Learning goal 1 (case2) Flashcards
nucleic acids
DNA, RNA
building blocks of DNA, and nucleic acids
Nucleotides.
Nucleotides
A,T,G,C,U
Ribose,
Phosphate group
purine
adenine (A) and guanine (G).
pyrimidines
cytosine (C), thymine (T), and uracil (U).
A, T bonds
two hydrogen bonds
G, C bonds
three hydrogen bonds
monosaccharide
D-ribose. RNA
2-deoxy-D-ribose. DNA
sugar and base
nucleoside
bond between the phosphate group and the nucleoside
ester bond (-o-)
Primary structure
sequence nucleotides
backbone of DNA
stability, Monosaccharide and the phosphate group
deoxyribose and phosphate groups that are throug phosphodiester (5’-o-(o=p-oh)-o-3’) bonds connecting through the oxygen on the 5’ carbon of one to the oxygen on the 3’ carbon of another deoxyribose.
Bases function
carries information for protein synthesis
the asymmetrical ends of DNA
5’ prime (phosphate terminal(end), oh )
3’ prime ( deoxyribose, OH terminal(end) )
twisting of the DNA Alpha-Helix and the geometry of the bases impact on the DNA structure
B-DNA form:
creats wide gaps, minor and major grooves, its important binding sites for proteins that maintain DNA and regulate gene activity.
largest rna
mRna
secondery structure RNA
single stranded, or often single and souble stranded RNA becasue they can fold to peforme there functions, they also contain stem loops like the ones in tRNA
3d structure of DNA
in the nuclei, 147 paired bases in a Alpha-Helix DNA(-) (2nm) coiled around 8 Histones proteins core (+) (11nm) = nucleosomes»_space;» Chromatin form when a 30 nm fiber form of 6 nucleosomes pers turn (solenoid) a repeating unit.
chromatine fiber»_space;> loops»» (bands)»» stacked minibands (18 loops flower) matrix in the middle»» ALMIGHTY SUPERSTRUCTURE OF CHROMOSOME!!! with centromere in the middle.
short arm, long arm
when are nucleosomes considered chromatine
when a 30 nm fiber form from nucleosomes (solenoid), 6 nucleosomes per turn
where the energy comes from for polymerisation of DNA
from the two terminal phosphate group on the deoxynucleotide triphosphate ,that disbond and become Pyrophosphate, and constantly hydrolsed to provide energy for polyrisation.
DNA strands names
sense (coding) which has the same sequence as mRNA and antisense (template) which is processed by Polymerases in transcription
what regulate DNA function
proteins that bind to the grooves and can alter the DNA structure, regulate replication, transcription.
where the DNA of prokaryotes is located
central region called Nucleoid
cell set of DNA (all DNA)
genome
octameer
the 8 histones core of a nucleosome, consists of two copies of each histone proteins (H2A, H2B, H3, H4), each histone has both C-terminal (COOH free in an amino acid) histone-fold and N-terminal(NH2 free group) tail,when its created from mRNA, its created from N-terminus to C-terminus.
Each loop in chromsome loop’s band, contains 50 turn of chromatine thethered by…..
Nonhistone scaffold protein
histones relations to genes
determines which genes are active
Dna form in prokaryotes comparing to chromsomes in Eukaryote
Supercoiling
forms of DNA
A-DNA (dehydrated non-physiolgical), Z-DNA, B-DNA
B-DNA + mtheylation= Z-DNA recognised by a protein binds to it, to regulate transcription.
denaturation
breaking the hydrogen bonds between the bases in a DNA helix by eposing it to high temperature
why DNA with more G=C bonds isharder to denaturate
more H bonds
vertical gene transfer
transmission of DNA info from mother to daughter cell through replication, DNA doesnt serve structural role in cells
Semi- conservative replication
two daughter DNA each with one Parental strand and a new daughter strand.
types od replication
semi conservative, conservative, dispersive
conservative replicatio
the re-basepair of the used pair parental DNA strands. and daughter DNA two new pair together
dispersive
alternating parental and new daughter DNA segments
what is a primosome
a primosome is a protein complex (DnaG primase, DnaB helicase, DnaC helicase assistant, DnaT, PriA, Pri B, and PriC.) formed by primase enzyme responsible for creating RNA primers, in prokaryotes.
why do wwe have two replication forks
two helicases bond, goes both directions
how are supercoilings resolved
through topoismerase, by causing temporary nicks in the DNA helix
initiation
Helicase opens up Dna helix, breaks hydrogen bonds + activate primase = forms primosome. A replication bubble with its two replications forks forms in the origin of replication nucleotides sequence.
free nucleotides provides energy from breaking two phosphate bonds, from its three phosphate. the energy is used to form phosphatdieseter bond between two nucleotides.
the opening of the helix causes overwinding or suopercoiling, ahead of the replication forks.
how many repication origins in both types cells
pro, one origins, approximately 245 base pairs long wich with AT sequences.
euk, multiple up to 100,000 origin
DNA polymerase lll
requiere a template and a primer, 5’ > 3’ synthesize, he moves 3 to 5
proofread ( remove nuleotides that are accedintly added)
lagging strand
the strand made of okazaki fragments, with each has its own primer
single strand binding protein
coat the seperated strand causing to not bind again temporary
Dna igase
Dna ligase, repairs the Okazaki fragments in lagging strand
Sliding clamp
helps DNA polymerase to stay bonded on the lagging strand
topoisomerase
prevent the DNA helix from getting to tightly wounded
makes temporary nicks in the helix to release the tension, then sealing the nicks to avoid permanent damage.
