Chapters 7, 8, 9 Flashcards
DNA is a simple molecule made up of only four building blocks called
nucleotides
Discovered double helical stucture
Watson & Crick
Who used a pneumonia-causing bacteria to discover that the genotype and phenotype can transformed by mixing it with heat-killed strain?
Frederick Griffith
Who discovered that DNA is the genetic material in bacteria?
Avery, MacLeod & McCarty
The demonstration that DNA is the transforming agent was the first evidence that genes (the hereditary material) are…
Composed of DNA
Who infected two E. coli cultures with many phage particles and found that the radioactivity ended up inside the bacterial cells, indicating that phage DNA entered the cells?
Hershey & Chase
3 components of DNA
1.) phosphate
2.) deoxyribose
3.) 4 nitrogenous bases
Name the 4 bases
adenine, guanine, cytosine, and thymine
The sugar in DNA is called “deoxyribose” because it contains ribose sugars that are…
Missing an oxygen atom
Two of the bases, adenine and guanine, have a double-ring structure characteristic of a class of chemicals called _____.
purines
Two of the bases, cytosine and thymine, have a single-ring structure characteristic of another class of chemicals called ______.
pyrimidines
All nucleotides have (3 things)
phosphate, sugar, base
The chemical subunits of DNA
deoxynucleotides
Who established certain empirical rules about the amounts of each type of nucleotide found in DNA?
Chargaff
DNA contains _____ of A and T nucleotides and G and C nucleotides
an equal amount
Organisms ____ in the relative amount of A + T versus G + C, but different tissues in the same organism have ____ relative amount of A + T versus G + C.
vary; the same
Whose X-ray data showed that DNA is helical, like a spiral staircase, long and skinny, and has two similar parts that are parallel to each other?
Rosalind Franklin
Nucleotide bases pair by:
Hydrogen bonding
complementary bases
Refers to specific pairing between adenine and thymine, guanine and cytosine, and adenine and uracil.
DNA is a ____-handed helix
right
On the outside of the double helix, the backbone of each strand is formed by alternating phosphate and deoxyribose sugar units that are connected by
phosphodiester linkages
Each sugar–phosphate backbone is said to have a ____ polarity, or direction
5′-to-3′
In double-stranded DNA, the two backbones are in ____ orientation
anti-parallel
A–T base pairs have ___ hydrogen bonds, and G–C base pairs have ___.
2; 3
Shallow _____ grooves occur where the sugar–phosphate backbones are far apart, and deep ____ grooves occur where they are close together
major, minor
Function of grooves
Protein binding
semiconservative replication
The established model of DNA replication in which each double-stranded molecule is composed of one parental strand and one newly polymerized strand.
the original strand
parental molecule
the new strand
daughter molecule
two other modes of replication that were also hypothesized
1.) conservative replication
2.) dispersive replication
Whose experiment set to allow parental DNA containing nucleotides of one density to replicate using nucleotides of a different density?
Meselson & Stahl
base linked to a sugar
nucleoside
Bacterial chromosomes are (shape)
Circular
The ends of the thick curve of dots defined two sites of ongoing DNA replication and are referred to as
replication forks
Whose experiment provided additional evidence for semiconservative replication and also demonstrated that replication in bacteria begins at one site in the genome and spreads bidirectionally by means of two replication forks?
Cairns
enzymes that disrupt hydrogen bonds that hold the two strands of the double helix together
Helicase
Prevents overwinding
topoisomerases
Unwound DNA is stabilized by
single-strand DNA-binding (SSB) proteins
Example of topoisomerase
DNA gyrase
The point of a specific sequence at which DNA replication is initiated.
origin of replication
it is easier to separate (melt) the double helix at stretches of DNA that are enriched in ___ base pairs
A-T
Who isolated a DNA polymerase from E. coli and demonstrated its enzymatic activity in vitro?
Kornberg
A bacterial enzyme that synthesizes DNA to connect Okazaki fragments during DNA replication.
DNA polymerase I
A bacterial enzyme that is the primary DNA polymerase during DNA replication.
