bios 350 unit 4 and 5

genotype

The genetic constitution of an organism, consisting of the alleles inherited from its parents, which influences its traits and characteristics.

phenotype

The observable physical or biochemical characteristics of an organism, determined by both its genotype and environmental factors.

what do cell receptors do

Cell receptors bind to specific molecules, initiating cellular responses and communication within the organism.

prokaryotic genomes

are typically smaller and consist of a single circular DNA molecule, lacking introns and complex packaging found in eukaryotic genomes.

units of genes

single gene vs operon

monocistronic vs polycistronic

regulons

are groups of genes or operons that are coordinately regulated by the same regulatory protein, allowing for coordinated expression in response to environmental changes.

steps of transcription

include initiation, elongation, and termination processes that convert DNA into RNA.

coding (+) strand

has the code for the protein

template (-) strand

is the DNA strand that is complementary to the coding strand and serves as the basis for RNA synthesis during transcription.

sigma factor

changeable subunit of RNA polymerase. Once it binds to the core RNA polymerase (consists of five subunits), it allows RNA polymerase to bind the promoter at a conserved genetic sequence that is 35 bases upstream of the start site for transcription. This region is called the -35 sequence. The sigma factor is essential for the initiation of transcription, helping RNA polymerase to recognize and bind to specific promoter sequences, thus facilitating the correct synthesis of RNA from DNA.

upstream

nucleotides before a site

downstream

nucleotides after a site that are transcribed into RNA during gene expression.

eukaryotes do not have

operons

elongation

synthesis of mRNA in 5’ to 3’ direction

termination

dna template has nucleotide sequences that signal RNA polymerase to stall and fall off

rho dependent termination

is a process in transcription where the rho protein recognizes specific sequences on the RNA transcript, facilitating the release of the RNA polymerase from the DNA template.

sense vs antisense strand

Sense strand is the DNA strand that has the same sequence as the mRNA, whereas the antisense strand is the complementary DNA strand that serves as the template for mRNA synthesis.

stop codons

are nucleotide triplets in mRNA that signal the termination of protein synthesis during translation.

every three rna nucleotides (codons) can be translated into

one amino acid

reading frame

each codon after the start is translated in a systematic fashion until a stop codon

initiation

First, the 30S subunit (specifically bases in the 16S rRNA) binds to a conserved sequence, called the Shine-Dalgarno sequence, immediately upstream of the start codon. Then, it scans the mRNA until it reaches the first start codon. Then, a tRNA binds the start codon before the 50S subunit completes the ribosomal structure. Then, elongation can begin.

elongation

The stage in protein synthesis where tRNAs bring amino acids to the ribosome, and the polypeptide chain is extended as ribosomes move along the mRNA. The ribosome reads the mRNA from 5' to 3' during elongation.

termination

During the termination of translation, only the release factor can recognize a stop codon. After binding the stop codon, the release factor (RF-1/2) causes the ribosome to stop and fall off.

exons

encode for functional polypeptide

introns

do not encode for functional polypeptide

rna splicing

removal of introns

where does translation occur

outside nucleus at ER (membrane destined) or cytoplasm (cytosol destined)

kosak sequence

found in most eukaryotic transcripts and includes start codon

main aim in dna replication

to produce a copy of the entire bacterial genome for binary fission

where does DNA replication start?

OriC or origin of replication and it is bidirectional and semiconservative

RNA polymerase unwinds and seperates DNA at the

-10 sequence

what recognizes the stop codon?

release factor

tRNA’s

bind codons via an anticodon and add the corresponding amino acid the polypeptide chain

during elongation mRNA is

capped with 5’ cap and 3’ poly- A tail

DNA A

is the genetic material that carries information for the development and functioning of living organisms. It is composed of two chains forming a double helix, containing nucleotides made up of a sugar, phosphate, and nitrogenous base. INITIATES REPLICATION.

DNA B

comprises the second strand of the DNA double helix, often complementary to DNA A. helicase

DNA C

helicase loader

DNA gyrase

releases pressure on DNA

SSB

Single-stranded binding protein that stabilizes single-stranded DNA during replication, preventing it from re-annealing.

