Nucleic Acids

Roles 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