exam #2: quiz 1 Flashcards by tori livelli

genome

all the genetic information that defines an organism

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with the exception of RNA viruses, microbial genomes are encoded by?

DNA (deoxyribose nucleic acid)

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two types of gene transfer

vertical and horizontal transmission

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genomes vary in ____

size

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DNA function depends on ____

its chemical structure

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bacterial chromosomes are compacted into a ____

nucleoid

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___ supercoil DNA

topoisomerase

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prokaryotic genomes contain?

relatively small, topically circular, chromosomes and plasmids

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the genomes of some microbes include ______ elements that replicate ____

extrachromosomal DNA ; autonomously

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plasmids
-copy number per cell ____
-contain ____ that often play critical roles in certain situations (ex. _____)

-varies widely
-nonessential genes ; antibiotic resistance

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the coding content in a chromosome is broken up into function units called ?

genes

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____ code for proteins

structural genes

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noncoding content includes regulatory sequences like ___ and ___ that control the expression of ____
-does not encode ____

noncoding content includes regulatory sequences like promoters and enhancers that control the expression of coding genes
-does not encode RNA

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-prokaryotic genomes are _% noncoding
-eukaryotic genomes are _% noncoding

-<15%
->90%

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functional units of genes
-a gene can operate ___ of others
-or, it may exist in tandem with other genes in a unit called ____

-independently
-operon

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what is the monomer unit of DNA? polymer?

monomer = nucleotide
polymer = nucleic acid

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each nucleotide consists of three parts

deoxyribose sugar
phosphate group
nitrogenous base
-purines: adenine(A) and guanine(G)
-pyrimidines: cytosine(C) and thymine(T)

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how do eukaryotes compact their chromosomes?

DNA is tightly wound around a histone

bacteria pack their DNA into a series of ____, collectively called a ____
-the loops are over- and undertwisted, or ____, and then anchored by ___ proteins

loops or domains, nucleoid
-supercoiled, histone-like

in general, supercoils are introduced into chromosomes in a 3-step method

-produce a double-strand break in the circular chromosome
-pass an intact region of the DNA through the break
-seal the ends to generate a twist in the chromosome

supercoiling changes the ___ of DNA
-thus, enzymes that change DNA supercoiling are called _____

topology
-topoisomerases

to maintain proper ___, a cell must delicately balance the activities of two types of topoisomerases:

DNA negative supercoiling levels
-topoisomerase I and II

type I topoisomerase
-proteins
-cleavage
-relieves

-usually single proteins
-cleave one strand of DNA
-relieves negative supercoiling

type II topoisomerase
-subunits
-cleavage
-use ATP how
-example
-targeted by

-have multiple subunits
-cleave both strands of DNA
-use ATP to introduce negative supercoils
-example: DNA gyrase
-targeted by quinolone antibiotics

DNA replication -____ of biology -DNA replication needs to occur when?

-central dogma -each time a new generation of cells is produced by binary fission

DNA replication is fully/semi/not conservative? -give definition

semiconservative -each new double helix is composed of one parental strand and one newly synthesized strand

bacterial DNA replication

-origin (oriC) -replication bubble: two replication forks, bidirectional replication -termination (ter) sites

DnaA

initiator protein; binds to origin (oriC)

DnaB

helicase; unwinds helix to expose template strands

DnaG

primase; synthesizes RNA primers

DNA polymerase III

major replication enzyme

DNA polymerase I

replaces RNA primer with DNA

DNA gyrase

relieves positive DNA supercoiling

initiation controlled by ____, and by the binding of ___ to ____ -the ____ is a 245-bp sequence that includes a series of repeats bound by ____

initiation controlled by DNA methylation, and by the binding of DnaA initiator protein to the origin -the oriC origin is a 245-bp sequence that includes a series of repeats bound by specific replication factors

stage 1: initiating replicator _____ melts the DNA at ____ and assembles a replication machine called a _____ -___ (helicase loader) loads ___(helicase) -___ recruits ___ (primase); primase synthesizes a short ___ against each ____ -the ___ is completed by the addition of ___, which is held in place by a ____

DnaA melts the DNA at oriC and assembles a replication machine called a replisome -DnaC (helicase loader) loads DnaB (helicase) -DnaB recruits DnaG (primase); primase synthesizes a short RNA primer against each template strand -the replisome is completed by the addition of DNA polymerase III, which is held in place by a sliding clamp protein

stage 2: elongation of replicating DNA -____ "read" the nucleotide sequence of a ____ and synthesize a _____ -however, these enzymes are unable to start synthesis de novo; they all require a _____ via a primer for a nucleotide addition -thus, new DNA is always synthesized in the __ to __ direction -RNA primers are removed by ____ or the exonuclease activity of ___ -____ then synthesizes a DNA patch using the ___ end of the preexisting DNA fragment as a priming site -finally, ____ repairs the remaining phosphodiester nick

-DNA polymersases "read" the nucleotide sequence of a DNA template and synthesize a complementary DNA strand -however, these enzymes are unable to start synthesis de novo; they all require a free 3' OH group via a primer for a nucleotide addition -thus, new DNA is always synthesized in the 5' to 3' direction -RNA primers are removed by RNase H or the exonuclease activity of DNA polymerase I -DNA polymerase I then synthesizes a DNA patch using the 3' OH end of the preexisting DNA fragment as a priming site -finally, DNA ligase repairs the remaining phosphodiester nick

direction of replication -____ adds nucleotides only to the __ end of growing strand -replication can only go from __ to __

-DNA polymerase adds nucleotides only to the 3' end of growing strand -replication can only go from 5' to 3'

leading v.s lagging strand -okazaki fragments -synthesized simultaneously by a ___ with two ___ enzymes

leading strand: continuous towards replication fork lagging strand: discontinuous away from replication fork -okazaki fragments: discontinuously synthesized short DNA fragments forming the lagging strand -synthesized simultaneously by a replisome with two DNA polymerase III enzymes

____ operates ahead of each fork to relieve the torsional strain caused by ___ activity

DNA gyrase operates ahead of each fork to relieve the torsional strain caused by helicase activity

stage 3: terminating replication two replication forks meeting each other at the _____ -there are as many as ten ___ on the E.coli chromosome -__ binds to these sequences and ensures that the __ do not escape and continue replicating DNA -ringed __ formed at the completion of replication are separated by ___

two replication forks meeting each other at the termination site -there are as many as ten terminator sequences (ter) on the E.coli chromosome -Tus (terminus utilization substance) binds to these sequences and ensures that the polymerase complexes do not escape and continue replicating DNA -ringed catenases formed at the completion of replication are separated by topoisomerase IV

chromosomes in eukaryotic microbes -nucleus? -linear or circular? -larger or smaller than bacteria? -require ___ -pack with ___ -have ___ -mitosis or meiosis

-nucleus -linear -generally larger than bacteria -require telomerase to maintain ends of linear chromosomes -pack with histones -introns -mitosis

archaeal chromosomes -nucleus? -linear or circular? -one or multiple origins? -pack with ___ -replication proteins more closely related to?

-no nucleus (true prokaryote) -circular -multiple origins -pack with histones and alba -replication proteins more closely related to eukaryotes

DNA replication divided into three phases -what they are and where they occur

1. initiation: occurs at the origin (oriC) 2. elongation: occurs at the replication forks 3. termination: occurs at the terminus (ter)