MICRO 2050 Exam 2 Study Guide-Noel MIlton

Structure of DNA

is double stranded and held together by hydrogen bonding between bases. two strands have complementary base sequences.

Topoisomerase

they insert and remove supercoils

DNA gyrase

introduces supercoils into DNA via- double strand breaks

Central Dogma

genetic information flow can be divided into three stages, DNA to RNA to proteins

Types of rRNA

catalytic and structural ribosome components

Genetic elements other than chromosome

virus genomes (contain either RNA or DNA genomes)

plasmids (circular or double stranded DNA that replicate separately from chromosome)

transposable elements (segments if DNA inserted into other DNA molecules that move from one site to another site on the same of a different DNA molecule)

Helicase

an essential enzyme involved in DNA replication. Its primary role is to unwind the DNA double helix by breaking the hydrogen bonds between complementary base pairs

primase

synthesizes short RNA primers. These primers serve as starting points for DNA polymerase, which requires a free 3'-OH group to begin adding nucleotides.

polymerase

responsible for synthesizing new DNA strands by adding nucleotides to a growing chain. It builds the new strand in the 5' to 3' direction by reading the template strand in the 3' to 5' direction.

ligase

joins broken or discontinuous DNA strands by forming a phosphodiester bond between adjacent nucleotides.

Semiconservative Replication

Each new DNA molecule consists of one original (parental) strand and one newly synthesized strand. This preserves half of the original DNA in each new molecule, ensuring genetic continuity.

Initiation

Begins at specific sites called origins of replication where helicase unwinds the DNA.

Elongation

DNA polymerase extends the new strands by adding complementary nucleotides.

termination

Replication ends when the entire DNA molecule is copied, and enzymes ensure the new strands are properly sealed and proofread.

leading vs. lagging strand

The leading strand is synthesized continuously in the same direction as the replication fork movement.

The lagging strand is synthesized discontinuously in short segments called Okazaki fragments, which are later joined by DNA ligase.

replication fork

the DNA double helix is unwound to allow the synthesis of new DNA strands. It represents the active site of replication, where the parental DNA strands are separated, and new complementary strands are synthesized.

proofreading

helps to ensure high fidelity

what is transcription of DNA?

RNA synthesis off DNA template yields messenger, transfer, and ribosomal, regulatory RNAs

what is the cell doing in transcription of DNA?

the cell is synthesizing messenger RNA (mRNA) from a DNA template. This process is the first step in gene expression, converting genetic information stored in DNA into a readable RNA format that can guide protein synthesis.

RNA polymerase?

carries out the process of transcription

promoters; pribnow box

are specific DNA sequences recognized by sequences vary but two highly conserved regions

sigma factors

a protein that plays a crucial role in prokaryotic transcription by guiding RNA polymerase to the correct starting point on the DNA.

operons

functional unit of prokaryotic DNA that consists of a cluster of genes under the control of a single promoter and regulated as a group.

termination

he final stage of transcription, where the synthesis of the RNA strand concludes, and the newly formed RNA molecule is released from the DNA template.

TATA box in eukarya

most important recognition sequence 6-8 base pair

functional groups

hydroxyl, carbonyl, barboxyl, amino, phosphate, and sulfhydryl

structure of proteins

are polymers of amino acids: organic compounds containing both amino and carboxylic acid

primary

linear array of amino acids in a polypeptide

secondary

from hydrogen bonding (alpha helix or beta sheet)

tertiary

three dimensional shape of polypeptides from hydrophobic and other interactions

quaternary structure

number and types of polypeptides (subunits)that make a protein

tRNA

anticodon matches codon on mRNA; encodes for a specific amino acid

start codon, stop codon, shine-delgarno sequence

start codon: translation begins with AUG, endoces N-formylmethionine in bacteria and methionine in Archaea and Eukarya

Stop (nonsense) codons: terminate translation (UAA, UAG, UGA) sometimes unusual amino acids selenocysteine and pyrrolysine can be encoded by stop/nonsense codons

Shine-delgarno sequence: or the ribosome binding site, ensures proper reading frame in bacteria

ribosomes

large complexes of proteins and RNA where proteins are biosynthesized

how basic translation works

the process by which cells use the information encoded in messenger RNA (mRNA) to build a polypeptide chain (protein).

a, p, e sites on tRNA; energy comes from GTP

The A site is where the incoming aminoacyl-tRNA (a tRNA carrying an amino acid) binds to the ribosome.

The P site holds the tRNA that carries the growing polypeptide chain.

