Studied by 14 peopleRoles of what:
long-term genetic info storage in organism + species
genetic info transmission from cells + generations
genetic info expression by rna + protein synthesis
DNA
Roles of DNA carried out through replication during __________ and transcription during _____________
dna repair, before cell division
gene expression
Transcription
gene expression, RNA synthesis (and mRNA by translation)
Differences bw genetic info in nucleus vs mitochondria
nucleus - low # long linear DNA molecules mitochondria - high # circular small DNA molecules
DNA is a long polymer made of __________ joined by ____________
nucleotides, ester bonds
DNA backbone is made of
alternating sugars and phosphate groups
Attached to the backbone of each sugar, there is
one of 4 types of nitrogen bases, encodes specific genetic info
In the mitochondria the DNA doesn't have proteins, but in the nucleus it does and forms the :
chromatin and chromosome structures during interphase + cell division
N-base of nucleotide can be either
purine - A or G pyrimidine - C or T
Roles of nucleoside triphosphates (ATP + GTP) vs nucleotides
energy carriers in pathways components of coenzymes
The sugars of DNA backbone are joined together by
phosphate groups that form phosphodiester bonds bw 3' and 5' carbon atoms of neighbouring sugar rings
Asymmetric ends of DNA has 5' ______ end and 3' _______ end
5' - terminal phosphate group 3' - free terminal hydroxyl group
N-bases are attached through their 1 or 9 nitrogen atoms in purine or pyrimidine rings to _____________ by _______
1' carbon atom of sugar by N-glycosidic bonds
Secondary structure of DNA
Two anti-parallel strands twist into a double helix, stabilized by hydrogen bonding between complementary bases (A-T & G-C) and hydrophobic interactions.
2 complementary nucleotides in 2 strands bind together with _____________ and are called a ___________
h+ bonds, base pair
A and T form ______ H+ bonds G and C form _________ H+ bonds
2, 3
strength of association bw 2 dna strands is determined by
% GC base pairs length of double helix
DNA structure is _____parallel and ____axial
antiparallel, coaxial
Alternate DNA structures found in functional organisms
B (Watson-Crick) and Z DNA
Traits of biological importance of B-DNA structure
complementarity
sugar-phosphate backbone externally to protect N-bases
bases in major groove exposed
Z-DNA
double helix winds to left in zigzag, elongated
Single-stranded DNA may appear during
replication and transcription
Triple-stranded DNA may appear in
displacement (D-) loop of the mitochondrial DNA
G-quadruplex DNA
guanine tetrad stabilizied by Hoogsten h+ bonding
RNA
ribonucleic acid w/ ribonucleotides as repeating units, pentose sugar w/ ribose and U-A
RNA primer
short rna sequence copied from DNA by RNA primase, priming for dna synthesis
messenger RNA
carries genetic info to cytoplasm, translated by ribosomes into amino acid sequences of coded protein
pre-mRNA
transcript of protein coding genes w/ introns, splices in nucleus to remove non-coding intros + joins exons
snRNA
involved in - splices introns during mRNA maturation + processing of functional RNA
snoRNA
small rna molecules that guide posttranscriptional base modifications in tRNA, rRNA, snRNA
tRNA
transports amino acid to place of translation
structure of tRNA
"T"-shaped, has anticodons complementary to the mRNA opposite of the amino acid
ribosomal RNA
rna part of ribosome, protein manufacturing
micro RNA
small RNAs of 21-33 nucleotides that bind to target mRNA at 3' UTR sequence, gene silencing (no translation)
siRNA (small interfering)
double stranded RNA, involved in RNA interference and gene silencing by binding to mRNA and digesting them
scRNA (small cytoplasmic RNA)
involved in specific protein selection and transportation
RNA component of telomerase
template for reverse-transcription so telomere sequences can be made
7SL RNA
rna component of SRP (signal recognition particle), recognizes and translocates ribosome-mRNA-nascent peptide complex to ER
large non-coding RNA molecules coded by XIST in the XIC
transcribed on inactivated X chromosome and involved in gene silencing and X chromosome inactivation during lyonization
traits of biological importance of nucleic acids
uv absorbance
chemical properties for genetic engineering
uv absorbance of nucleic acids
due to N-bases that are exposed in single stranded DNA
UV light induces the formation of
pyrimidine dimers (bind T or C), lesions that alter dna structure - inhibit polymerase cause skin malignancies
pyrimidine dimers may be repaired by
NER (nucleotide excision repair) or photoreactivation (w/ photolyase)
What leads to inability to repair damage by UV light
inherited mutation of gene coding for endonuclease of NER system
Denaturation
2 complementary strands of DNA in double helix separate by H+ bond breakage
Tm or melting temp
temp at which half of dna molecules is double-helicated and half is in random-coil single stranded
higher Tm associated w/ higher
GC content
Renaturation
reverse process of denaturation, reassembly of 2 complementary strands leading to normal conformation
Cot (concentration time analysis), study of dna reassociation kinetics
the more repetitive sequences the dna has, the faster the reassociation
Molecular hybridization
establishment of non-covalent sequence-specific interaction bw complementary strands of nucleic acids into 1 hybrid molecule
H+ bonding of single stranded nucleic acid is dependent on
complementarity
High vs low stringency of sequence detection
high - high hybridization temp and low salt in buffers, permits only hybridization low - low temp and high salt, allows hybridization when sequences are less similar
chromatin
packaged nuclear dna in the form of a nucleoprotein complex
In which mitosis phase is chromatin structured to make DNA template accesible
interphase
Identical molecules that differ only in supercoiling state are called
topoisomers
2 types of dna supercoiling
dna twisted in direction or opposite direction of helix
type of DNA supercoiling most prevalent
negative/opposite supercoiling, makes unwinding easier for replication/transcription by use of topoisomerases
histones function
provide structure on which dna winds + folds, involved in gene expression
Histones are small proteins that are highly
conserved (few differences among amino acid sequence in diff species)
Why do histones have high affinity to DNA
dna is negatively charged and histone is strongly alkaline + rich in Lys, Arg, His
Why do non-histone nuclear proteins (hertones) have a neg charge
they're rich ini Glu and Asp
non-histone nuclear proteins are associated with the ________ and involved in
chromatin dna and histone modifications
Chromatin function
package DNA into a small volume to fit into the nucleus of a cell and protect the DNA structure and sequence
types of chromatin
euchromatin (active and extended) and heterochromatin (inactive and condensed)
What stains lightly, has unmethylated DNA + histones, rich is GC and presents early replication?
