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DNA Biochemistry Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Lecture Outcomes

A
  • List hypotheses on the origin of life on earth.
  • Know the main events which led to the discovery of DNA.
  • Be able to describe the main features of DNA.
  • Understand how the genetic code works.
  • Know what is meant by “The Central Dogma”.
  • Know the terminology for bases, nucleotides, nucleosides, deoxy, ribo.
  • Be able to define the terms antiparallel, complementary base pairing, coding strand, codon, right-handed helix, major groove.
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2
Q

Four hypotheses on origin of life on earth

A
  1. Organic chemical synthesis in a reducing atmosphere
  2. Carriage by meteorites
  3. Organic chemical
    synthesis
    deep ocean vents
  4. RNA world
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2
Q
  1. Organic chemical synthesis in reducing
    atmosphere
A
  1. Was thought that early earth had
    a reducing atmosphere, rich in hydrogen and methane.
  2. Miller, S.L. (1953) subjected methane, ammonia & hydrogen gas
    mixture to electrical discharges presence of water (famous Miller-Urey experiment).

Prebiotic soup resulted (amino acids and nucleotides).

  1. No data on how soup forms organic networks encompassed by a membrane.
  2. But was primitive atmosphere reducing? Current consensus is that it was not.
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2
Q
  1. Carriage by meteorites/comets
A
  • “Panspermia” - attractive theory due to sudden appearance of life on earth and its amazing uniformity (but no data).

> Organic compounds common in space.

Amino ace sanine fundin comet 2088. Than, based on studies simulating its atmosphere (2013, NASA).

  • Mars rocks blasted into space by meteor impacts, carrying microbes?
  • Only moves the question backwards - how did life originate
    e sewnere.
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2
Q
  1. Synthesis on metal sulphides in deep
    sea vents
A
  • Vents are sites of abundant biological activity, much of it independent of solar energy.
  • Energy source, chemical source leads to another prebiotic soup.
  • Prebiotic soup self-organizes into life-supporting networks on metal sulphide surfaces.
  • Networks incorporate into membranes (no data).
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2
Q

Discovering the DNA structure

A

Watson and Crick 1953

The Cavendish Laboratory, Cambridge UK.

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3
Q
  1. RNA world
A
  • Was the first self-replicating entity simpler than a cell?
  • Short RNA molecules were discovered that can store information and catalyse chemical reactions (ribozymes)
  • RNA molecules have been synthesised that are capable of self-replication
  • How did lipid membrane form around RNA?
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3
Q

Behind the Discovery

A
  • James Watson sees X ray diffraction image of DNA shown by Maurice Wilkins (Kings College London) at conference in Naples.
  • Frances Crick works on helical diffraction in proteins in the same laboratory.
  • November 1951 better X ray data from Rosalind Franklin (Kings College).
  • Watson and Crick produce a three-stranded DNA model.
  • Franklin points out this model’s inconsistencies with her data.
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4
Q

Moving back & Moving on

A
  • DNA is the genetic material
  • DNA is a base-paired, anti-parallel, right-handed double helix
  • The code is cracked (triplets of A, T, G and C code for individual amino acids, the building blocks of proteins
  • Gene to protein relationships established
  • Control of gene expression partly elucidated
  • Large scale sequencing of genomes now common
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5
Q

How does the genetic code work?

A

Taken three at a time, combinations
64 are possible, which is enough to characterise the 22 amino acids plus ‘stop’.

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6
Q

How does the genetic code work?

A
  • Backwards explanation with an example
  • Highly active neuropeptide present in human brains: met-enkephalin
  • The amino acid sequence is
    (N) Met Tyr Gly Gly Phe Met (C)
  • The DNA code is
    (5’) ATG TAT GGT GGT TTT ATG (3’)
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7
Q

How does the DNA code look in context?

