Nucleotides + human genome Flashcards
Which bases are considered purines?
Structures.
NOTE: heterocycles, rings labelled counterclockwise
- adenine
- guanine
MNEMONIC: <span>P</span>ure <span>A</span>s <span>G</span>old
What are the oxidation products of purines?
Structures.
- adenine → hypoxanthine
- guanine → xanthine
Which bases are considered pyrimidines?
Structures.
NOTE: heterocycles, labelled counterclockwise
- cytosine
- uracil
- thymine (= methylated uracil)
MNEMONIC: <u>CUT</u>
Which kind of tautomerism is exhibited by purines and pyrimidines?
- amine - imine
- keto (oxo) - enol
⇒ physiologically amino + keto forms favored
What are nucleosides?
sugar linked to a ring -N of purine/pyrimidine by β-N-glycosidic bond (usually at N-1, N-9 position)
- in DNA: 2-deoxy-D-ribose (indicated by prefix “d”)
- in RNA: D-ribose
(add. -OH in DNA could be dangerous due to add. formation of H-bonds)
nucleo<strong>S</strong>ide is the<strong> s</strong>maller molecule
What is the reason for different conformations?
Differentiate.
no freedom of rotation about β-N-glycosidic bond btw purine/pyrimidine base + sugar
- syn = on same side
- anti = on opposite side (predominates in nature)
(similar to cis-/trans configuration)
What is a nucleotide?
nucleoside + phosphate esterified to a -OH of sugar (either 3’ or 5’) → mononucleotide
additional phosphates connected by acid anhydride bond → di-/trinucleotide (macroergic bonds)
nucleo<strong>S</strong>ide is the <strong>s</strong>maller molecule
What are the names of all bases?
Their ribonucleosides, deoxyribonucleosides resp.?
- base = -ine
- ribonucleoside = -osine/-idine
- deoxyribonucleoside = deoxy-
only exception: thymine - thymine - thymidine
Why are nucleotides as in DNA and RNA acidic?
due to phosphate diester bonds similar structure to phosphoric acid, slightly acidic
BUT: can act as buffers in pH btw 7 +/-2
How do you call the molecule formed by multiple nucleotides?
Biological function?
polynucleotid, nucleotides connected by 3’,5’-phosphodiester bonds
- phosphoester bond formed at 5’ carbon
- second nucleotide esterified to phosphate at 3’ carbon
→ forms the backbone of RNA and DNA
formed in condensation reaction
How is polynucleotide backbone of DNA/RNA broken down?
Which nucleic acid is more stable?
hydrolyzed by phosphodiesterases
→ RNA less stable b/c additional 2’-OH of ribose acts as nucleophil (e- donor) during hydrolysis
Describe the general layout of the DNA double helix.
strand backbones closer together on one side of the helix than on the other
-
major groove: where backbones far apart
NOTE: DNA binding proteins interact here - minor groove: where close together
⇒ grooves twist around the molecule on opposite sides
What does the Chargaff rule state?
describes ratio of bases
- [adenine] = [thymine]
- [guanine] = [cytosine]
BUT: [A+T] ≠ [G+T] in isolated DNA
Okay, now we have 2 polynucleotide strands connected by phosphodiester bonds…
But which types of bonds do the bases of both strands form to create a double stranded DNA molecule?
form H bonds on minor groove side
- 2 btw A-T
- 3 btw G-C (remember G looks like a mirrored 3)
⇒ G-C more resistant against denaturation
Explain the meaning of the 2 common terms that are used to further describe the structure of the DNA double helix:
- polarity
- antiparallel
- polarity: 2 different strand ends (5’, 3’) with different behavior
- antiparallel: strands bind to each other in opposite directon (5’ end to 3’ end and vice versa)
What are the 3 major forms of DNA?
- B-form: right-handed Watson-Crick structure, physiological form
- A-form: dehydrated form
- Z-form: left-handed
Which bonds, mechanisms stabilize the right handed structure of the double helix?
