3' end the other end is the 5' end |
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*** nucleotides can only be added to the...**** |
3' end w/ the removal of the hydroxyl group. |
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extention of a DNA molecule can only go... |
from the 5' to 3' direction |
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Antiparallel |
describes how the two strands are oriented in opposite directions |
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leading strand |
synthesized continuously in the 5' to 3' direction |
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lagging strand |
synthesized in small (okazaki) fragments which are joined together later each fragment is added in the 5' to 3' direction |
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unwinding enzymes |
DNA helicases gyrases topoisomerases these open up the helix exposing each strand |
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stabilizing proteins |
bind to single stranded DNA (SSB-single stranded binding proteins) ONLY & stabilize the strand while new daughter strand is being formed. |
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DNA polymerase |
CANNOT begin in the middle of a DNA strand and add nucleotides in a 5' to 3' direction b/c RNA Primase must come in 1st and begin adding complementary RNA nucleotides in 5' to 3' direction and be a primer for DNA polymerase. |
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Using the 3'-OH of the RNA Primer,... |
DNA polymerase is able to extend the 2nd strand using complementary DNA nucleotides in the 5' to 3' DNA polymerase continues until it runs into RNA primer, it then removes the primer. |
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5' to 3' exonuclease activity |
what DNA polymerase has that allows it to cut out RNA nucleotides and replace them with complementary DNA nucleotides |
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DNA polymerase falls of when... |
it bumps into the daughter DNA strand infront of it. |
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DNA Ligase |
joins the gaps in the backbone between the segments of DNA (okazaki fragments) in the lagging strand, which were added in 5' to 3' direction |
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IN bacterial DNA, which is circular, DNA replication process begins at some site associated with the cytoplasmic membrane then... |
continues BIDIRECTIONALLY (two replication forks) eventually they meet and separate |
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The attachment site in the membrane assures... |
that during binary fisson, the two chromosomes migrate into separate daughter cells. |
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DNA synthesis is very fast occuring at .... |
1000 nucleotides per second w/ very few mistakes |
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3' to 5' exonuclease activity |
the proofreading ability of DNA polymerase. if incorrect nucleotide is add, it can recognize the mistake, back up, remove it and replace it with the correct one. |
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Bacterial cell can actually undergo binary fission... |
at a much faster rate than DNA replication b/c of the BUBBLES (bidirectional replication and multiple replication forks) |
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Transcription |
process by which a complementary strand of RNA is made from a DNA template |
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3 kinds of RNA |
mRNA-messenger, carries the info from the GENE to the ribosome rRNA-ribosomal, forms an important part of ribosomes tRNA-transfer, protein synthesis, transfers amino acids to ribosomes |
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Messenger RNA (mRNA) |
will have URACIL instead of thymine and is always complementary to the gene from which is was generated. |
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Transcription requires... |
the 4 RNA nucleotides (G,U,A,C) and RNA polymerase |
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Transcription begins.... |
when the RNA polymerase binds to a promoter. Only one of the strands of DNA (the coding strand) serves as a template. It is synthesized in the 5' to 3 ' direction |
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Terminator |
a signal in the DNA that stops transcription when RNA polymerase runs into it. the mRNA and the polymerase are then released from the DNA |
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transcription and translation are... |
coupled, since both occur in the cytoplasm |
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In eukaryotes, often mRNA must be processed before entering the cytoplasm b/c of the intervening sequences called______________, which do NOT code for a protein product. |
-INTRONS the coding sequences are called exons. After introns are removed , exons are spliced together. |
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Spliceosome |
a complex of enzymes including including ribozyme and the mRNA molecule. |
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Translation |
is the process by which each nitrogenous base of a mRNA molecule dictates which amino acids are joined together to form a protein. -1st 5' end of the mRNA associates w/ a ribosome( composed of rRNA into protein subunits) |
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Before an amino acid can be added to build a protein it must first... |
Be activated by attachment to a tRNA molecule. This is called charging and is accomplished by an enzyme called aminoacyl tRNA synthetase |
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Codon |
A set of three nucleotides in mRNA which specifies one amino acid |
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Anticodon |
The set of three nucleotides associated with the tRNA molecule.
