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Biochemistry > Nucleic Acids: DNA/RNA > Flashcards

Nucleic Acids: DNA/RNA Flashcards

1
Q

DNA

A

Storage unit of genetic info “genome”

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2
Q

RNA

A

Mediates genome expression

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3
Q

Nucleoside

A

C5 sugar + nitrogenous base

  • C5 sugar
    1. Ribose
    2. Deoxyribose (more stable)
  • Nitrogenous bases
    1. Purines = 2 rings
      * adenine (A)
      * guanine (G)
    2. Pyrimidine = 1 ring
      * Cytosine (C)
      * Thymine (T)
      * Uricil (U)
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4
Q

Nucleotide

A

Nucleoside + PO4 group

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5
Q

Building DNA/RNA Polymers

A
  • Dehydration reaction
    1. 3’-5’ Phosphodiester bond: between -OH on C3 of one sugar and C5 of next one
  • link nucleotides to form backbone
    2. N-glycosidic bonds: nitrogenous base and C1 of sugar
    3. Orientation:
  • 5’ end = PO4 group
  • 3’ end = -OH group
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6
Q

DNA structure

A

Double helix- Watson and Crick model

  • 2 antiparallel comp. strands
  • N-bases H-bond
  • 10 nt per 360 degree turns
  • major and minor grooves
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7
Q

DNA structural forms

A
  1. B-DNA (Watson and Crick): majority of DNA in humans
    * right-handed helix
  2. A-DNA:
    * right-handed
    * 11 bp/turn (more compact)
  3. Z-DNA:
    * left-handed
    * 12 bp/turn
    * fxn not well understood
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8
Q

Base complementary

A
  • A = T (2 H-bonds)

* C = G (3 H-bonds)

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9
Q

DNA denaturation

A
  • change in pH
  • temperature
    1. Tm = T at which 50% of DNA is denatured
    • dependent on C-G/A-T ratio
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10
Q

Nucleosomes

A
  • 146 bp
  • Histone proteins
    1. High % Arg and Lys (basic)
    2. 8 core histones
    3. H1-linker histone
  • other minor proteins help keep form
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11
Q

Euchromatin

A

Relaxed, transcriptionally active

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12
Q

Heterochromatin

A

Highly condensed, no transcription

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13
Q

DNA modifications

A

Methylation- more condensed

Acetylation- relaxes histones

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14
Q

Mitochondrial DNA

A
  1. Circular, double-stranded
  2. Contains ~17kb (small)
  3. Fxn = encodes:
    * 13 proteins of ETC
    * large (16S) and small (12S) mt rRNAs
    * 22 mt tRNA molecules
  4. Very few untranslated sequences
  5. Genetic code differs from standard
  6. High mutation rate
  7. Provides evidence for evolutionary origins
  8. Passed from mother to offspring
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15
Q

RNA structure

A

Single-stranded linear
5’ -> 3’
U instead of T
Can fold on self to make hairpin

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16
Q

Types of human RNA

A
  1. Messenger (mRNA)- carries genetic info from DNA -> ribosomes for protein synthesis
  2. Transport (tRNA)- present a.a. To ribosomes to make proteins
  3. Ribosomal (rRNA)- form ribosomal subunits w/ proteins
  4. Micro (miRNA)- regulatory
  5. Others: regulatory
    * snRNA, snoRNA, piRNA, IncRNA, siRNA
17
Q

mRNA

A
  1. Fxn: carry genetic information from DNA to ribosomes
  2. Structure:
    * most diverse in length and base sequence
    * moncystronic in eukaryotes
    * produced as larger precursor (hnRNA)
    * modifications:
  3. 5’- G cap and 3’ poly-A tail - protect from cytoplasmic nucleases
  4. Intron splicing
  5. 5’ and 3’ UTRs - reg. Localization, stability, translation efficiency
18
Q

*tRNA

A
  1. Fxn: present a.a. To ribosomes for polypeptide synthesis
  2. Structure:
    * smallest (~80 nt)
    * 1< tRNA for each a.a.
    * high % unusual bases: hydroxy, dehydro, pseudo
    * secondary and tertiary structure -> cloverleaf
    1. 3’ acceptor end- aa attachment
    2. Anticodon loop- complement to respective codon on mRNA
    3. D and TYC loops- modified bases
    4. Variable loop
19
Q