- H bonds: btw purine/pyrimidine bases
- van der Waals bonds + hydrophobic interactions: btw stacked adjacent base pairs
- anti-configuration of glycosidic bonds
- predominant tautomerism of bases
What is a palindromic sequence?
What can it cause?
inverted sequence on both strands
⇒ self complementary within each of the strands, can form hairpin (if single strand) or cruciform (if double strand) structures, virtually found in every large DNA molecule
How is a mirror repeat sequence different from a palindromic sequence?
also called: inverted repeat
inverted sequence on 1 strand
⇒ do NOT have complementary sequences within the same strand and CANNOT form hairpin or cruciform structures
What is H-DNA?
DNA triple helix that can form spontaneously within long sequences containing only pyrimidines (or only purines) in one strand
- 2 normally paired purine/pyrimidine strands via Watson-Crick base pairing
- 1 additional pyrimidine strand binding to purines via Hoogsteen base pairing
NOTE: this strand is parallel to purine strand
What is a guanine tetrade, quadruplex resp.?
formed in nucleic acids by sequences that are rich in guanine
⇒ Four Gs associate through Hoogsteen hydrogen bonding to form a square planar G tetrad
⇒ 2+ G tetrads can stack on top of each other to form a G quadruplex
(quadruplex structure further stabilized by the presence of a cation, especially K+, which sits in a central channel between each pair of tetrads)
What is the reason for UV-absorption of purines and pyrimidines?
absorbed by conjugated double bonds present in purines/pyrimidine
(this is responsible for mutagenic effect of UV light on DNA causing chemical modifications)
absorption spectrum = pH-dependent
BUT: at pH 7 all common nucleotides absorb at 260 nm
⇒ conc. often expressed as “absorbance at 260 nm”
How can the DNA be denaturated?
- increasing temperature
- decreasing salt concentration
What is DNA hyperchromicity?
incr. absorbance of denaturating DNA double strand at 260nm
Explain the temperature dependence of denaturation.
base pairs seperate when melting temperature TM reached
⇒ 50% hyperchromicity reached at ~ 70°C
NOTE: increased TM in DNA rich in G-C (3 H-bonds instead of 2 as for A-T pairing) → more stable
Why does a decreased salt concentration cause denaturation of DNA?
lower [cations] decreases TM b/c increased interchain repulsion btw neg. charged phosphates of phosphodiester backbones
→ increased denaturation
Explain the 3 phases of renaturation of ssDNA to dsDNA.
happens when physiological temperature/salt concentration regained
- joining of short, homologous sites on two strands
→ fast - reversible zipping of repeated sequences
→ slightly slower - zipping of single copy base pairs
→ slow
What is hybridization?
ssDNA can form double stranded hybrid molecule w/ non-DNA molecule, such as complementary RNA
Explain the semiconservative model of DNA replication.
How was this model proven to be valid?
parent DNA molecule denaturates, so that each strand can serve individually as template for the synthesis of a new complementary DNA strand
⇒ 2 identical, daughter DNA molecules created
proven by Meselson-Stahl experiment using “heavy” 15N DNA
Which 2 components comprise the human genome?
Differentiate btw types of sequences on the human genome.
nuclear (+ mitochondrial genome)
- 30% of DNA transcribed into RNA (introns + exons)
-
2% are exons, coding for proteins, rRNA, tRNA
(approx. 25,000 protein coding genes) - 50% are repetitive sequences
- 20% not categorized yet
NOTE: much more proteins (150 - 200k) can be synthesized due to alternative splicing
What are introns and exons?
- intron = region of DNA that does not code for protein
- exon = region of DNA that codes for protein
→ introns cut out for protein synthesis during process called splicing
Differentiate btw types of repetitive sequences.