A
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8
Q

The Central Dogma/Overview photo

A
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9
Q

Nucleotides: The building blocks of
DNA/RNA photo

A
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10
Q

Terminology Continued

A
  • If sugar is deoxyribose, prefix names with deoxy
    -ex
  • Deoxyadenosine monophosphate (dAMP)
  • Deoxyadenosine triphosphate (dATP)
  • If sugar is ribose, prefix names with ribo - Riboadenosine triphosphate (rATP)
  • DNA (deoxyribonucleic acid) contains deoxyribose
  • RNA (ribonucleic acid) contains ribose
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11
Q

deoxyribose sugar photo

A
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12
Q

Terminology for nucleotides and
nucleosides photo

A
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13
Q

How The Chain Is Linked photo

A
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14
Q

Important features to remember:

A

Important features to remember:

  1. Strands are opposite directions (i.e. ANTIPARALLEL)
  2. Strands are COMPLEMENTARY. Sequence of one strand defines the seauence of the other strand from base pairing rules (A=T & G=C)
  3. Information encoded by order of bases 5’ to 3’ One CODING strand & other is NON-CODING
  4. THREE bases = ONE codon (i.e. codes for 1 amino acid) e.g. ACG encodes for threonine, TTC encodes for phenylalanine
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15
Q

Important features to remember:
dna photo

A
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16
Q

DNA Helix is Right-handed photo

A
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16
Q

What’s happening with DNA now?

A
  • Genes have been/are being patented

> Update: in 2013 the US Supreme Court has ruled that human
genes cannot be patented

  • “Junk DNA” has been patented

> (87% of the human genome)|

  • Transgenics and gene KO/KI developed
  • Knock-out mutants: loss/inactivation of gene

> Knock-in mutants: addition of gene

  • Genetic screening moves into medicine
  • Viruses and living cells created from synthetic DNA constructs
  • “Bioinformatics” is born
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17
Q

DNA interaction with Proteins

A

Proteins can interact with bases in “major groove”

Proteins can recognise specific base sequences

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18
Q

Is there still research on DNA?

A
  • “Junk DNA” is not junk
  • DNA can change to other forms (Z and G) in vivo and such changes alter gene expression
  • Z DNA has a left-handed helix
  • Chromosomal position and movement within the nucleus is preserved across species and affects gene expression
  • Confocal microscopy of living cells reveals DNA in real-time as a “demonic dancer”
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19
Q

Lecture Outcomes:

A
  • Define the terms describing DNA replication: semiconservative, origin, bidirectional, replication fork, Okazaki fragment.
  • Understand the mechanism of leading and lagging strand replication and role of the RNA primer.
  • Understand the functions of the proteins at the DNA replication fork.
  • List major DNA polymerases of prokaryotes and eukaryotes and their functions.
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20
Q

general features applying to all chromosome replication

A
  • Complementary base-pairing enables SEMICONSERVATIVE DNA
    replication
  • DNA synthesis initiates at ORIGINS
  • Synthesis usually moves BIDIRECTIONALLY away from an origin via two REPLICATION FORKS, thus producing a REPLICATION
    BUBBLE
  • Synthesis of new DNA is always 5’→ 3’
  • Synthesis of new DNA always requires a PRIMER
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21
Q

Complementary base-pairing enables accurate DNA replication

A
  • Each strand of a dsDNA molecule serves as a template for synthesis of a new complementary strand
  • A binds only with T
  • G binds only with C
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22
Q

DNA replication is semiconservative

A
  • Each strand of a dsDNA molecule serves as a template for synthesis of a new complementary strand
  • Each daughter molecule has a parental strand plus a new strand
  • Accuracy and speed - 1000 nucleotides per second without error
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23
Q

DNA synthesis initiates from origins (ori)

A
  • dsDNA pried apart at replication origin by helicase, at position identified by particular DNA sequence = ori
  • Group of proteins meet to operate as a protein machine moving along
    replication fork
  • DNA polymerase adds nucleotides to 3’ end of new strand
  • DNA polymerase has proofreading property to reduce error rate
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24
Q

bidirectional synthesis from origins

A
  • Circular (short) chromosomes of prokaryotes e.g. E. coli have a single origin of replication

Parental strands orange, new strands red → direction fork is moving

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25
Q

bidirectional synthesis from origins photo

A
25
Q

Bidirectional synthesis from origins photo

A
26
Q

Structure of a replication fork

A
  • Both daughter strands polymerized in 5’ to 3’ direction
  • Leading strand is synthesized continuously
  • Lagging strand is synthesized discontinuously, made as series of short Okazaki fragments
27
Q

