Chapters 16-18 Flashcards
purine
nitrogenous base with two rings, includes adenine and guanine
phosphodiester bonds
bonds formed between the phosphate on the 5’ carbon of one nucleotide and the 3’ carbon of the next nucleotide
pyrimidine
nitrogenous base with single ring structure, includes thymine, cytosine and uracil
nucleotide
3 phosphate groups + pentose sugar + nitrogenous base
nucleoside
pentose sugar + nitrogenous sugar
nucleotide residue
1 phosphate, pentose sugar, and nitrogenous base
the bond holding phosphates breaks to make energy for building process
first scientists credited with DNA structure
James Watson and Francis Crick
polarity of nucleotide chain
one end contains the roof of the pentose sugar (5’ carbon) and the other end is the left base of the pentose sugar (3’ carbon)
how many nucleotides chains are in RNA?
1
how many nucleotide chains are in DNA?
DNA is a double helix formed by combining two chains
how are two nucleotide chains linked?
hydrogen bonds between their bases (A,G,T,C)
antiparallel
run in opposite directions. 5’ end and 3’ end of opposite nucleotide chains are side-by-side
DNA is antiparallel
how does the sugar-phosphate backbone remain straight?
A purine always bonds with pyrimidine. always 3 rings in any pair, providing consistent width
What complementary base pair has 2 hydrogen bonds?
Adenine and Thymine
NOT URACIL because only DNA does this
What complementary base pair has 3 hydrogen bonds?
Guanine and Cytosine
angstrom
equal to 0.1 nanometers. used to measure wavelengths of EM radiation
distance between base pairs (steps of ladder)
3.4 angstroms
distance between sugar-phosphate backbones
20 angstroms
distance between every complete twist of helix
34 angstroms
3.4 angstroms between pairs, so 10 pairs per twist
Chargaff’s Rule
#purines = #pyrimidines #adenines = #thymines #cytosines = #guanines
ratio is very unlikely to be 1:1:1:1
Scientists used to think genetic material was ______
proteins
First proof that nucleic acid was genetic material and not protein
Bacterial transformation studies ny Frederick Griffith - 1928
Involved bacteria with glyco protein coats and without
Denaturation study by Oswald Avery, Colin Macleod, and Maclyn McCarty - 1944
Protein was destroyed with enzyme but bacteria transformation occurred
RNA was destroyed but bacteria transformation occurred
DNA was destroyed and transformation didn’t occur
Genetic material must be DNA
bacteriophage labeling by Hershey and Chase - 1952
radioactive sulfur was put into bacteriophage making protein coat radioactive
radioactive phosphorous was put into virus making nucleic acid radioactive
phosphorus was found in new phages, so DNA is genetic material
Tobacco Mosaic Virus Study by Fraenkel-Conrat and Singer - 1957
TMV protein coat put onto HRV RNA to make hybrid.
When virus replicates it is HRV RNA and protein coat. Therefore RNA was genetic material.
replication
when DNA makes copies of itself during synthesis stage of the cell cycle
semiconservative
Conservative
Two strands of DNA reassociate, therefore parental double helix is always together.
semiconservative
two strands of parental DNA molecule separate and act as a template for new complementary strand.
therefore each DNA strand is half parental and half new material
dispersive
each strand of DNA contains both old and newly synthesized DNA
old is dispersed throughout the strand
Matthew Meselson and Franklin Stahl - 1958
Grew E. coli in heavy isotope of nitrogen N (15) for several generations to make DNA heavy
Allow heavy DNA to replicate one time in normal nitrogen (14). Take sample and let it replicate one more time in normal nitrogen and take another sample.
Centrifuge spins DNA in Cesium Chloride
results: There was a single band midway in the tube after first replication. There were two bands, one midway and one higher up, in the tube after second replication
First replication was half and half heavy and nonheavy, second replication was one half and half and one all normal. Therefore semiconservative.
Replication is bidirectional
DNA strands unzip in opposite directions from the origin (where the DNA first opens)
replication forks/Y-junctions
opposite areas of unzipping
Number of origins in small molecules
only one origin for small chromosomes, such as E. coli
number of origins in larger chromosomes
there are multiple origins in larger chromosomes
replicon
area under control of 1 origin
there are multiple replicons in replicating eukaryotic DNA
Rates of replication
~25,000 bp/min in E. coli
~2,000 bp/min in eukaryotes (slower due to histones that get in the way)
Replication is semidiscontinuous
one strand replicates continuously, the other replicates in fragments (discontinuously)
leading strand
replicates in one piece
lagging strand
replicates in fragments
Okakazi fragments
new DNA fragments on the lagging strand
DNA ligase
later stitches together Okakazi fragments
Why is replication semidiscontinuous?
DNA can only build in the 5’ –> 3’ direction, with the phosphate on the 5’ carbon of the newly arriving nucleotide bonding to the 3’ carbon of the last nucleotide in the chain. Because the DNA molecule is antiparallel, the two new strands cannot be former in the same direction.
DNA proofreading
DNA Polymerase III proofreads while it builds the new DNA strand. If it has put it in an incorrect nucleotide, it has an exonuclease region that will remove the incorrect nucleic acid and replace it with the correct one.
error rates of replication
~1 incorrect nucleotide per 100,000 basepairs
post-proofreading ~1 incorrect nucleotide per 10 billion base pairs
In a nucleotide, the nitrogenous base is attached to the sugar’s _____ carbon and the phosphate group is attached to the sugar’s _____ carbon.