DNA polymerase l
DNA repairing enzyme.
able to catalyse multiple polymerisation before releasing the template DNA.
filliling okazaki fragments with DNA
removes RNA primers from 5 to 3
proof reading from 3 to 5 exonuclease activity
exonuclease activity meaning
Exonucleases are enzymes that catalyze the removal of nucleotides in either the 5-prime to 3-prime or the 3-prime to 5-prime direction from the ends of single-stranded and/or double-stranded DNA. Removal of nucleotides is achieved by cleavage of phosphodiester bonds via hydrolysis
Dna polymerase ll
DNA replication
3 to f proofreading exonuclease activity
5 to 3 polymerase activity
interacts with DNA polymerase 3 to maintain the fidelity (accuracy) and processitivity of DNA replication
ORC
origin recognition copmplex, initiator protein by eukaryotes
ORC binds to two different areas at one end of the replicator durng G1 phase + recruits other replication proteins to foprm prereplicative complexes that get ativated between g phase and S phase
Pol ε
synthesizes the leading strand
Pol δ
synthesizes the lagging strand
what hapens when the primers are removed from the 5’ end of the new strand
overhang of the parental DNA, cant filled with complimentary DNA becasue DNA polymerase needs primer, this why the DNA get shorter after each repliation
eukaryote telomerase
has a complementary RNA sequence to the 3’ Overhang parental DNA strand after replication,
The RNA sequence s used to SYnthesize the complemantary strand
telomerase shift and the process is repeated
Primase and dna polymerase
continue the synthesize of the strand
RNA synthesized in … to … direction
5 to 3
molecules in replications
dNTP’s datp dctp etc…
which ion is needed for optimal DNA polymerase activity
Mg+ Magnesium
Molecules in Transcription
ATP GTP CTP UTC
Reverse transcriptase
DNA polymerase synthesiz double stranded DNA from RNA
is RNA polymerase rimer dependent
no
prokaryote transcription
initiation:
promoter sequence, signles the RNA polymerase to start transcription.
RNA- coding sequence, coding region for the RNA polymerase, determines the Amnio acids sequence.
terminator sequence, where the process stops
general transcription factors activate transcription
RNA polymerase has sigma factor to recognize the promoter
holoenzyme in the RNA polymerase contacts the -35 sequence and then binds to the full promoter (closed promoter complex)
untwists DNA in the -10 region (open promoter complex)
transcription elongation pro
o Transcription bubble
o Transcription factors unzip the double
helix by breaking the hydrogen bonds
o Sigma factor is released and RNA polymerase moves along the DNA
o Core enzyme can complete the transcription of the gene alone
o RNA polymerase continues to untwist the DNA ahead of it (behind the translation bubble the DNA strands reform into double stranded DNA)
o RNA exits the enzyme single stranded
o Two proofreading mechanisms:
1. replacing an incorrect nucleotide for a correct nucleotide (RNA polymerase reverses its synthesis reaction);
2. Enzyme moves back one or more nucleotides and cleaves the RNA at that position
termination transcription pro
terminator sequence (repetiton of a sequence)
core RNA polymerase terminate the process
RNA polymerase transcribes the terminator sequence > RNA folds into a hairpin loop structure
Rna polymerase dissociate from template
termination pro transcription hairpin loop stracture function
causes RNA polymerase to slow down and then pause in its catalysis of RNA synthesis
types of terminators in Pro transcription
Rho-depndent recognised by RNA polymerase and the Rho factor
Rho- independent: only RNA polymerase hairpin loop structure
transcription eukaryotes PRODUCT
pre-mRNA with introns (NON-CODING FOR AMINO ACIDS) and exons
Regions ofthe promotor in euk
core promoter , promotor proximal elements
core promotor function euk
ensure the start of transcription at the correct site
promotor proximal elements function
Short sequence element called Inr (initiator) which spans the transcription initiation start site;
2. The TATA box at position ca. -30; they determine where transcription will begin
TATA boxfunction
determines where transcription begin
Activators
regulate how and when a gene is expressed
enhancers
modulate the transcription form distance
the three mRNA parts
5’ UTR, untranslated region or leader sequence at the 5’ end, upstream
protein coding sequence
3’ UTR, trailer sequence, downstream
UTR can regulate gene expression
initiation transcript euk
RNA Pol ll, and GTF’s (general transcription factors) on the core promoter.
GTF bind and then RNA form complex
with other GTF’s
Preinitiation complex (PIC): GTFs and RNA polymerase 2 bind to promoter elements in a particular order
transcription begins
5’ end modification
5’ caping after RNApolymerase 2 made 20-30 nuc pre-mRNA
capping enzyme add guanine nucleotide (7-methyl guanosine) to the 5 end
it protects the transcript from being broken down. It also helps the ribosome attach to the mRNA and start reading it to make a protein
3 modification
poly a tail 50-250
The tail makes the transcript more stable and helps it get exported from the nucleus to the cytosol
ribonuclease
When a sequence called a polyadenylation signal shows up inan RNA molecule during transcription, an enzyme(ribonuclease) chops the RNA in two at that site.
Another enzyme adds about 100-200 adenine (A) nucleotides to the cut end, forming a poly-A tail.
splicing
introns chop chop, exons recombination occur occur, boom gigtrilion propapility amino acid sequence from one mRNA
are all genes transcriped
transcription for each gene is controlled individually
Cells carefully regulate transcription, transcribing just the genes whose products are needed at a particular moment
in prokaryote each group of genes are transcriped together
types of RNA
tRNA, rRNA
tRNA function
match mRNA codon and bring its aminoacid
L shape
has anti codon
attachment site of the amino acid
differ slightly in structure, cause each tRNA has its own amino acid
rRNA
responsible for most of the structure and function of the ribosome