*rRNA

A
  1. Fxn: forms ribosomal subunits w/ proteins
  2. Structure:
    * 80% of all RNAs
    * 4 sizes in eukaryotes
    * from larger precursors in nucleolus and modified
    • 47S precursor for 28S, 18S, and 5.8S
    • 5S produced separately
20
Q

Ribozymes

A

RNA catalysts
1. Small RNAs w/ catalytic activity
2. Diverse structure and mechanism- not well understood
3. Fxn:
A. Nuclease: processing rRNA, tRNA, and mRNA
B. Peptidyltransferase: catalyze polypeptide form. As part of lg. Ribosomal subunit

21
Q

Homologous chromosomes

A

Contain genes coding for same proteins

*variation because one inherited from each parent

22
Q

Diploid (2n)

A

2 allele for each gene
somatic cells
Humans: 223=46 chromosomes

23
Q

Haploid (n)

A

One allele per gene

*only in mature gametes

24
Q

Eukaryotic DNA

A
  1. Linear chromosomes
  2. Chromosome= 10k -100k bp
    * 100s - 1000s of genes
  3. Many origins of replication
  4. Centromeres: recog. Site for kinetochore proteins
  5. Telomeres: keep DNA from being recog. As broken
  6. Repetitive sequences common, esp. at ends
25
Q

Gene structure

A
  1. Regulatory region- tells transcription where to start
  2. Promoter- transcription factor binds
  3. Exons - expressed/protein coding
  4. Introns- spliced out
  5. Terminator poly-A tail
  6. 3’ and 5’ UTRs
26
Q

Types of DNA in human genome

A
  1. Single copy genes
  2. Repetitive DNA
    * *very small % of DNA codes for proteins
27
Q

Single copy genes

A
  • Protein coding
  • 20-25 x 10^3 genes (code for >100k proteins)
    1. Tissue specific: expressed as part of specific tissues
    2. House-keeping: expressed in all cell types (eg. actin)
28
Q

Repetitive DNA

A
  • not sure about fxn
    1. Satellite DNA
    2. Dispersed repetitive DNA
29
Q

Satellite DNA

A

Generally not transcribed

  1. Alpha
  2. Mini
  3. Micro- trinucleotide repeats
    * expansion w/ certain diseases
30
Q

Dispersed repetitive DNA

A
  1. LINES- long interspersed elements
  2. SINES- short interspersed elements
  3. Transposons
31
Q

DNA replication

A
  • before mitosis in euk.
  • Mech: semiconservative- parent strand + new strand
    1. Strands separate -> 2 forks (helicase and single-strand binding protein)
    2. Primer allows DNA polymerase to synth. DNA (leading and lagging strands)
    3. Okazaki fragments connected by ligase
32
Q

Topoisomerase

A

Relieves supercoil during replication

  • I and II in euk targeted by anti cancer drugs
  • gyrase in prok. Target for antibiotics
33
Q

DNA polymerase activity

A
  1. 5’->3’ Polymerase activity: builds new DNA strands

2. 3’->5’ exonuclease activity: proofreads new strand and fixes mistakes during replication

34
Q

Telomerase

A

Complex of TERT protein and piece of RNA template

  • reverse transcriptionase: uses RNA to make DNA 5’->3’
  • makes telomere to protect ends
  • active in germ cell lines and stem cells
  • not active in somatic cells (can be reactivated in diseased state)
35
Q

Reverse transcriptionase

A
  1. In retroviruses
  2. Uses ssRNA to make DNA copy (cDNA)
  3. cDNA used to make dscDNA
  4. dscDNA integrated into genome
  5. Viral genes upon integration:
    * inactive
    * transcribed- causes disease
  6. Integration can disrupt adjacent cellular gene -> disease
36
Q

DNA inhibitors

A
  • Mech: can’t add more nucleotides
    1. Azidothymidine: anti-retroviral, used as anti-cancer therapy
    2. Didanosine: anti-retroviral, anti-cancer
    3. Cytarabin: chemo
    4. Vidarabin: antiviral

Biochemistry (8 decks)

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