chapter 5 microbio

what is a genome?

entire collection of genetic material in a cell or virus

what is a gene

heritable unit of genetic material that determines a particular behavior

what is genotype

genetic makeup of an organism

phenotype

physiological and physical traits of an organism

differences in prokaryotic and eukaryotic genomes

prokaryotic: simple genomes/ chromosomal DNA and plasmids, few or one circular chromosome/ location of chromo is in nucleoid region/ DNA is organized by histone like proteins

eukaryotic: more complex/ chromosomal DNA, plasmids, and DNA in mitochondria and chloroplasts/ many chromosomes are linear/ chromosomes in nucleus/ DNA organized by histones

plasmid

pieces of DNA that exists outside of the chromosomal DNA in bacteria and a number of eukaryotic cells

three parts of nucleic acid

phosphate, a sugar (deoxy in DAN or ribose in RNA) and a nitrogen base

four nucleotides that make DNA & RNA

DNA: adenine, guanine, cytosine, thymine

RNA: adenine, guanine, cytosine and uracil

ATGC (uracil replaces thymine in RNA)

which nucleotide is different when comparing DNA and RNA nucleotides?

DNA= thymine

RNA-uracil

three main types of RNA

Messenger RNA, transfer RNA and ribosomal RNA

what type of RNA is translated

mRNA

which types of RNA are transcribed

mRNA, tRNA, rRNA

which types of RNA is/are not translated but used directly as functional molecules or RNA

tRNA and rRNA

differences between structure and function of RNA & DNA

 Unlike DNA, RNA doesn’t serve as the genome in cells (although, it can in certain viruses). Instead, in cells RNA mainly serves a an essential intermediate for building proteins. The nucleotides in RNA (ribonucleotides) are built using the sugar ribose, as opposed to the deoxyribose sugar found in DNA’s nucleotides. Recall that RNA uses uracil instead of thymine, leading to AU base pairs in RNA instead of AT base pairs. RNA is often single- stranded, while DNA tends to be a double-stranded helix

what is the central dogma of general flow of genetic info & exceptions

refers to the general flow of genetic information from DNA - RNA - protein; the revised central dogma considers that the RNA can be used as a template for DNA.

What is DNA replication

the process by which a cell copies its genome before it divides

why is there a low rate of DNA mutation during DNA replicationq

DNA polymerase has “proofreading” ensuring that the correct nucleotide is in the replicated DNA

what is an enzyme (end in ‘ase'')

proteins that facilitate chemical reactions in a cell

helicase

unwinds DNA helix

primase

builds RNA primers, multiple primers are requies to build the lagging strand

DNA polymerase III

main enzyme that copies DNA on the leading and laggin strand

DNA polymerase I

Replaces RNA primers with DNA also has a role in DNA replair

liagase

forms phosphodiester bond to seal nicks in the DNA sugar-phosphate backbone; important in DNA replication + repair

what is difference between leading and lagging strand in DNA replication

leading strand is the side of the parent DNA molecule that is copied in the same direction as helix unwinding. Laggin strand is the complementary strand of the parent DNA molecule that is copied/replicated in the opposite direction of helix unwinding -built in chunks Okasaki fragments

Which DNA strand has continuous replication?

leading

Which DNA strand has discontinuous replication?

lagging

okasaki fragments

segments/chunks of DNA that are built on the lagging strand during DNA replication; segments are glued by ligase to form a continuous DNA strand

gene expression & end product?

AKA Protein synthesis- cellular process in which genetic info within a cell is read and used to create proteins (end product)

transcription

first stage of protein synthesis in which genes in DNA are copied into a new format RNA

what enzyme is used from transcription

RNA polymerase

where does transcription occur in prokaryotes vs eukaryotes?

prokaryotes: cytoplasm

eukaryotes: nucleus

What is reverse transcription, and what enzymes that is used

Another form of PCR that is useful for detecting RNA in a sample, such as the genome of an RNA virus; in RT-PCR, the enzyme reverse transcriptase is used in conjunction with primers to build DNA that is complementary to RNA molecules in a sample

function of mRNA

contains codons that code for either an amino acid or stop signal; translated to build protein

function of tRNA

contains an anticodon loop complementary to the codon; carry the correct amino acid to a ribosome to build proteins

function fo rRNA

fold into 3D structures and combine w/ proteins to form ribosomes

when are all thre types of RNA produced?

during transcription but only mRNA is transcribed into protein. tRNA and rRNa are used directly in their RNA form to perform their functions

difference between exons and introns in eukaryotes

exons: in eukaryotic cells, certain segments of mRNA that are decoded to build a protein

introns: intervening sequences in mRNA that are clipped out before transcription; genetic material that is not decoded to build protein

How many STANDARD amino acids are encoded by the genetic code

20

what is redundancy in the genetic code mean

protects cells from genetic changes (mutations)

what is translation?