The E site is where the now empty tRNA (after transferring its amino acid to the growing chain) exits the ribosome.

chaperone proteins

catalyze macromolecular folding events

a type of heat shock protein

protein secretion

some proteins must be transported outside cytoplasmic membrane into periplasm or inserted into cytoplasmic/outer membrane

sec translocases vs. Tat translocases

The Sec system specializes in moving unfolded proteins with ATP-driven energy, while the Tat system is designed for fully folded proteins and relies solely on the proton motive force. Both systems are crucial for bacterial survival, aiding in processes such as enzyme secretion, cell wall construction, and adaptation to environmental conditions.

activator vs repressor

activator- turns on transcription and binds DNA and recruits RNA polymerase or sigma factors to promoter region.

repressor- turns off expression and binds operator region of DNA downstream of promoter

inducers vs corepressors

inducers turn on transcription

corepressors turn off transcription

where does the repressor bind? what does it do?

binds to the operator region. it acts as a regulatory switch , and the repressors binding prevents transcription

repression used for anabolic pathways

In anabolic pathways, repression is controlled through a negative feedback mechanism involving a corepressor — the end product of the pathway itself.

induction-making the repressor fall off: negative control

a gene regulation mechanism in which a repressor protein is actively bound to the operator, preventing transcription. In this system, transcription is initiated only when an inducer molecule causes the repressor to detach from the DNA.

activation-where does the activator do and bind to?

binds DNA. Recruits RNA polymerase or sigma factor to promoter region

what is a regulon?

multiple operons controlled by the same regulatory protein

signal transduction

external sign may be detected by sensor and transmitted to regulatory machinery

what does kinase do?

detects environmental signal and autophosphorylates at specific histidine residue.

what is quorum sensing? examples of when it is used

regulatory mechanism by which bacteria and some archaea assess their population density

E Coli, Staphylococcus aureus,

catabolic repression

controls use of carbon sources if more than one present glucose always used first . can lead to diauxic growth

when there is more than one sugar present does the cell utilize all of them at the same time?

no the best carbon and energy source is used first

diauxic growth

two exponential growth phases if two energy sources available

cyclic AMP and CRP proteins

Cyclic CRP- an activator protein, and is a form of activation CRP is allosteric and binds to DNA only if it has first bound cyclic cAMP.

Cyclic AMP- regulatory nucleotide derived from adenosine synthesized bu adenylate cyclase

two ways that lac operon is regulated

Cyclic AMP and Cyclic CRP proteins

what is heat shock response?

global control mechanism to protect cells from protein denaturation resulting from heat, high solvent levels, osmotic stress, ultraviolet light

RpoH and DnaK repsonse are?

sigma factors

stopping transcription before it finishes?

attenuation

post translational regulation?

refers to the control of a protein’s activity, stability, or location after it has been synthesized during translation.

the product of an anabolic pathway becomes an inhibitor

feedback inhibition

allosteric site vs. active site on enzyme

binding at allosteric site changes conformation, preventing substrate binding

does not prevent substrate binding or change conformation

wildtype vs mutant

wildtype-isolated from nature

mutant- a cell or virus derived from wild type that carries a nucleotide sequence change

genotype

designated by three lowercase letters followed by capital, all italicized

phenotype

observable properties may also be altered

selective vs nonselective mutations

selective- do not affect sequence of encoded polypeptide or phenotype

nonselective-

auxotrophs

loss of enzyme in biosynthetic pathway. inability to grow on medium lacking the nutrient

spontaneous mutations vs induced mutations

spontaneous- occur without external intervention

induced- caused environmentally or deliberately

point mutations; silent; missense; nonsense

point- change only one base pair

transitions vs transversions

transitions are purines substituted for other purines or pyrimidines substituted for other pyrimidines

transversions are purines substituted for pyrimidines or vice versa

frameshift mutations

single base pair deletions or insertions that result in a shift in the reading frame

mutagens

chemical, physical, or biological agent that increase mutation rates, induce mutations

chemical mutagens vs radiation mutagens

chemical- induce chemical modifications or frameshift mutations

radiation- can cause mutations by damaging the DNA structure in cells

SOS system to repair DNA

stalled replication or major DNA damage activated this

LexA and RecA

regulators

what is genetic recombination?

physical exchange of DNA between genetic elements

genetic recombination competence

he rearrangement of genetic material to form new gene combinations.

regulation of genetic recombination competence

a tightly controlled process that ensures bacterial cells become competent only under specific environmental conditions or stages of growth.

what is transformation?

genetic transfer process by which free DNA is incorporated into a recipient cell and brings about genetic change

Competence of transformation

a cell that can take up DNA and be transformed; genetically determined

regulation of transformation competence

a bacterial cell's ability to take up extracellular DNA and integrate it into its genome.

generalized vs specific transduction

generalized- DNA from any portion of the host genome is packaged inside the virion

specific- DNA from a specific region of the host chromosome is integrated directly into the virus genome, typically replacing some viral genes

F Plasmid Conjugation

a type of horizontal gene transfer in bacteria that allows genetic material to pass directly from one cell to another via conjugation

formation of Hfr strains

The formation of an Hfr strain occurs through a process where the F plasmid integrates into the bacterial chromosome via homologous recombination.

transposable elements

Transposable elements (TEs), also known as "jumping genes," are DNA sequences that can move (or "transpose") from one location to another within the genome.