euchromatin
What stains dark, aggregates, has methylated DNA and histones, rich in AT + repetitive sequences, doesn't participate in genetic recombination and presents late replication?
heterochromatin
constitutive vs facultative heterochromatin
-Constitutive: C-banding stained, stable, has satellite DNA, no genes, in well-defined places, polymorphic -Facultative : is reversible (to euchromatin), has LINE sequences
where is constitutive vs facultative heterochromatin present
constitutive - Y chromatin or fluorescent body, distal 2/3 of long arm of chromosome Y facultative - X chromosome in interphase
X sex chromatin is the result of _______, which is
dosage compensation, mechanism that equalizes gene expression on X chromosome according to the sex
Lyonization
random inactivation of the maternal or paternal X chromosome during mitosis of daughter cells
Heterochromatinization is mediated by
histone methylation on H3 and ubiquitination of H2A
Sequences at the __________ control the inactivation/lyonization process
X inactivation center (XIC) on the X chromosome, has Xist and Tsix + binding sites for regulatory proteins
X-inactive specific transcript (XIST)
gene which becomes active only on the chromosome that will become the Barr body, codes for 2 non-coding RNA molecules that gene silence (coats the inactive X chromosome)
Tsix
inhibits transcription of Xist on active X chromosome, encodes for large RNA
Basic repeating unit of chromatin
nucleosome
what does nucleosome have
histone proteins and dna sequence
Most basic organization level of double helix
beads (nucleosome) on a string (double stranded dna, negative supercoil), histone octamer core
nucleosomes in the basic double helix organization level are connected by
sections of double stranded spacer dna bw successive nucleosomes there is linker dna (w/ H1 type histone protein attached)
chromatosome
nucleosome + H1 histone
solenoid structure
made up of 6 nucleosomes w/ linker dna and h1 in bw (internally)
solenoid structure appears due to
successive H1 proteins binding together
where is solenoid structure found
interphase chromatin + mitotic chromosomes
levels of organization of chromatin
nucleosome, solenoid, scaffold, supercoil, chromosome
chromosome loops/scaffolding structure of chromatin
30 nm fiber/solenoid structure that forms loops, fixed by non-histone nuclear proteins (topoisomerase II)
genetic material reaches its peak level of packaging at which level
metaphase
in the chromosome, condensins and cohesins are ______ that
SMC (structural maintenance of chromosome) proteins induce positive supercoiling, aid condensation and sister chromatid binding at the centromere
mandatory structures on chromosome
chromatid
primary constriction
centromere
arms
telomere
chromatid
2 subunits carrying 2 linear dna double helices
centromere
Area where the chromatids of a chromosome are attached
what is removed in anaphase for chromosome to give rise to 2 chromosomes
sister chromatid separation protein (ISS), by ubiquitin
at the level of the centromere dna is made of
satellite dna and alphoid dna
telomere
2 ends of linear dna in chromatid, prevent chromosomes to attach, made of repetitive sequences
facultative elements on chromosome
satellites
terminal secondary constrictions
interstitial secondary constrictions
fragile sites
satellites
round terminal structures at the end of the short arm of the human acrocentric chromosomes in group D and G
terminal secondary constrictions
connect satellites to the rest of the short arm on the human acrocentric chromosomes from group D and G
interstitial secondary constrictions
on long arm of chromosomes 1,9,16, Y
fragile sites
non staining gaps on chromatids where they break spontaneously
Which type of band: rich in AT, resistant to nucleases, early condensation, late replication, poor in genes and Alu, rich in line
dark (G+) bands
Which type of band: rich in GC, sensible to nucleases, late condensation, early replication, rich in genes + Alu, poor in LINE
light (G-) bands
for replication, what must be done to dna structure
opening of chromatin fibers and histones removed so that active genes are in relaxed chromatin regions and inactive genes are in compact chromatin genes
Note
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