Quiz 3 Flashcards
genome
set of DNA in a living organism
genes
sequences of DNA that encode specific proteins
gene expression
transcription plus translation
How is DNA replicated?
- unwind helix
- Add complementary base pairs
phosphodiester bonds
phosphate groups are linked together by these bonds and the phosphate groups link carbon 5’ in on sugar to another 3’ in another sugar
Origins of replication (ORI)
-must unwind the DNA first
multiple points of origins of replication
-replication in both directions in bubble until the bubbles meet each other
-unwound and replication proceeds in both directions, which form replication forks
DNA helicase
uses energy from ATP hydrolysis to unwind the DNA
Single-strand binding proteins
keep the strands from getting
back together
Topoisomerase
prevents twisting, relieves pressure by cutting DNA and putting it back together
leading strand
continuous synthesis of DNA
lagging strand
discontinuous
DNA polymerase
requires a primer which is a short RNA starter. primer is complementary to the DNA template and is synthesized by an enzyme called primase.
okazaki fragments
Synthesis of the lagging strand
occurs in small, discontinuous
stretches. Each fragment requires its own primer
DNA polymerase III
adds nucleotides to the 3’ end until reaching the primer of the previous fragment
chromosome
lots of DNA packed together in a strand
translation
-nucleotide to amino acids
-process of which info from mRNA is used to build proteins
codon
sequence of 3 bases that code for/specify for an amino acid
genetic code
specifies which amino
acids will be used to build a protein.
- given a codon we can determine which specific amino acid is made/used
- multiple codons for one amino acid but theres no multiple amino acids for the same codon
start codon
AUG
tRNA
binds to specific amino acid
-anticodon= complementary to mRNA codon
- each is charged by a specific enzyme (amino acid has been added to tRNA which makes it charged)
- once it gives up one amino acid, it can attach to a new one
ribosome
- associate with mRNA
initiation
- an initiation complex forms around mRNA (small subunit of ribosome)
-first amino acid is always methionine which can be removed after translation
elongation
labelled as A, P, and E site
- large subunit catalyzes two reactions
P site
first RNA is located
- amino acid is then transferred and taken to the new tRNA that is in the A site
A site
new amino acid is located here (incoming tRNA
- after amino acid from P site is transferred, growing polypeptide bond starts forming
E site
for exit, tRNA leaves from e site
termination
stop codon in A site
- no amino acid matches up with stop codon
- stop codon binds to release factor which is a protein (cuts polypeptide off of tRNA)
What happens to a protein after translation?
- Proteins have specific functions, so it has to go to the right location
- Some proteins are modified (post-translational modification)
signal sequence
allows for protein to get to the right place in the cell
- translation starts from mRNA
- moved to rough ER
post translational modification
- phosphorylation: Addition of phosphate
groups catalyzed by
protein kinases. - Glycosylation: Addition of sugars to form
glycoproteins. - Proteolysis:
Polypeptide is cut by
proteases (e.g., signal
sequence is removed)
how/when can gene expression be regulated ?
Before transcription
* During transcription
* After transcription but before
translation
* At translation
* After translation
transcriptional control
are we starting transcription or not? best time to figure out if we are going through transcription
- allows for control of making of certain proteins
Constitutive genes
expressed in all cells at a constant rate
inducible genes
genes can be turned on/turn on expression of these genes
- control catabolic pathways
- genes turned on when needed to make protein
repressible genes
- genes can be turned off
- controls anabolic pathways
- turned off when product/protein production is sufficient
prokaryotic gene regulation
- regulation occurs when environmental changes need to be responded to (adapt to nutrients available in environment)
- Coordinate expression of genes with related functions
- Conserve energy by making certain proteins only when needed
sigma factors
-bind to RNAP and direct it
to certain promoters
-separate genes can have the same promoter sequence
- help regulate/start transcription with certain promoters
operon
-several genes can come together an be controlled by one promoter (make proteins needed for a certain function, might as well make them all together)
- includes, operator, promotor, and structural genes
structural genes
- 2 or more structural genes are part of the operon
-make proteins that do the thing that we want to do
-core of operon
operator
- all about regulation of proteins
- part of DNA that is the binding site for regulatory proteins
regulatory gene
makes regulatory proteins
- proteins are separate from operon
- can be active or inactive
lac operon
-An inducible operon regulated by a repressor protein (turn on when needed)
- ex. e. coli must quickly adjust in the intestine and quickly adjust to changes in food supply. they need lactose to use as energy source. Three proteins that e coli needs are only present if lactose is
- made up of 3 beta galactoside (structural genes). Must know z, y, and a genes
trp operon
A repressible operon regulated by a repressor protein
- the genes code for enzymes that
synthesize tryptophan (anabolic pathway)
- 5 enzymes needed to make tryptophan and when it is present the operon can be turned off
repressor protein
has two binding sites: one for operator that can block transcription
ex. if lactose is absent, the repressor prevents binding of RNA polymerase
What happens if lactose is present?
-binds to repressor and changes the repressors shape
-repressor can’t bind to
operator
-RNA polymerase can bind to
the promoter, and the genes
are transcribed.
how does lactose get broken down?
when lactose is present, there is a lot of it. It creates proteins and then those proteins will continue to break down the rest of the lactose.
- must know that whenever lactose is present you must break it down (catabolic reaction)
co repressor
when repressor is made it is inactive. the co repressor activates the repressor
- ex. tryptophan is the co repressor and activates repressor then binds to operator, then RNA polymerase cant bind and then no transcription occurs
allosteric regulation
allows for rapid changes in pathways
TATA box
Many eukaryote promoters contain this sequence
general transcription factors
RNA polymerase can only bind to the promoter
after general transcription factors bind to the
TATA box
Basal transcription apparatus
group of proteins that bind to DNA to start transcription
activators
increase transcription
repressors
decrease transcription
DNA sequences
enhancers (activators bind to and activate transcription) or silencers (DNA sequence that repressors bind to and repress transcription)
what determines rate of transcription?
The combination of factors present
determines the rate of transcription
How do eukaryotes coordinate expression of sets of genes?
EUKARYOTIC GENES ARE NOT ORGANIZED IN OPERONS
-Most genes have their own promoters, and may be far apart in the genome.
-If the genes have common regulatory sequences within promotors, they can
be regulated by the same transcription factors.
Epigenetic modification:
how we change the DNA structure and the accessibility of the DNA
histones
Protein that DNA wraps around
- there is an attraction between DNA and protein
-positively charged amino acids which attract the DNA negative charges from phosphates
nucleosome
made up of DNA wrapped around a core of eight histone proteins
How DNA is packaged
influences gene expression
Expression depends on
1. Modification of histone
proteins
2. Methylation of bases
heterochromatin
tightly packed and not expressed
euchromatin
loosely packed and expressed
What is a HAT?
Reduces ionic attraction and weakens
association of histone and DNA, and
“opens” the chromatin
Histone acetylation
promotes transcription
Histone deacetylases
can repress
transcription by removing acetyl groups
DNA methylation
natural process of
adding methyl groups to parts of DNA
-Methylated DNA is not expressed
-gives a stable long term silencing of genes
alternative splicing
take out introns but can also take out exons as well
- allows for different proteins
-complexity, more proteins we can make
- introns always spliced out
