Unit 6 - Gene Expression and Regulation Flashcards
function of nucleic acids
- hereditary information
- store and transmit genetic expression
structure of nucleic acids
- double stranded
- alpha helix
nucleotide composition
- nitrogenous base
- phosphate
- pentase sugar
how do nucleotide monomers join together to form a polymer
- complementary bases are bonded with hydrogen bonds
purines
A-G
- double rings
pyramidines
C-T
- single rings
how many hydrogen bonds between A-T
2 hydrogen bonds
how many hydrogen bonds between C-G
3 hydrogen bonds
what is meant by “DNA is antiparallel”
DNA runs in opposite directions
how are bases added to a DNA strand
- bases are added 5’ -> 3’
building of nucleic acids: arrival with 3 P groups
- nucleotides arrive with 3 phosphate groups
- that nucleotide is energy
building of nucleic acids: DNA polymerase III
- use the energy from breakin the 3-phosphate to bond nucleotides together
- energy coupling
energy coupling
- exergonic gives energy for endergonic reaction
when does DNA replicate
s-phase in mitosis
why does DNA replicate
- growth
- repair
- reproduction
topoisomerase
- loosens DNA, unwinds DNA
helicase
- breaks hydrogen bonds between bases
- “unzips DNA”
replication fork
dna helicase unzips here
DNA polymerase III
- adds complementary bases on the new daughter strand
**cannot start strand
primase / rna primase
- starts the replication process
- adds rna primer
templet strand
- original strand
leading strand
- continuous replication at DNA
- replicated in the direction of the replication fork
lagging strand
- opposite the direction of the replication fork
- replicated in fragments
- okazaki fragments
- DNA ligase binds these fragments together
- forms phosphodiester bonds
DNA polymerase I
- removes rna primers
- adds the correct nucleotides in place of primers (only in lagging strand)
what about the first RNA primers on the leading strand?
- they are removed and not replaced with nucleotides
telomeres
- repeating sequences of DNA (TTAAGGG)
- they get shorter everytime DNA replicates
- as they get smaller, eventually it will enter apoptosis
dna polymerase??
- add nucleotides
- proof read/check
- remove primers
- add bases
shape of prokaryotic DNA
circular DNA
semi-conservative replication
- the original parent strand is always going to be in at least one offspring
where does RNA processing occur?
in the nucleus
does RNA processing occur in prokaryotes and eukaryotes?
no, only eukaryotes
- prokaryotes do not have a nucleus
3 events in RNA processing
- modified guanine cap is added
- introns are removed and exons are spliced together
- poly a tail is added
RNA Processing: guanine cap
- 3 phosphates added to it
- function: attaches to the ribosome (for protection)
RNA Processing: introns and extrons
- introns are removed and exons are spliced together
introns
- noncoding regions of mRNA
- “in the way”
- these are removed using an SnRNP
exons
- coding regions for amino acids
SnRNP
- small nuclear RNA and proteins
- cut out introns
spliceosomes
- groups of SnRNPs
- splice = cut out introns and attach exons
RNA Processing: poly A tail
- poly A tail is added
- 50 to 250 adenine bases are added to the 3’ end of mRNA
- used for protection
alternate RNA splicing
- we can use different combinations of exons to produce different proteins
mRNA
instructions to make proteins
ribosomes
- reads mRNA 3 bases at a time (codon)
how many RNA bases call for an amino acid
3 RNA bases call for 1 amino acid
steps for translation
- initiation
- elongation
- termination
anti codon
initiation
- mRNA binds to ribosome (small ribosomal subunit)
- ribosome calls for an amino acid
- tRNA will bring amino acid, and bind with mRNA codon
elongation
-polypeptide is made, peptide bonds formed through dehydration synthesis
primary structure of a protein
polypeptide chain
termination
- a stop codon is reached
- polypeptide is released
** mutations
how many nitrogenous bases are in a polypeptide made from 219 amino acids
219 * 3 = 657
657 + 3 (stop codon) = 660 total bases
tRNA
transfer RNA that carries amino acids to the ribosome
prokaryotic translation
- no nucleus; DNA gets transcribed and RNA gets translated at the same time
what is the source of heritable information found in cells?
DNA and (sometimes) RNA are the primary sources of heritable information
what are the characteristics of DNA and RNA that allow them both to be used as hereditary materials?