DNA methylation

allows for precise control of replication

seqA

is a protein involved in regulating the timing of DNA replication in bacteria by interacting with the origins of replication. inhibits replication.

replication bubble

contains two replication forks that move in opposite directions around the chromosome

DnaG

primase, works 5’ to 3’

adds rna primers to strands as start point

DNA Pol III (1 of 5)

a DNA polymerase enzyme responsible for synthesizing new DNA strands during replication by adding nucleotides complementary to the template strand.

leading strand

synthesis of DNA is continuous

lagging strand

synthesis of DNA is discontinuous

DNA Pol III can

proofread

DNA Pol I and II are

required for DNA repair

Rnase H

removes RNA primers

DNA ligase

ligates pieces of DNA together

Tus

forms complex with ter site to stop replication

3 polymerases involved in elongation

Pol alpha : primase

Pol delta : lagging

Pol Epsilon: leading

end replication problem

refers to the inability of DNA polymerases to fully replicate the ends of linear chromosomes, leading to progressive shortening with each cell division.

telomere

end of linear chromosome

homologous recombination

integration of outside DNA with similar region in recipients genome

transformation

the process of importing free DNA into cells

natural competence

cells capable of natural transformation

natural competence in gram negatives

either are competent or not

can become more competent during starvation

natural competence gram positives

utilize transformasomes to import DNA across cell wall and membrane

use quorum sensing aka competence factors

artificial competence

chemical treatment to “force” cells to take in larger pieces of DNA

use of salt solutions (CaCl2) or electric current (electroporation) to “open” membranes to DNA

gene transfer by conjugation

plasmid transfer by cell-to-cell contact

requires f plasmid and f pilus

f+ cells are the genetic donors

f- cells are the recipients

rolling circle replication

a process by which a circular DNA molecule is replicated, creating a single-stranded DNA that can be transferred to another cell.

hfr cell

a type of bacterial cell with the F plasmid integrated into its chromosome, enabling efficient gene transfer during conjugation.

F’ plasmid

a modified F plasmid that carries chromosomal genes along with the fertility factor, allowing for more diverse gene transfer during conjugation.

R plasmids and R factor

are plasmids that carry antibiotic resistance genes, enabling bacteria to withstand the effects of antibiotics.

transposons

segments of DNA that can move between locations within a genome, facilitating genetic diversity and adaptation in organisms.

CAN INSERT RANDOMLY

CAN CREATE KNOCKOUT MUTATIONS

CAN CONTAIN ANTIBIOTIC RESISTANT AND ADAPTABILITY GENES

transduction

the process in which bacteriophages (bacterial viruses) carry host DNA from one cell to another

generalized transduction (lytic)

can transfer any gene from a donor to a recipient cell

specialized transduction (lysogenic)

can transfer only a few closely linked genes between cells

conjugation

the process by which genetic material is exchanged between bacterial cells through direct contact, often via a pilus.

transduction

the transfer of genetic material from one bacterium to another by a virus.

transformation

the uptake and incorporation of free DNA by a bacterial cell from its environment.

transposition

the movement of DNA segments within and between DNA molecules, often resulting in changes to gene expression.

from human to bacteria dna transfer

neisseria gonorrhoeae contain human derived sequences

from bacteria to plants

agrobacterium tumefaciens : transfers dna to plants

crown gall disease

a plant disease caused by the transfer of T-DNA from Agrobacterium tumefaciens, leading to tumor formation.

treatments of crown gall disease

destroy infected plants

prune infected stem (s)

treat roots with control bacteria

mutation

heritable change in the DNA

point mutation

change in a single nucleotide position

substitution

one or more bases are replaced by the same number of bases

inversion

DNA is flipped in orientation

insertion

one or more bases are added to a DNA sequence

deletion

removing one or more bases

(true) reversion

dna mutates back to original sequence

silent mutation

DNA change does not change the amino acids or function of the protein

missense mutation

changes the amino acid to another and can affect enzyme function

conditional mutation

only apparent under certain conditions

reversion mutation

a true reversion or suppressor mutation reverts the protein to its original function

nonsense mutation

changes the amino acid sequence to a stop codon

frame shift mutation

changes the open reading frame. occurs with insertion/deletion of nucleotides not divisible by 3

in frame mutation

occurs when nucleotides are inserted or deleted in multiples of three, maintaining the reading frame.

spontaneous mutation

typically a mistake in DNA replication that later affects transcription and translation

induced mutation

exposure of DNA to a mutagen

mutagens

chemicals or radiation that increase rate of mutation

chemical mutation

a mutation caused by chemical agents that alter DNA structure.

electromagnetic radiation mutation

ionizing and non-ionizing

proofreading

dna pol double checks new bases to make sure its a match

mismatch repair

sometimes dna pol misses and another set of enzymes check after replication machine moves

nucleotide excision repair

removes a set of nucleotides upstream and downstream a thymine dimer. then DNA pol I and dna ligase come and fill in the gap

ames test

a test to assess mutagenic potential of chemical compounds by observing their effects on bacteria. uses salmonella with mutation in hisG needed for histidine synthesis, and this means the bacteria cannot grow on media lacking histidine (amino acid) and if salmonella can grow on media without histidine, your chemical is a mutagen.