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Biochemistry I > Nucleotides + human genome > Flashcards

Nucleotides + human genome Flashcards

1
Q

Which bases are considered purines?

Structures.

A

NOTE: heterocycles, rings labelled counterclockwise

  • adenine
  • guanine

​MNEMONIC: <span>P</span>ure <span>A</span>s <span>G</span>old

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2
Q

What are the oxidation products of purines?

Structures.

A
  • adenine → hypoxanthine
  • guanine → xanthine
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3
Q

Which bases are considered pyrimidines?

Structures.

A

NOTE: heterocycles, labelled counterclockwise

  • cytosine
  • uracil
  • thymine (= methylated uracil)

​MNEMONIC: <u>CUT</u>

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4
Q

Which kind of tautomerism is exhibited by purines and pyrimidines?

A
  • amine - imine
  • keto (oxo) - enol

⇒ physiologically amino + keto forms favored

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5
Q

What are nucleosides?

A

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​

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6
Q

What is the reason for different conformations?

Differentiate.

A

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)

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7
Q

What is a nucleotide?

A

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

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8
Q

What are the names of all bases?

Their ribonucleosides, deoxyribonucleosides resp.?

A
  • base = -ine
  • ribonucleoside = -osine/-idine
  • deoxyribonucleoside = deoxy-

only exception: thymine - thymine - thymidine

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9
Q

Why are nucleotides as in DNA and RNA acidic?

A

due to phosphate diester bonds similar structure to phosphoric acid, slightly acidic

BUT: can act as buffers in pH btw 7 +/-2

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10
Q

How do you call the molecule formed by multiple nucleotides?

Biological function?

A

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

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11
Q

How is polynucleotide backbone of DNA/RNA broken down?

Which nucleic acid is more stable?

A

hydrolyzed by phosphodiesterases

→ RNA less stable b/c additional 2’-OH of ribose acts as nucleophil (e- donor) during hydrolysis

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12
Q

Describe the general layout of the DNA double helix.

A

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

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13
Q

What does the Chargaff rule state?

A

describes ratio of bases

  • [adenine] = [thymine]
  • [guanine] = [cytosine]

BUT: [A+T] ≠ [G+T] in isolated DNA

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14
Q

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?

A

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

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15
Q

Explain the meaning of the 2 common terms that are used to further describe the structure of the DNA double helix:

  • polarity
  • antiparallel
A
  • 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)
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16
Q

What are the 3 major forms of DNA?

A
  • B-form: right-handed Watson-Crick structure, physiological form
  • A-form: dehydrated form
  • Z-form: left-handed
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17
Q

Which bonds, mechanisms stabilize the right handed structure of the double helix?

A
  • 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
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18
Q

What is a palindromic sequence?

What can it cause?

A

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

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19
Q

How is a mirror repeat sequence different from a palindromic sequence?

A

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

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20
Q

What is H-DNA?

A

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
21
Q

What is a guanine tetrade, quadruplex resp.?

A

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)

22
Q

What is the reason for UV-absorption of purines and pyrimidines?

A

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”

23
Q

How can the DNA be denaturated?

A
  • increasing temperature
  • decreasing salt concentration
24
Q

What is DNA hyperchromicity?

A

incr. absorbance of denaturating DNA double strand at 260nm

25
Q

Explain the temperature dependence of denaturation.

A

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

26
Q

Why does a decreased salt concentration cause denaturation of DNA?

A

lower [cations] decreases TM b/c increased interchain repulsion btw neg. charged phosphates of phosphodiester backbones

→ increased denaturation

27
Q

Explain the 3 phases of renaturation of ssDNA to dsDNA.

A

happens when physiological temperature/salt concentration regained

  1. joining of short, homologous sites on two strands
    → fast
  2. reversible zipping of repeated sequences
    → slightly slower
  3. zipping of single copy base pairs
    → slow
28
Q

What is hybridization?

A

ssDNA can form double stranded hybrid molecule w/ non-DNA molecule, such as complementary RNA

29
Q

Explain the semiconservative model of DNA replication.

How was this model proven to be valid?

A

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

30
Q

Which 2 components comprise the human genome?

Differentiate btw types of sequences on the human genome.

A

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

31
Q

What are introns and exons?

A
  • 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

32
Q

Differentiate btw types of repetitive sequences.

A
  • 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
33
Q

What are transposons?

A

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)
34
Q

What are SNPs?

A

single nucleotide polymorphism​

chromosomes of diff. individuals identical for most DNA sequences → SNPs are variations of single bases

35
Q

What are the 2 functions of DNA?

A
  • source of information for synthesis of protein molecules
  • information inherited by offspring
36
Q

What is chromatin?

Components.

A

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
37
Q

Differentiate btw the terms haploid and diploid.

How many chromosomes does the human haploid genome have?

A
  • *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)
38
Q

Differentiate btw the 2 types of chromatin.

A

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
39
Q

Explain the structural levels of DNA compaction in a chromosome during metaphase.

A

compact transportable form, forming classical 4 arm structure

  1. dsDNA
  2. winds around histones to form nucleosome →“beads-on-a-string” (10-nm chromatin fibril)
  3. supercoiled fibrils form 30nm-chromatin fiber
  4. forms more and more supercoils

⇒ eventually 2 sister chromatids connected at centromere, terminally attached telomeres

40
Q

What is crossing over?

A

2 homologous chromosomes align and chromatides exchange genetic information → recombination

⇒ incr. g_enetic variation_, one mechanism how evolution happened

41
Q

What is a nucleosome?

A

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

42
Q

Differentiate btw the types of histones.

A

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

43
Q

What is special for histone genes?

A

do NOT contain introns, are fully transcribed, unspliced

44
Q

What is phasing?

A

preference of nucleosomes to certain regions

45
Q

What are the advantages of supercoiled DNA structures?

What are negative supercoils?

A

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)
46
Q

Where can we find circular DNA?

In which forms does it exist?

A
  • in mitochondria
  • in bacteria, bacteriophages
  • in many DNA-containing animal viruses

⇒ either in relaxed or supercoiled form

47
Q

What is the function of mitochondrial genome (mtDNA)?

Clinical relevance?

A

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

48
Q

Describe the structure of mtDNA.

A
  • 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

Biochemistry I (13 decks)

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