- they store information as nitrogen base sequences
- base pairing occurs with specific pyramidines always pairing with specific purines
what differences exist between the heritable information found in prokaryotes and eukaryotes
- prokaryotes typically have circular chromosomes while eukaryotes have linear chromosomes
how is genetic information stored
- stored as a sequence of bases in DNA and RNA
in what ways are DNA and RNA structurally similar
- both are polymers containing nucleotides
- both are chain like
- both follow base pairing rules
pyramidines: rings
single ring structure
purines: rings
double ring structure
what is the purpose of DNA replication
- to ensure the continuity of hereditary information
- allows transmission of genes from one gen to the next
what does it mean for the replication process to be semiconservative
- results in a DNA molecule containing one og strand and a newly synthesized compliment
how does the directionality of a DNA molecule influence the replication process
what are the specific enzymes involved in replication and what is the function of each?
- helicase
- topoisomerase
- DNA Polymerase
- ligase
structure of DNA molecule in terms of phosphate and hydroxyl
- each DNA strand has a terminal phosphate group on one end and a terminal hydroxyl group (OH) on the other end
what is the phosphate terminus referred to as
5’ end
what is the hydroxyl terminus referred to as
3’ end
in what direction can nucleotides be added
- nucleotides can only be added to a growing strand in a 5’-3’ direction
- this means one strand will continously be made (leading strand)
which strand will always be synthesized continuosly
- leading strand
which strand will always be synthesized discontinuously, in fragments
- lagging strand
helicase
unwinds DNA strand
topoisomerase
- relaxes the supercoil at the replication fork
replication fork
- the location where the two strands are separated
DNA polymerase
- synthesizes new strands
- requires RNA primers to initiate synthesis
- attaches to the 3’ end of the template strand
- builds strands in the 5’-3’ direction
ligase
joins DNA fragments on the lagging strand
what is meant by the flow of genetic information
- genetic information flows from DNA to RNA to protien
what is transcription
- the process in which RNA polymerase uses the noncoding strand of DNA as a template to produce an mRNA molecule
RNA polymerase directionality
- RNA polymerase synthesizes mRNA in the 5’-3’ direction while reading DNA in the 3’-5’ direction
what are the diff types of RNA molecules and what is the function of each
- mRNA
- tRNA
- rRNA
mRNA
- carries genetic information from DNA to the ribosomes
- information is used to direct protein synthesis at the ribosomal site
- codons are found on mRNA
tRNA
- recruited to the ribosomes to help create a specific polypeptide sequence as directed by mRNA
- various tRNA molecules, each carrying a specific amino acid
- anti codon
anti-codon
- a 3-base sequence on tRNA
- correct base pairing of tRNA anti-codons with mRNA codons will result in the release and addition of an amino acid to a growing polypeptide
rRNA
- Ribosomal RNA
- functional units of ribosomes responsible for protein assembly
what are the mRNA transcript modifications that occur in eukaryotic cells
- addition of a poly-A tail
- addition of a GTP cap
- introns and exons
what is alternative splicing?
- when introns are excised from a primary mRNA transcript and exons are retained and joined together
how does alternative splicing result in different proteins
- different combinations of exons can be retained in a mature mRNA transcript
- diff exon combinations encode for different proteins
what does addition of a poly-A tail do
- 100-200 adenine nucleotides
- increases stability
- helps with exporting from nucleus
what does the addition of GTP cap do
- modified guanine nucleotide
- protects the transcript
- helps ribosome attach to mRNA
introns
- sequences of mRNA transcript that DO NOT CODE for amino acids
- these are removed during RNA processing
- not included in mature mRNA transcript
what is translation
- the process of generating polypeptides using the information carried on an mRNA molecule
exons
- sequences of mRNA transcript that code for amino acids
- retained during RNA processing
- different exons are connected in the mature mRNA transcript
what are the main steps of the translation process
initiation, elongation, termination
when does translation occur in prokaryotes
protein synthesis objective
- this is how we get the directions from DNA about how to make proteins and bring them to the ribosomes so that the ribosomes can join amino acids in a specific order to synthesize a protein
what are phenotypes dependent on
they depend on presence or absence of particular proteins
how do we get the directions from our genes into an actual protein
transcription and translation
where does translation / transcription occur in prokaryotes
the cytoplasm at the same time
miRNA
- Micro RNA
- promotion of genes
transcription simply put is just
- copying the code from DNA to RNA
DNA is read in what direction
3’-5’
coding strand
- 5’-3’
- codes for the proteins
template strand
- non coding strand
- minus strand
- antisense strand
- DNA that is used for transcription (3’-5’)
how does RNA polymerase know where to attach to begin transcription?