The nitrogenous base is attached to the sugar’s 1’ carbon and the phosphate group is attached to the sugar’s 5’ carbon.
The first step in the replication of DNA is catalyzed by
helicase. The first step of the DNA replication is unwinding the DNA double helix.
The action of helicase creates
Replication forks and replication bubbles
replication fork
transition region between paired and unpaired DNA strands
origin
area in middle of DNA where replication occurs bidirectionally
theta structure
structure when half of bacteria circular chromosome is replicated and the chromosome looks like the letter theta
histone
protein balls that DNA wraps around to keep DNA from getting tangled
its difficult for enzymes to build DNA around histones
core DNA
DNA that wraps around histones
linker DNA
DNA between histones
nucleosome
half linker DNA and histone and core DNA
Flow of genetic information (replication, transcription, translation) is called
central dogma
transcription is controlled by which enzyme?
RNA polymerase
Steps of Transcription
Initiation, Elongation, Termination
initiation
- RNA polymerase searches for and binds to the promoter site on the DNA.
- RNA polymerase melts the DNA strand open.
where is the region of the promoter located in eukaryotic cells?
approximately 25 base pairs up stream from where transcription of RNA from the DNA template will begin.
wht is the TATA box
region of promoter site containing several thymine-adenine bonds
Elongation
Transcription continues as nucleotides are added to the growing RNA strand by RNA polymerase in the 5’ -> 3’ direction according to the rules of complementarity until a terminator sequence is reached
Termination
- RNA polymerase detects a termination signal AAUAAA on the pre-mRNA strand
- The pre-mRNA drops free from the DNA template.
- Both ends of the pre-mRNA are capped to protect RNA from being destroyed by hydrolytic enzymes. A 5’ cap protects the leading edge of the mRNA and also helps the ribosome know where to attach to the mRNA. The 3’ end is protected by a poly-A tail (50-250 adenine)
Prokaryotic vs Eukaryotic transcription
prokaryotic cells do not have a nuclear envelope, transcription and translation can occur simultaneously
in eukaryotes transcription occurs in nucleus and translation occurs in the cytoplasm
introns
parts of pre-mRNA cleaved out of mRNA before leaving nucleus
exons
pieces of eukaryotic RNA that leave nucleus and travel to ribosomes for translation
spliceosomes
nuclear organelles that remove the introns and splice the exons together
how do spliceosomes work?
complementary base pairs of RNA inside spliceosomes connect to pre-mRNA and pull the pieces together
messenger RNA
carries genetic message from the DNA template in the nucleus to ribosomes in the cytoplasm where proteins are made
transfer RNA
brings amino acids (monomers of polypeptides) to the ribosomes where they will be linked together into a polypeptide
anticodon
area of transfer RNA where it connects to codon on mRNA
ribosomal RNA
forms a structural component of ribosomes
small nuclear RNA (snRNA)
tiny pieces of RNA combined with protein that are found in the nucleus of eukaryotic cells. they form a structural component of the spliceosome
Translation
using the genetic message transcribed in a strand of mRNA to code for the arrangement of amino acids into a polypeptide
Enzyme that attaches amino acid onto appropriate tRNA
aminoacyl-tRNA synthetase
Aminoacyl tRNA
a “charged amino acid”. amino acid attached to RNA
codon
sequence of 3 nucleotides on the mRNA strand. Each codon codes for the placement of one amino acid in the growing peptide strand.
there are 4 nucleotides and 3 nucleotides per codon so there are 64 (4 x 4 x 4) possible codons
regions of ribosome (3 letters)
EPA
A site of ribosome
aminoacyl-tRNA binding site; receives the newly arriving tRNA
P-site of ribosome
peptidyl-tRNA binding site; holds the tRNA with the growing peptide chain
e-site of ribosome
exit site; releases the empty tRNA
steps of translation
initiation, elongation, termination
Initiation of translation
- mRNA is threaded into the small ribosomal subunit (initiation factors aid this step)
- The first tRNA carrying methionine (Met) attaches to the start codon (AUG) of the mRNA strand
- The large ribosomal subunit combines with the small subunit. GTP is the energy source that combines the ribosomal subunit.
Elongation of translation
- Next tRNA arrives at a-site
- amino acid chain is added to new tRNA with peptidyl transferase
- translocase moves the ribosome down 3 nucleotides, putting old tRNA in e-site and exiting it
peptidyl transferase
enzyme used to form peptied bond between amino acid chain and new tRNA
translocase
enzyme that moves ribosome down three nucleotides
termination of translation
- a stop codon (UAG, UAA, or UGA) hits A-site
- further peptide elongation is blocked
- The last tRNA is released from ribosome
- Polypeptide chain is releases from ribosome
- mRNA is releases from ribosome
- Ribosomal units dissociate and are available to start process again
Release factors aid the release of tRNA, polypeptides and mRNA from ribosome
evolution
changes in the frequences of alleles in a population from one generation to the next
population
members of a species that occur together in a localized region; have a good probability of interbreeding
species
organisms potentially capable of interbreeding and producing viable, fertile offspring; often spatially separated
gene pool
sum of all alleles in a population
hardy-weinberg equilibrium
allelic frequences stay the same across generation
conditions of H-W equilibrium
P - Large population size R - Random Mating I - Isolation (no immigration or emigration) S - No selection (survival) M - no mutations
genetic drift
random shifts in alleles due to small population sizes
two equations of HW values
p + q = 1.0
p2 + 2pq + q2 = 1.0
p is dominant (power)
q is recessive (quiver)
