Molecular biology Flashcards
nucleic acids are..
found in the nucleus and possess many acidic phosphate groups
What are nucleotides built from
a sugar, an aromatic nitrogenous base, and 1-3 phosphate groups
What is the variable part of the DNA building block
the base
Watson crick dna model
cellular DNA is a right handed, antiparallel double helix held together by hydrogen bonds between bases
What is true about dna structure
It is also coiled and the double helix is stabilized by van Der Waals interactions between bases
What are prokaryotic genomes composed of
A single circular chromosome
What does dna gyrase do?
type of topoisomerase that uses energy of ATP to reduce strains and create super coils of double stranded DNA
How is dna packed
It is wrapped around histones to form nucleosomes which compose chromatin.
kinetochores
act as anchor attachment sites for spindle fibers
telomere function
they are the ends of linear chromosomes,
prevents chromosome deterioration and prevents fusion with neighboring chromosomes
They are eventually consumed and shorten during cell division
single nucleotide polymorphisms
mutations
Copy-number variations
structural variations in the genome that lead to different copies of DNA sections
tandem repeats
where short sequences of nucleotides are repeated one right after the other
Central Dogma
DNA leads to RNA via transcription and this RNA is used as a template during translation through ribosomes to create proteins
Degeneracy and (un) Ambiguity
Degenerate - multiple codons can code for the same amino acid
unambiguity- each codon specifies only a single amino acid
Meselson and Stahl experiment
showed that replication is semiconservative, meaning one strand of the helix is parental and one is newly synthesized daughter DNA.
origin of replication
specific place where helices begins to unwind the double helix
topoisomerase
cuts one or both of the strands and unwrap the helix to release excess tension created by helicases
single strand binding proteins
protects unpackaged DNA in preparation for replication and helps keep strand separated
primase
synthesizes RNA primer
DNA polymerase
catalyzes elongation of daughter strand using parental template
Where does polymerization occur?
Always in the 5 to 3 direction
What does DNA pol require
A template and a primer
lagging strands
wait until the replication fork widens before beginning to polymerize, comprised of Okazaki fragments discontinuous replication compared to continuous replication of leading strand
What direction do replication forks grow?
Away from the origin in both directions
What are RNA primers replaced by and how are fragments joined?
They are replaced by DNA and the fragments are joined by DNA ligase.
DNA polymerase III
does very fast elongation of leading strand, has proofreading function
DNA polymerase I
adds nucleotides at RNA primer, slower than III, capable of proofreading, also important for excision repair
theta replication
Replication of prokaryotes
telomerase
adds repetitive nucleotide sequences to ends of chromosomes
mutagens
any compound that can cause mutations
point mutations
single base pair substitutions
missense mutation
causes one amino acid to be replaced by another
nonsense mutation
stop codon replaces a regular codon and prematurely shortens the protein
silent mutation
codon is changed into a new codon for the same amino acid, causing no change
frameshift mutation
mutations that cause a change in reading frame
inversion
a segment of a chromosome is reversed end to end
Chromosome amplification
when a segment of a chromosome is duplicated
translocations
when recombination occurs between nonhomologous chromosomes
transposons
can jump around the genome through the cut and paste activity of transposase
hemizygosity
haploid expression in a diploid organisms can lead to increased effect of mutation on chromosomes
homology dependent repair pathways
Mutations on one strand of DNA can be repaired using the undamaged complementary info on the other strand
happens before dna replication (excision repair) or after dna replication (post replication repair)
mismatch repair pathway
targets mismatched watson crick base pairs that weren’t repaired by DNA polymerase proofreading during replication
Rna characteristics
single stranded, contains uracil instead of thymine, pentose ring is ribose
mRNA
carries genetic info to ribosome
monocistrionic
each piece of mRNA encodes only one polypeptide
tRNA
responsible for translating the genetic code
rRNA
major component of the ribosome
promoter
sequence of nucleotides on a chromosome that activates RNA polymerase to begin the process of transcription
sigma factor
required along with core enzyme to form holoenzyme that is responsible for initiation of prokaryotic transcription
helps polymerase find promoter
Three stages of transcription
initiation, elongation, termination
Eukaryotic vs prokaryotic transcription
Eukaryotic - takes place in nucleus, splicing out of introns by splieceosome, addition of 5’cap and 3’ poly A tail
primary transcript of prokaryotic transcription is mRNA ready to be translated.
The three rna polymerases
RNAP I - transcribes most rRNA
II - transcribes hnRNA (mRNA), most snRNA, and some miRNA
III - transcribes tRNA, long ncRNA, siRNA, some miRNA, and a subset of rRNA
anticodon
sequence of three ribonucleotides which is complementary to the mRNA codon the tRNA translates
amino acid acceptor site
where the amino acid is attached to the tRNA
wobble hypothesis
states that the first two codon-anticodon pairs obey normal base pairing rules but the third position is more flexible
trna loading/ amino acid activation
hydrolyzing two high energy phosphate bonds to provide the energy to attach an amino acids to its tRNA molecule
Ribosome binding sites
A site - where each new tRNA delivers its amino acid
P site - where the growing polypeptide chain is still attached to a tRNA
E site - exit tRNA site
tRNA moves from A to P to E
Shine Dalgarno sequence
the ribosome binding site of prokaryotic translation
prokaryotic translation steps
- initiation - small ribosomal subunits binds two initiation proteins
- elongation - has three steps, last step is translocation where an empty tRNA moves into the E site, tRNA with the growing polypeptide moves to the P site, and the next codon to be translated moves to the A site
- termination - stop codon appears in the A site
cap independent translation
when eukaryotes can start translation in the middle of an mRNA molecule
epigenetic
changes in gene expression not due to changes in DNA sequences, includes dna methylation, chromatin remodeling, and rna interference
genomic imprinting
when only one allele of a gene is expressed
lac operon vs trp operon
lac operon is inducible, since it codes for catabolic enzymes and trp is repressible since it codes for an enzyme that mediates anabolism.
lac operon only has high transcription when lactose is present and glucose is absent
trp genes are off in presence of tryptophan
transcription factors
crucial in transcription regulation
chaperones
fold proteins into their correct 3D shape
What is the reading direction of translation
5 to 3 on RNA template