-
SSRs (simple sequence repeats):
- repetitive sequences (2-500 bps)
-
STRs (short tandem repeats):
- very short repetitive sequences (2-5 bps)
- satellite DNA, microsatellites
- can be used for paternity tests, forensics
-
clustered repeats:
- form centromeres and telomers of chromosome
What are transposons?
group of interspersed repeats
gene sequences that are able to change position in genome (form an RNA intermediate, reverse transcriptase forms again DNA)
- make up approx. 45% of entire genome
- 2 groups: SINEs and LINEs (short/long interspersed nuclear elements)
What are SNPs?
single nucleotide polymorphism
chromosomes of diff. individuals identical for most DNA sequences → SNPs are variations of single bases
What are the 2 functions of DNA?
- source of information for synthesis of protein molecules
- information inherited by offspring
What is chromatin?
Components.
complex of macromolecules in eukaryotic cells, packaged into chromosome
consists of:
- dsDNA (= double stranded)
- histones: condense DNA
- non-histone proteins: enzymes resp. for DNA replication, repair, transport process of RNA
- RNA
Differentiate btw the terms haploid and diploid.
How many chromosomes does the human haploid genome have?
- *haploid** = number of chromosomes, in a gamete
- *diploid** = number of chromosome pairs, in somatic cells
- 22 autosomal chromosomes (number 1-22)
- 1 gonosomal chromosome (either X or Y)
Differentiate btw the 2 types of chromatin.
structure depends on stage of cell cycle
- euchromatin = accessible (“turned on”) chromatin that is actively transcribed during interphase
-
heterochromatin = highly condensed chromatin, w/ lower level of “activating” histone PMTs, untranscribed (“turned off”), either:
- constitutive: always inactive
- facultative: can be converted to euchromatin
Explain the structural levels of DNA compaction in a chromosome during metaphase.
compact transportable form, forming classical 4 arm structure
- dsDNA
- winds around histones to form nucleosome →“beads-on-a-string” (10-nm chromatin fibril)
- supercoiled fibrils form 30nm-chromatin fiber
- forms more and more supercoils
⇒ eventually 2 sister chromatids connected at centromere, terminally attached telomeres
What is crossing over?
2 homologous chromosomes align and chromatides exchange genetic information → recombination
⇒ incr. g_enetic variation_, one mechanism how evolution happened
What is a nucleosome?
basic unit of DNA packaging in eukaryotes, consisting of
- a segment of DNA wrapped around eight histone protein core twice in left-handed fashion
- connected to next “core particle” by stretches of linker DNA
NOTE: H1 associates individually w/ DNA at each octomer
Differentiate btw the types of histones.
decrease in size/molecular weight w/ increasing number (1 = largest/heaviest, etc.)
- H1 = stabilizes 30-nm chromatin fiber, associates w/ DNA at each octomer
- H2A + H2B = form dimer
- H3 + H4 = form tetramer
⇒ 2 dimers + 1 tetramer form histone octomer core of nucleosome
What is special for histone genes?
do NOT contain introns, are fully transcribed, unspliced
What is phasing?
preference of nucleosomes to certain regions
What are the advantages of supercoiled DNA structures?
What are negative supercoils?
energy is stored in supercoils (= torsional stress)
→ transition to another form that needs energy provided by underwinding
- negative supercoils: DNA twisted in direction opposite from the clockwise turns of B-DNA (ergo: left-handed)
Where can we find circular DNA?
In which forms does it exist?
- in mitochondria
- in bacteria, bacteriophages
- in many DNA-containing animal viruses
⇒ either in relaxed or supercoiled form
What is the function of mitochondrial genome (mtDNA)?
Clinical relevance?
tiny part of human genome
37 genes coding for:
- 2 mito.-specific rRNAs
- 22 mito.-specific tRNAs
- 13 proteins that play an important role in the resp. chain
⇒ inherited maternally, hence passed on to all children
Describe the structure of mtDNA.
- strands different in base composition
→ 1 H (heavy) + 1 L (light) strand, more genes encoded on H strand - D (displacement) loop = DNA triple helix w/ 2 overlapping copies of H strand, most of replication/transcription controlled here
- no introns