Structure of a replication fork

A
  • New strands are synthesized in the 5’ to 3’ direction.
  • The lagging strand of DNA must be made initially as a series of short DNA strands called Okazaki fragments, these are later joined together.
  • DNA strand that is synthesized discontinuously is called the lagging strand.
  • The other strand is synthesized
    continuously and is called the leading strand.
28
Q

DNA synthesis is catalysed by DNA
polymerase

A
  • DNA polymerase adds each deoxyribonucleotide to the 3’ end of a primer strand attached to the template strand.
29
Q

DNA synthesis is catalysed by DNA
polymerase photo

A

IDK why but its always called deoxyribonucleoside triphosphate and never deoxyribonucleotide triphosphate

30
Q

Primers for DNA synthesis

A
  • DNA primase is an enzyme that synthesizes a short strand of RNA on a DNA template
  • During lagging strand synthesis, each Okazaki fragment is primed by an RNA primer, which is synthesized in a template dependent manner by DNA primase
  • DNA ligase joins fragments by their sugar-phosphate backbones
31
Q

The proteins at a replication fork cooperate to form a replication machine

A
32
Q

The proteins at a replication fork cooperate to form a replication machine

A
  • Single-strand DNA-binding proteins stabilise ssDNA and aid the helicase
  • Helicase pries apart (unwinds) the double helix to form ssDNA for replication
  • Sliding clamp holds DNA polymerase firmly on the DNA during DNA replication
  • Clamp loader assembles the clamp on the DNA using ATP energy
32
Q

Current view of the arrangement of replication fork

A

Lagging strand DNA is folded to bring its DNA polymerase into a complex with leading strand DNA polymerase.

33
Q

Current view of the arrangement of replication fork

A
34
Q

DNA polymerases of Escherichia coli photo

A
34
Q

DNA polymerases in mammals photo

A
35
Q

Lecture Outcomes

A
  • Explain mutation of DNA
  • Describe the processes that result in the mutation of DNA
  • Describe the consequences of depurination, deanimation, thymine dimer formation and double stranded breaks on DNA replication
  • Understand how transposable DNA elements and infectious agents introduce mutations into DNA
  • Explain the two mechanisms for DNA repair: MisMatch repair system and homologous recombination
36
Q
  • Definition of Mutation
A

 Any permanent and heritable change in the DNA sequence
of an organism

37
Q
  • Consequences
A

 Damaged DNA will cause problems with DNA replication, lethal

38
Q
  • Repair restores DNA replication
A

 Restoration of correct nucleotide sequence

 Repair can result in incorrect nitrogenous base being incorporated

  • To overcome these problems, all living cells have mechanisms for DNA repair
39
Q
  • How do changes in DNA sequence occur?
A

‒ Replication errors (Very Rare)

 DNA replication is referred to as
“HIGH FIDELITY”

 Incorrect copying by DNA polymerases results in only 1
error in 1,000,000,000 bases (1:109 or one in a billion)

39
Q
  • This high fidelity is caused by:
A

‒ Base paired structure of DNA

‒ The primer requirements of all DNA polymerases

‒ The “proof-reading” of DNA polymerases

40
Q

fidelity pho5o

A
40
Q

Mutation of DNA: Environmental factors photo

A
40
Q

Mutation of DNA: Nucleotide Instability photo

A
41
Q

Mutation of DNA: Nucleotide Instability

remember the consequences

A

Outcome: DNA polymerase randomly assigns nucleotides to match damaged nucleotide, therefore, a change in the nucleotide sequence becomes fixed and inherited.