promoter region - RNA polymerase attaches and begins transcription
how does the RNA polymerase know where the promoter is
TATA box
TATA box
a repeating sequence of TATA nucleotides
how does RNA polymerase know where to stop
termination sequence
transcription factors
- proteins that grab RNA polymerase (this attaches to them) in order to start transcription
transcription initiation complex
- transcription factors, promoter, RNA polymerase - all bind to start transcription
RNA Processing
- results in mature mRNA
- only happens in eukaryotes
RNA Processing: 1
- modified guanine cap is added for protection
RNA Processing: 2
- introns are removed and exons are spliced together
what are mutations that could occur during termination in translation
how is it possible to have over 200 different types of human cells if we all start from one cell
- different genes are turned on and off (expressed)
histones
- proteins that DNA coils around
- 8 Histones coiled up is a nucleosome
what regulates gene expression in eukaryotes
- transcription factors (proteins that help RNA polymerase bind to the promoter)
- DNA coiling
euchromatin
- loosely/unwounded chromatin
- able to do transcription or translation
heterochromatin
- densly packed chromatin
- hidden
- no transcription therefore no translation
how do we modify the histone proteins and DNA
- add acetyl groups to the histone proteins
- relaxes the histone so that DNA is available for transcription
what happens if you remove the acetyl group from histones
- DNA ends up as heterochromatin
what happens during histone acetylation in relation to transcription
- if you acetylate the histone, gene transcription can be turned on
deacetylation in relation to transcription
- gene transcription is turned off
what is DNA methylation
- CH3
- add a methyl to the actual DNA
- brings you from euchromatin to heterochromatin
- **turns off gene transcription
how does DNA polymerase replicate DNA
- DNA polymerase reads the template strand in the 3’-5’ direction and carries complementary base pairs to create a new strand
how does DNA polymerase build the complimentary strand
- DNA polymerase reads the parent strand from 3’-5’ then builds the complementary strand from 5’-3’
role of the DNA polymerase
- DNA polymerase proofreads and corrects errors with the help of nucleases
- incorrect base pairs are removed, and correct ones inserted
DNA Ligase
bonds the nucleotides and the okazaki fragments together
helicase function
unwinds the parental double helix
DNA Replication - leading strand
- the DNA polymerase reads the parent strand from 3’-5’ and synthesizes continuosly in the leading strand in 5’-3’ direction, moving towards the replication fork
telomeres
- ends of eukaryotic DNA molecules
- protects coding genes from being eroded during multiple rounds of DNA replication
DNA replication vs Transcription + Translation
- DNA replication occurs only when the cell is ready to divide
- Translation and Transcription occur constantly to make proteins needed as the cell carries out metabolic activities
where does transcription occur in eukaryotes
transcription of DNA to RNA occurs in the nucleus
where does translation of RNA occur in eukaryotes
the cytoplasm
transcription: promoter
- TATA Box
- the part of the DNA where RNA Polymerase binds to start transcription
- noncoding DNA
transcription: transcription factors
- in eukaryotes
- proteins that bind to the promoter region and ease the binding of RNA polymerase to the promoter
why does the RNA get modified before it exits the nucleus into the cytoplasm?
purpose of 5’ cap and poly-A tail: prevent enzymatic degradation of the mRNA when it moves out of the nucleus into the cytoplasm
purpose of RNA splicing
removes the introns so that only the exons will remain in the mRNA that goes out into the cytoplasm to be translated
length of final mRNA vs. og mRNA
final mRNA is much shorter than the initial RNA transcript due to the removal of introns
function of mRNA
- carries the instruction for making a protein from a gene and delivers it to the site of translation (ribosome)
- this mRNA is a complementary copy of a segment of DNA
ribosomal RNA (rRNA) function
- part of the structure of the ribosome
mutations are caused by…
- a change in the sequence of DNA nucleotides
- error in DNA replication or as a result of environmental factors (mutagens)
phenotypic plasticity
- the ability of one genotype to produce several phenotypes when exposed to different environments
what are the bonds between nucleotides
phosphodiester bonds formed by dehydration synthesis
translation: initiation
- mRNA binds to small ribosomal subunit
- ribosome calles for tRNA to bring amino acid
- tRNA will bring amino acid and bind with mRNA codon
start codon is
AUG
translation: elongation
building a polypeptide by forming peptide bonds
explain why a normal polypeptide may have 100 amino acids whereas a mutated polypeptide may only have 10
there was a stop codon earlier in the sequence so the mutated polypeptide ended up shorter
