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MC Biochem 1 > Chpt 4 > Flashcards

Chpt 4 Flashcards

1
Q

Central Dogma of Molecular Biology

-What part is replication, Transcription, and Translation?

A

DNA->RNA->Protein

Replication= DNA to DNA or DNA directed DNA synthesis
Transcription=DNA to RNA or DNA directed RNA synthesis
—>Processing of mRNA capping, polyadenylation, splicing
Translation=RNA to Protein or RNA directed protein synthesis

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2
Q

Where does replication, transcriptions and translation take place? (In a eukaryotic cell)

A

Eukaryotic cell has a nucleus
Nucleus:
-replication
-transcription

Cytoplasm:
-Translation

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3
Q

Functions of Nucleic Acids (3)

A

Building blocks of DNA and RNA

  • DNA=Genetic Material
  • RNA=Adaptor molecule between DNA and protein

Transport chemical energy within the cell
-ATP

Signal Molecules
-Cyclic AMP

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4
Q

Nucleic Acids

A

-linear, non branched polymer of nucleotides

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5
Q

What are the classes of nucleic acids?

A

1) RNA=ribonucleic acid

2) DNA= 2’ deoxyribonucleic acid

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6
Q

What does. a nucleotide contain?

A
  • Pentose sugar
  • Nitrogenouse base
  • Phosphate (one or more)
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7
Q

What are the nucleotides? and the two classes of nucleotides?

A

Pyrimidines:
Thymine (T)
Cytosine (C)
Uracil (U)

Purines:
Adenine (A)
Guanine (G)

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8
Q

Thymine

A

Pyrimidine Base
5-methyl-2,4-dioxypyrimidine
DNA only

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9
Q

Cytosine

A

Pyrimidine Base
4-amino-2-oxypyrimidine
DNA and RNA

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10
Q

Uracil

A

Pyrimidine Base
2,4-dioxypyrimidine
RNA only

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11
Q

Adenine

A

Purine
6-aminopurine
DNA and RNA

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12
Q

Guanine

A

Purine
2-amino-6-oxypurine
DNA and RNA

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13
Q

Sugar Phosphate Backbone

A

Nucleotides connected by 3’ to 5’ phosphodiester bond

Imparts uniform negative charge to DNA/RNA

  • negative charge repels nucleophilic species (ex hydroxyl) thus the phosphodiester bond resists hydrolytic attack
  • Seperation by agarose gel electrophoresis

Creates 3’ and 5’ end (directionality)
-nucleotide sequences are written 5’ to 3’: L to R

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14
Q

How are bases attached to sugars?

A

Beta Glycosidic linkage

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15
Q

Nucleotide vs Nucleoside

A

Nucleoside:
sugar + nitrogenous base

Nucleotide
sugar + nitrogenous base + phosphate

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16
Q

What data did Watson and Crick use to determine the structure of DNA

A
  • xray diffraction photograph of DNA crystals
  • Chargraff’s rule
  • Bond Angles from reference books
  • Built models
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17
Q

Chargraff’s rule

A

Edwin Chargraff determined the composition of DNA from many organisms

  • [A]=[T]
  • [G]=[C]

rules:

  • the four nucleotides are not present in equal amounts
  • relative ratios of the four bases are not random, and vary from one species to another
  • A=T and G=C
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18
Q

X-ray diffraction photograph of DNA crystals

A

Maurice Wilkins and Rosalind Franklins
-two chains that wind in a regular helical structure

DNA is a HELIX- 3.4 A spacing

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19
Q

MP of DNA factors on?

A

nucleotide content determines melting point of DNA (# of h bonds)
G to C = 3 bonds
A to T= 2 bond

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20
Q

Who received the Nobel Prize in Physiology or Medicine in 1962?

A

Francis Crick
James Watson
Maurice Wilkins

DNA!

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21
Q

What holds DNA together?