If anticodon is complementary to the codon on the MRNA then the tRNA will transiently hydrogen bond to the message. This base pairing only occurs in a region where mRNA is associated with the ribosome |
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Start codon |
The first codon in the mRNA. this is where the first tRNA associates, and this occurs in the P site(peptidyl site) of the ribosome |
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A site (aminoacyl site) |
The 2nd position in the ribosome. When the 2nd tRNA fills the A site, a peptide bond is formed between the amino acids When this happens the first tRNA molecule then exits the ribosome leaving the amino acid behind. The ribosome then shifts down by one codon. The released tRNAs are recycled in new amino acids are charged to them |
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There are 64 possible codons |
61 in code for amino acids 3 are stop codons |
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The most common start codon is... |
AUG coding for methionine |
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Degeneracy |
The phenomenon of more than one codon for each amino acid because the 61 codons code for only 20 amino acids |
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Housekeeping genes(constitutively expressed genes) |
Genes expressed at a constant rate which encode proteins needed to maintain the cell |
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Repression |
A mechanism by which gene expression is inhibited genes are turned off. Regulatory proteins performing this job are called repressors |
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Repressors |
In gene regulation . they block the ability of RNA polymerase to transcribe the DNA |
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Induction |
A process which turns on expression of genes. The regulatory protein that turns on gene expression is called an INDUCER |
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Operon model |
Developed by Jacob and Monod Describes the way related genes are controlled by a single regulatory region |
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In addition to beta-galactosidase the lactose operon contains |
a permease gene: involved in transport of lactose into the cell and a Thiogalactoside transacetylase (involved in transport of galactose waste out of the cell) |
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The three structural genes are located... |
Next to each other in the DNA |
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Control region |
Contains an -operator determines whether transcription will occur or not & -promoter the region in which RNA polymerase binds to initiate transcription |
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Operon |
Composed of the structural genes in the control region |
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Lacl gene |
Another Gene involved in lactose utilization. It encodes a repressor protein which is constitutively synthesized |
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When lactose is NOT present... |
The repressor binds the operator site and prevents transcription |
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When lactose is PRESENT... |
It diffuses into the cell and is converted to allolactose |
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The allolactose (an inducer).... |
Activates the operon by binding to the repressor protein in doing so, the repressor CANNOT associate with the operator & transcription of the operon occurs |
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When glucose and lactose are BOTH present... |
Cell prefers to use glucose so LAC OPERON is shut off (repressed) |
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When glucose is used up... |
ATP is converted to cyclic AMP(cAMP)
which is an alarm to let the cell know that an alternate carbon Source must be used |
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Global regulation |
The ability of cAMP or any other molecule to control the expression of a wide variety of genes |
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If glucose is absent and lactose is present... |
Lac operon is turned on |
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If both lactose and glucose are present... |
Lac operon is turned off |
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Catabolite repression (the glucose effect) |
The affect glucose has on operons. This is governed by a protein called CAP and a region of DNA upstream of the lac operon called CRP |
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When glucose is low |
cAMP concentrations are high |
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CAP binds... |
cAMP |
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The CAP -cAMP vomplex binds the CRP site and lac operon is.... |
TURNED ON!! |
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CAP alone cannot find the CRP site |
When this site is empty Lac operon is off |
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When glucose is present it does not matter if... |
Lactose and thus allolactose is present b/c lac operon will still be OFF |
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Point mutation (single base change) |
The most common mutation. Mistake is carrying on to the daughter strand b/c of degeneracy of the genetic code it is likely that this will not result in change at the amino acid level |
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Mutations |
Changes made at the DNA level(mistakes) |
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Missense mutation |
When a codon is changed so that different amino acid is inserted |
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nonsense mutation |
When a stop codon is formed as a result of a point mutation |
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Frameshift mutation |
When one or more bases are inserted or deleted in DNA resulting in the shift in the 3 by codon reading frame.
This type of mutation affects every codon further down the line.
A frameshift mutation almost always results in inactive gene products |
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Mutagens |
Environmental agents that cause mutations |
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Ionizing radiation |
Gamma and x-rays Can cause DNA damage in the form of breaks in the chromosomes Can also cause errors in DNA replication and in repair mechanisms which lead to mutations |
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Non ionizing radiation |
UV light Can form covalent bonds between the thymines. Thymine dimers can be repaired by cutting them out and replacing them with bases according to the complementary strand. |
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Methods for detecting mutations |
-Direct selection -Indirect selection (using the replica plating technique): useful for identifying auxotrophs, bacteria which following mutation have specialized requirements for growth |
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Bacteria auxotrophs are used... |
In the Ames test to identify possible carcinogens |
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Genetic recombination |
Is the exchange of genes between DNA molecules to form a new molecule. In organism which is undergoing this process is called a recombinant |
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Transformation |
DNA is transferred from one bacterium to another in the form of naked DNA in solution. Recipient cell has now acquired new characteristics from donor cells & is thus transformed. |
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Competency |
When the recipient cell is in a physiological state in which it can receive DNA, it is called competent. Very few cells are naturally competent but competency can be forced in a laboratory |
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Conjugation |
Another mechanism of transferring DNA from one cell to another usually plasmid mediated. Differs from transformation in that it requires direct cell-to-cell contact, and the two conjugating cells are of opposite mating type. One cell must contain a plasmid that encodes for sex pilli which allows the direct transfer of single-stranded plasmid DNA to a recipient cell. |
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Transduction |
Is the infection of a bacterial cell by a bacteriophage |
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Generalized transduction |
Involves the lytic cycle of a bacteriophage during which the host cell's chromosomal DNA is chopped up into small fragments which may be packaged into a phage capsids. Defective phage can then transmit the chromosomal DNA of one cell to another cell |
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Specialized transduction |
Occurs following lysogeny when a prophage excises from the host's DNA and take some host chromosomal DNA along with it |
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Transposons |
Small segments of DNA which can move or be transposed from one region of DNA to another. Also called jumping genes May carry genes for antibiotic resistance or toxin production |
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Insertion sequences |
Regions which only in code for an enzyme called transposase(responsible for cutting and ligating DNA during transposition) |
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Recognition sequences |
Target specific sequences in target DNA for insertion |