DNA polymerase III
DNA synthesis must be initiated by this short chain of nucleotides that forms a segment of duplex nucleic acid:
Primer
Primers are synthesized by a set of proteins called a
Primosome
a central component of primosome is an RNA polymerase called
Primase
In DNA replication, the strand that is made in the 5′-to-3′ direction by continuous polymerization at the 3′ growing tip.
leading strand
A small segment of single-stranded DNA synthesized as part of the lagging strand in DNA replication.
Ozaki fragments
In DNA replication, the strand that is synthesized apparently in the 3′-to-5′ direction by the ligation of short fragments synthesized individually in the 5′-to-3′ direction.
Lagging strand
Because DNA replication is continuous for the leading strand and discontinuous for the lagging strand, the overall process is described as
semidiscontinuous
An enzyme involved in DNA replication and repair that seals the DNA backbone by catalyzing the formation of phosphodiester bonds.
DNA ligase
Responsible for proofreading
DNA pol I and DNA pol III
the _____ is more likely than DNA to contain errors
RNA primer
A molecular machine called the _____ carries out DNA synthesis
Replisome
A protein that encircles the DNA, keeping the enzyme DNA pol III attached to the DNA molecule at the replication fork, converting it from a distributive to a processive enzyme.
𝛃 clamp / sliding clamp
An enzyme that can add only a limited number of nucleotides before falling off the DNA template.
distributive enzyme
the behavior of DNA polymerase III, which can perform thousands of rounds of catalysis without dissociating from its substrate (the template DNA strand).
processive enzyme
The β clamp converts DNA polymerase III from a _____ to a _____ enzyme.
distributive; processive
Replication proceeds in both directions from hundreds or thousands of origins on
linear eukaryotic chromosomes.
DNA synthesis takes place only in ___ (synthesis) phase of the eukaryotic cell cycle
S
A eukaryotic complex that binds to origins of replication to initiate DNA replication.
origin recognition complex (ORC)
DNA replication in eukaryotes requires ____________, proteins that are only available during late mitosis (M) and G1 phase, ensuring that the genome is only replicated once per cell cycle.
Cdc6 and Cdt1
An enzyme that, with the use of a small RNA as a template, adds repetitive units to the ends of linear chromosomes to prevent shortening after replication.
Telomeres
An enzyme that, with the use of a small RNA as a template, adds repetitive units to the ends of linear chromosomes to prevent shortening after replication.
Telomerase
The discovery that the ends of chromosomes are made up of sequences repeated in tandem was made in 1978 by
Blackburn & Gall
An enzyme that catalyzes the synthesis of a DNA strand from an RNA template.
reverse transcriptase
A structure at the end of a telomere that masks the end from the factors that detect DNA breaks.
telomeric loop
Telomeres and telomerase are associated with _____ and _____
aging; cancer
Unlike DNA, RNA has a ____ rate of turnover within cells.
high
RNA has ____ sugar in its nucleotides
ribose
What replaces thymine in RNA?
Uracil
single-stranded but base pairs to itself to form double-stranded regions.
RNA
An RNA molecule transcribed from the DNA of a gene; a protein is translated from this RNA molecule by the action of ribosomes.
mRNA (messenger RNA)
RNA that is not translated into protein.
noncoding RNA (ncRNA)
A class of small RNA molecules that carry specific amino acids to the ribosome in the course of translation; an amino acid is inserted into the growing polypeptide chain when the anticodon of the corresponding tRNA pairs with a codon on the mRNA being translated.
tRNA (transfer RNA)
Several different noncoding RNAs that are components of the ribosome and are essential for protein synthesis.
ribosomal RNAs (rRNAs)
snRNA
small nuclear RNA
lncRNA
long noncoding RNA
miRNA
micro RNA
siRNA
small interfering RNA
The site at which the double helix is unwound so that RNA polymerase can use one of the DNA strands as a template for RNA synthesis.
transcription bubble
The strand of DNA that is copied (i.e., transcribed) by RNA polymerase.
template / noncoding strand
The nontemplate strand of a DNA molecule having the same sequence as that in the RNA transcript.
coding strand
An enzyme that catalyzes the synthesis of an RNA strand from a DNA template
RNA polymerase
The three distinct stages of transcription
initiation
elongation
termination
A DNA sequence that defines where transcription by RNA polymerase will begin.
promoter
Refers to a DNA or RNA sequence located on the 5′ side of a point of reference.
upstream
A _____ site is located closer to the 3′ end of a transcription unit.
downstream
Nucleotide positions upstream of the initiation site are indicated by a _____ sign
negative
In bacteria, promoters are bound by RNA polymerase ____ factors
sigma
A type of transcription termination mechanism in bacteria that involves the protein Rho.