A

Hydrogen bonding between base pairs

Hydrophobic interactions (Van Der Waals) due to base stacking

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22
Q

B form of Double Helix

A

Normal Form-Watson and Crick Form

Diameter of Helix- 20 A
10.4 Base pairs per turn
1 Base pair is 3.4 A

Characteristics:
Complementary base pairing
Major Groove
Minor Groove
Antiparallel
Hydrogen bonding between complementary BP
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23
Q

A form of Double Helix

A
  • dehydrated B form

- nucleotide tilted 20 degrees relative to helical axis

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24
Q

Z form of Double Helix

A

Zig Zag Form
stretches of alternating purine and pyrimidine
-base pairs flip 180 degrees
-left handed helix

25
Q

what is DNA organized into?

A

Gene

26
Q

Gene

A
  • discrete functional unit of DNA
  • when expressed (transcribed), yields a functional product->rRNA, tRNA, snRNA, and mRNA is translated into a polypeptide sequence (protein)
  • open reading frame->long stretch of nucleotides that can encode polypeptide due to absence of stop codons
27
Q

Karyotype

A
  • Photograph of chromosomes from a single organism
  • Arranged by size (Largest #1 to smallest #22)
  • Homo sapiens- 46 chromosomes, 23 pairs
28
Q

What are the parts of a chromosome

A
  • Centromere
  • Kinetochore
  • Telomere
29
Q

Centromere

A

Site that connects sister chromatids

30
Q

Kinetochore

A

attachment site of spindle to chromosome

31
Q

Telomere

A

nucleotide repeat at the end of linear chromosome

  • TTAGGG x 1000
  • synthesized by telomerase
32
Q

Properties of DNA

A
  • Melt/Anneal/ Reanneal
  • Hypochromic effects
  • Supercoiled/Relaxed
33
Q

Double Stranded DNA and Heat

A

Double stranded DNA can reversibly melt

  • Heating DNA breaks hydrogen bonds between base pairs (acid or base also works)
  • At melting Temperature half of the helical structure is lost
  • Single stranded DNA absorbs light more efficiently than double stranded
34
Q

Hypochromic Effect

A

or Hypochromism

  • DNA can melt than reanneal
  • If sequences are similar they will reanneal or hybridize
35
Q

In what organisms are DNA circular and what organisms are there DNA linear?

A

Prokaryotic, mitochondrial, and chloroplast genomes are circular
-circular molecules may exist in topological isomers (relaxed and supercoiled)

Eukaryotic genomes are linear

36
Q

Single Stranded Nucleic Acids (DNA or RNA) can form complex structures

A

Stem loops

  • are produced by H-bonding between complementary regions in DNA and RNA
  • H-bonding stabilizes more complex structures
  • mismatches are observed
  • often observed in ribosomal RNA molecules
37
Q

Testing the Semiconservative Replication Hypothesis

A

-Grew E. coli in 15NH4Cl until DNA was completely labeled
-transferred E. coli to 14NH4Cl containing media
-Followed labeling pattern of DNA through several generations using density gradient equilibrium sedimentation
By 4 Generations you get Density 14, Hybrid and Density 15 gene

38
Q

DNA replication: DNA polymerase

A
  • adds deoxyribonucleotide units to an existing DNA molecule in a template directed fashion in the 5’ to 3’ direction
  • Requires: Four dNTPs- (dATP, dGTP, dCTP, dTTP)
  • Divalent Cation (Mg2+)
  • Template DNA
  • Primer provides 3’ OH
39
Q

DNA polymerase Rxn mechanism

A

Nucleophilic attack by the 3’ OH on the alpha phosphate group of dNTP
-PPi (pyrophophosphate) is hydrolyzed to Pi + Pi (orthophosphate)

40
Q

Types of RNA

A
  • ribosomal RNA (rRNA)- part of the ribosome
  • transfer RNA (tRNA)
  • messenger RNA (mRNA)- sequence translated into protein sequence
  • small nuclear RNA (snRNA)- involved in splicing (spliceosome)
  • micro RNA (miRNA)- small RNA complementary of mRNA that inhibits translation of mRNA
  • small interfering RNA (siRNA)- small RNA that binds to mRNA causing destruction of mRNA
41
Q

Transcription: RNA polymerase

A

-adds ribonucleoside triphosphate units to an existing DNA molecule in a template directed fashion in the 5’ to 3’ direction

requires:

  • four NTPs (A, U, G, C)
  • Divalent Cation (Mg2+)
  • Template DNA
  • no primer needed
  • lacks endo and eco nuclease activity
42
Q

What are the RNA polymerase’s for Eukaryotic and prokaryotic cells

A

Prokaryotic polymerase (1)- RNA polymerase

Eukaryotic polymerase (4)

  • RNA poly I
  • RNA poly II
  • mRNA
  • RNA poly III
43
Q

RNA transcribing

A

Genes may or may not be transcribed depending on the needs of particular cell type

  • gene is a functional region of DNA
  • expressed genes are TURNED ON
  • unexpressed genes are TURNED OFF
44
Q

RNA polymerase Rxn Mechanism

A

Nucleophilic attack by the 3’ OH on the alpha phosphate group of NTP (ribonucleoside triphosphates)
-PPi (pyrophophosphate) is hydrolyzed to Pi + Pi (orthophosphate)

45
Q

mRNA relationship to Template Strand and coding strand of DNA

A

mRNA is complementary to template strand

mRNA is identical (except for U to T changes) to the coding strand

46
Q

Prokaryotic Promotor Site

A

Pribnow box (also called TATA box)

  • 5’ TATAAT 3’ centered -9/-10
  • designated by the 5’ to 3’ sequence on the NONtemplate strand–> 8 to 10 nucleotides left (5’ or upstream) of transcriptonal start site (designated +1-there is no 0 nucleotide)

-35 sequence
5’ TTGACA 3’

47
Q

Eukaryotic Promotor

A

Class II genes
-those synthesized by RNA poly II (pre mRNA and snRNA)

Parts

  • TATA or Hogness box
  • GC box (GGGCGG)
  • CAAT box
48
Q

Transcriptional Termination

A

Rho dependent
-involves protein called RHO

Rho independent

  • involves stem loop structure in mRNA
  • stem loop is followed by UUUs
49
Q

prokaryotic and eukaryotic mRNA

A

prokaryotic mRNA are polycistronic
-may encode two or more proteins

eukaryotic mRNA are monocistronic
-encode only one protein

50
Q

eukaryotic mRNA post transcriptionally modified

A

Capping
-attachment of 7-methylguansine using 5’ to 5’ triphosphate linkage

Polyadenylation
-attachment of 40 to several hundred adenine nucleotides to 3’ end of mRNA

Splicing
-removal of introns

51
Q

Amino Acids and tRNA

A

Amino acids are attached to 3’ end of tRNA

-Aminoacyl-tRNA synthetase–> attach amino acid to tRNA

52
Q

Stages of Translation

A

Initiation
-assemble and align ribosome, mRNA, and tRNA^fmet

Elongation
-template directed synthesis of proteins

Termination

  • termination factors halt protein synthesis
  • ribosome, mRNA, and new protein dissociate
53
Q

Orientation of Translation

A
  • Ribosomes move 5’ to 3’ along mRNA

- protein is synthesized N to C

54
Q

Genetic Code

A

Specific Unambiguous

  • specific codon always codes for SAME amino acid
  • three nucleotides (codon)=one amino acid

Universal

  • conserved from species to species
  • main exception=mitochondria

Redundant (also called degenerate)
-amino acid may have more than one codon

Nonoverlapping and comma less (no punctuation)

  • read from fixed starting point (AUG)
  • lacks punctuation between codons
55
Q

Translation Start Site

A

AUG encodes Met (n-terminal amino acid)

  • Prokaryotes use a Shine-Dalgarno sequence to align a ribosome on the mRNA upstream (5’) of AUG
  • eukaryotes use the 5’ cap to align the ribosome on the mRNA
56
Q

Eukaryotic mRNA contain Exons and Introns

A

Exons-coding region

Introns- (intervening regions) nocoding regions

57
Q

How were Introns discovered?

A

introns were discovered by hybridizing mRNA to genomic DNA

58
Q

Splicing

A

removal of introns

  • spliceosome- specific proteins and small nuclear RNA
  • most introns start with GU and end with AG

MC Biochem 1 (30 decks)

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