second stage of protein synthesis, process that entails reading mRNA to build proteins

what is a start codon and typically what is its RNA sequence

in initiation step of translation a ribosome attaches to the mRNA and scans until it encounters a start codon; where it adds the first amino acid. Start codon is AUG and the first amino acid added by the initiator tRNA in prokaryotes formyl methionine (fMet)

what amino acid does the start codon code for in prokaryotes vs eukaryotes

prokaryotes: formyl methionine (fMet)

eukaryotes: methionine (Met)

what occurs when a ribosome reaches a stop codon

signals termination of translation; encourages termination factors to enter ribosome, end translation and release completed protein

Where does translation occur in prokaryotes vs eukaryotes?

in the cytoplasm for both

what is an operon

a collection of genes controlled by a shared regulartory element

What is an epigenome

the collection of all chemical changes to the genome; the DNA methylation patter of a genome

what happens when a gene is methylated

adding methyl groups (CH3) to specific regions in DNA enriched with cytosine; silences a gene by preventing transcription

what does quorum sensing allow bacteria to do

the collective sensing and responding to changes within a bacterial community. it allows bacteria to aler their protein syntheisis in reponse to changes in the density of the population

what are small non-coding RNA’s and how do they affect protein synthesis

eukaryotes: microRNAs, short interfering RNAs

prokaryotes: small RNA limit protein synthesis by binding to mRNA using complementary base pairing

what are riboswitches and how can they impact protein synthesis

 Built-in-switches in mRNA that act as protein synthesis controls (over 20 classes of them). The riboswitches folded structure changes when the sensor region associates with the target metabolite. These changes in structure serve as on-off signals that determine how the riboswitch will affect transcription or translation.

differentiate substitution, insertion and deletion mutations

Substitution mutations occur when an incorrect nucleotide is added. Example: adding a nucleotide that contains guanine instead of thymine. Cells may make this sort of error when replicating or repairing DNA (sometimes called point mutations)

Insertion mutations occur when a cell adds one or more nucleotides to its genome sequence. These mutations tend to lead to shifts in the mRNA reading frame. Deletion mutations occur when one or more nucleotides are removed from a genome sequence.

As with insertion mutations, deletions tend to lead to frameshifts in the mRNA nucleotide sequence that can drastically alter the protein sequence

what are nonsense mutations, missense mutations and frameshift mutations and what occurs

Nonsense: a mutation that causes a codon to go from encoding an amino acid to encoding a stop signal

Missense mutations: a mutation in which the meaning of the codon is changed in a way that the wrong amino acid is added to the growing protein

Frameshift mutation: a mutation in which the reading frame of an mRNA is altered due to nucleotides being inserted or deleted from the coding region of a genetic sequence

What is a mutagen

chemical, physical, or biological agents that increase the rate of mutation.

what is a carcinogen?

mutagens that cause a rate of mutation that promotes the development of cancers

What is the Ames test used for?

test to identify potential mutagens

what are thymine dimers and how are they remediated in the cell

interfere with DNA replication and transcription unless they are removed and repaired

difference between horizontal and vertical gene transfer

Horizontal: occurs when genetic information is passed between cells by a process independent of cell division, and therefore separate from reproduction.

Vertical: occurs when cells pass their genetic information to the next generation (from parent cell to offspring) as a result of sexual or asexual cell division

Plasmid genes are not essential for a cell’s survival, but they confer advantages to the cell. What are two advantages of having plasmid genes

The ability to make toxins or defend against antibiotics

which type of HGT uses a pilus to transfer plasmid DNA to another cell

conjugation

how is genetic material obtained in transformation

Transformation is a type of horizontal gene transfer in which bacteria are genetically altered when they take up DNA from their environment

what experiment performed in 1920s showed that bacteria could be transformed to gain certain pathological features?

Classic experiments performed in the 1920s by Fredrick Griffith showed that bacteria could be transformed to gain certain pathological features. Griffith exposed mice to four different combinations of Streptococcus pneumoniae, which causes bacterial pneumonia in humans. Griffith infected mice with a living strain of S.pneumoniae that tends to be dangerously virulent because of its capsule and as expected, the mice died. Then, he infected the mice with a nonvirulent, living strain of S.pneumoniae that does not make a capsule and the mice remained healthy. In the third scenario he infected mice with heat-killed, encapsulated S.pneumoniae and because the pathogens were dead the mice remained healthy. Finally he gave the mice the combined treatments from scenarios two and three, and the mice died. Griffith was then able to isolate living encapsulated S.pneumoniae from the dead mice

how is genetic material obtained in transduction?

 Generalized transduction: carried out by bacteriophages, this is one example of a horizontal gene transfer mechanism that can convey new genes to a bacterial cell; in this process a bacteriophage randomly takes up a bacterial gene and carries if from the prior host to the new host bacterium

What are bacteriophages

viruses that infect bacteria

which scientist described jumping genes called transposable elements

Barbara McClintock

Which class of transposons utilizes reverse transcriptase to make cDNA

 Retrotransposons, which are segments of DNA that get transcribed into RNA which is then reverse transcribed into cDNA by reverse transcriptase

which class of transposons use a copy-and paste or a cut and paste strategy?

The second class of transposons, DNA transposons, are mobilized as DNA and do not require an RNA intermediate. They can use a copy and paste or a cut and paste mechanism to move in the genome