Rho-dependent termination
Special sequences within the ____ of an mRNA direct transcription termination
3′ UTR
The abundance of an RNA in cells is determined by _____ and _______
transcription; decay
The first step of decay in bacteria is carried out by an _______, which cuts an RNA into two pieces
endonuclease
the next step of decay is carried out by ______, which digest the RNA pieces into single nucleotides starting at their 3′ end.
exonucleases
Eukaryotes have many genes that are
spaced far apart
Eukaryotes have ___ RNA polymerases
3
Transcription in eukaryotes takes place in the
Nucleus
DNA in eukaryotes is packaged with proteins into ______
chromatin
One of the main functions of ______ is to recruit a specific RNA polymerase and position it to begin RNA synthesis at the transcription start site.
general transcription factors (GTFs)
In the _____, initiation of rDNA gene transcription by RNA polymerase I is regulated by UCE and Core promoter elements and UBF, SL1, and TIF-1A regulatory factors.
nucleolus
A DNA sequence found in many eukaryotic genes that is located about 30 bp upstream of the transcription start site.
TATA box
About ____ of RNA polymerase II genes contain TATA box and/or Inr promoter elements.
half
The general transcription factors (GTFs) TFIIB and TFIID recruit RNA polymerase II and other GTFs to the promoter, forming a ______ and a transcription bubble.
pre-initiation complex (PIC)
Genes transcribed by RNA polymerase III are divided into three types, based on their
promoter elements
During elongation, the CTD of RNA polymerase II is chemically modified to serve as a _________ for other proteins involved in transcription and RNA processing.
binding site
A model proposing that transcription termination is caused by displacement of RNA polymerase II from DNA by an exonuclease.
torpedo termination model
A model proposing that transcription termination by RNA pol II is caused by a conformational change within its active site.
allosteric termination model
RNAs synthesized by RNA polymerase II, including mRNAs and snRNAs, are modified at their 5′ end by addition of a methylated guanine nucleotide, 7-methylguanosine (m7G), more commonly referred to as a
cap
The ____ end of a eukaryotic mRNA is modified to prevent decay and to serve as a binding site for factors that mediate mRNA processing and export
5’
______ of mRNAs is programmed to occur early in transcription through the association of capping enzymes with phosphorylated serine 5 on the CTD of RNA polymerase II.
Capping
The ___ end of mRNAs is modified by addition of a long stretch of adenosine nucleotides, which protects the mRNA from decay and supports translatio
3’
The _____ is added by a special type of RNA polymerase following mRNA cleavage at a site that is determined by protein factors that bind sequence elements in the mRNA.
poly(A) tail
A reaction that removes introns and joins together exons in pre-RNA.
splicing
_____ facilitate splicing by base pairing with conserved sequences in the pre-mRNA.
snRNAs
The first step is cleavage at the __ splice, and the second step is cleavage at the ___ splice site
5’; 3’
The joining of exons in different patterns via ____________ greatly expands the number of proteins encoded in the human genome and other eukaryotic genomes.
alternative splicing
RNAs are subject to ____ and _____
editing, modification
After removal of the poly(A) tail, mRNA decay by specialized enzymes occurs in
both directions
Researchers have taken advantage of the endogenous _____ machinery to knock down the expression of a specific gene by introducing into cells dsRNA that is identical in sequence to the target gene. (gene silencing)
RNAi
How many amino acids are there?
20
amino acids have which 3 groups
amino; carboxyl, R (side chain)
A codon of ____ nucleotides specifies an amino acid
3
The genetic code is _______; more than one codon can specify the same amino acid.
degenerate
The genetic code is _______; each nucleotide is part of only one codon.
nonoverlapping
The genetic code is ______; it is read from a fixed starting point and continues uninterrupted to the end of the open reading frame.
continuous
The genetic code contains how many codons
64