42
Q

Mutation of DNA: Nucleotide Instability photo

A
43
Q

Mutation of DNA: Mutagenic Chemical

A

Alkylation

Electrophiles add alkyl groups to nitrogenous bases, stalls replication
eg. carcinogens, methylmethane sulphonate (MEMS)

44
Q

Mutation of DNA: Mutagenic Chemical

A

Intercalation

Compound inserts into the double stranded helix leading to distortion

Does not change the bases
eg. Ethidium bromide

45
Q

Mutation of DNA: UV Light photo

A
46
Q

Mutation of DNA: Other forms of Radiation

A
  • Gamma and X-rays

‒ Attack DNA bonds by:

  • directly producing free electrons
    which attack DNA backbone
  • OR indirectly by generating hydroxide free radicals

‒ Both result in single and double stranded breaks

46
Q

Mutation of DNA: Other forms of Radiation photo

A
46
Q

Mutation of DNA: Infectious Agents

A
  • Mobile DNA, has the ability to insert or recombine into a target DNA molecule e.g:

 Infectious agents eg viruses, bacteriophages

 Transposons

  • Recombination, is the breaking and rejoining of DNA molecules to form new combinations

 Non-homologous recombination means no similarity between DNA molecules is required

o Site-specific (or targeted) recombination catalysed by enzymes called integrases and transposases

 Homologous recombination means both the donor and acceptor DNA molecules have extensive similarity in DNA sequences

46
Q

Mutation of DNA: Infectious Agents

A
  • Retroviruses such as HIV (cause of AIDS) and their equivalents in bacteria (bacteriophages) can integrate into host DNA
  • Parasites that utilize the host cell replication machinery
  • Lytic (enter and lyse host) and lysogenic (enter and integrate into host chromosome) life cycles
  • Insertion of foreign DNA physically disrupts a coding region (eg. Gene)

 HIV prefers to integrate into transcriptionally active genes

  • Not a common feature of all viruses
46
Q

Mutation of DNA: Transposons

A
  • Transposons

 Linear DNA molecule

 move within and between chromosomes

 insert into many different DNA sequences

  • Consequences

 Insertion into a gene will physically disrupt it

 Excision of transposon can result in small duplication of DNA - again disrupting a gene

 Common in bacterial DNA rearrangement

47
Q

Mutation of DNA: Transposons photo

A
47
Q

DNA repair: Basic Mismatch repair

A
  • DNA replication without mismatch repair - 1 mistake per 107 nucleotides copied
  • DNA replication with mismatch repair - 1 mistake per 10° nucleotides copied
  • “Mismatch” refers to mis-paired nucleotides
  • Repair - repair proteins recognise and excise strand of DNA containing the mismatch
48
Q

Mutation of DNA: Transposons photo 2

A
49
Q

Non-homologous recombination:
Transposition

A
49
Q

Non-homologous recombination:
photo

A
49
Q

Non-homologous recombination:

A

Non-homologous recombination between sites on bacterial DNA and phage DNA

  • Phage encoded Int (integrase) protein promotes recombination between the attachment sites (att), attP and attB
50
Q

DNA repair: Basic Mismatch repair steps

A
  • Four steps:
  • The repair proteins patrol the DNA and bind to the mismatched sequence
  • The mis-matched region is excised by nucleases, thus creating ssDNA patch

> Synthesis of the second strand by repair DNA polymerase using the free
3’OH group as a primer

  • Ligation of the DNA backbone by DNA ligase
50
Q

Repair mechanisms result in the restoration of the original sequence, two examples:

A
  • Mis-Match repair system repairs mutations in the newly synthesised DNA strand to restore it to the original sequence of the template strand
  • Homologous recombination repairs double-stranded breaks in the phosphodiester backbone of the DNA
  • this may result in restoration of the original sequence but can also result in rearrangements of local regions of the DNA sequence
50
Q

DNA repair: Basic Mismatch repair steps

A
51
Q

Homologous recombination

A
  • Double stranded break introduced into chromosome A
  • Exonuclease removes nucleotides from the 5’ to 3’ direction
  • The single stranded 3’ overhang can migrate into the recipient chromosome B where the sequences are homologous
51
Q

Repair of DNA by Homologous
Recombination

A
  • Homologous recombination
  • Regions of very similar sequences align
  • Double strands are broken then a cross over occurs
  • DNA repair, generate new combinations of DNA
52
Q

Homologous recombination photo

A
53
Q

Homologous recombination continued

A
  • DNA polymerase synthesises new complementary strands
  • Crossed strands also known as Holliday junction
  • Rotation of crossed strands to allow section of one strand to be joined to section of another strand (exchange of DNA)
  • Nucleotide sequence at site of exchange is unaltered (no additions or subtractions)
54
Q

Homologous recombination continued photo

A

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