TOPIC 1 - nucleic acids Flashcards
1
Q
what does DNA contain?
A
genetic information of most organisms required to make proteins
2
Q
B-form DNA
A
2 strands of DNA intertwine to form a double helix shape (most common)
3
Q
what directions do DNA strands run in?
A
antiparallel (opposite directions)
4
Q
what are the 2 DNA strands called and which which directions do they run?
A
Watson: 5’ -> 3’
Crick: 3’ -> 5’
5
Q
how often does a helix turn?
A
every 10 bps
6
Q
what helps maintain/stabilise regular double helix shape?
A
- hydrogen bonding
- base stacking causes pi-pi interactions as aromatic rings share electrons
7
Q
major grooves
A
- backbone far apart
- binding proteins can bind easier e.g. alter structure, regulate transcription/replication
8
Q
minor grooves
A
- backbones close together
- proteins cannot bind as easily
9
Q
how does the sugar-phosphate backbone form?
A
- phosphate group attached to 5’ carbon and 3’ oxygen of sugar
- forms covalent phosphodiester bond
10
Q
structure of RNA
A
- single stranded
- shorter than DNA
- larger grooves in helix
11
Q
how does a deoxyribonucleotide differ from a ribonucleotide?
A
ribose - hydroxyl groups in the 2 and 3 position of sugar
deoxyribose - lacks hydroxyl in 2 position of sugar
12
Q
how many H bonds form between A + T?
A
2
13
Q
how many H bonds form between C + G?
A
3
14
Q
what are pyrimidine bases + structure?
A
T, C, U
-single ring structure
15
Q
what are purine bases + structure?
A
A, G
-2 ring structure
16
Q
why can non-complementary bases not bind?
A
- lack geometry
- not form strong H bonds
- disturb double helix structure
17
Q
dna helicase
A
unwinds double helix at replication fork
18
Q
dna topoisomerase
A
relax and reintroduce supercoiling in DNA chain
19
Q
DNA polymerase III
A
elongates leading DNA strand in 5’ -> 3’ direction
20
Q
what is the role of polymerase III exonuclease activity?
A
- works in 3’ -> 5’ direction
- proofreads the strand being formed removing erroneous bases as strand synthesised
21
Q
RNA primase
A
creates primer RNA sequence
22
Q
DNA polymerase I
A
removes the RNA primer and replaces it with DNA
23
Q
DNA ligase
A
seals up gaps in Okazaki fragments
24
Q
single stranded binding proteins (SSBs)
A
keep DNA open and prevent it from annealing
25
how is DNA synthesised on the leading strand?
- RNA primase creates RNA primer sequence
- DNA polymerase III moves along DNA in 5' -> 3' direction
- adds nucleotides onto primer sequence
- DNA polymerase I degreades primers and replaces with nucleotides
- synthesised continuously
26
how is DNA synthesized on the lagging strand?
- RNA primase creates RNA primer
- DNA polymerase I adds short row of DNA nucleotides onto primer in 5' -> 3' direction up to previous fragment
- synthesised in Okazaki fragments
- DNA polymerase I degreades primers and replaces with nucleotides
- DNA ligase links fragments together
27
what effects could replication errors cause in germ and somatic cells?
germ cells - mutation could be heritable
somatic cells - cancer
28
how are DNA replication errors reduced?
- polymerase III exonuclease activity
- nucleotide excision repair
- base excision repair
- strand directed mismatch repair
29
base excision repair
- damaged base excised by DNA glycosylase
- gap recognised by AP endonuclease
- missing base resynthesised by DNA polymerase
30
nucleotide excision repair
- recognises/removes bulky DNA adducts (damage from UV light)
- missing segment resynthesised by DNA polymerase
31
strand directed mismatch repair
- inspects newly formed DNA (A + C undermethylated)
| - enzymes remove mismatched nucleotides
32
how can DNA be damaged after replication?
- cytosine: deaminated to uracil, recognised as thymine, base pairs with adenine -> mutation
- methyl cytosine: deaminated into thymine -> permanent mutation as thymine not recognised as foreign
33
how does the body protect replicated DNA from damage?
- uracil DNA glycosylase recognises uracil
- breaks bond between uracil + sugar
- mismatch repair enzymes detect lack of base + add cytosine
34
human genome
map of all DNA content in human body (included coding DNA and junk DNA)
35
how many nucleotides make up the human genome?
3x10⁹
36
how many protein coding genes are in the human genome?
20,000
37
allosomes
sex chromosomes
38
autosomes
non-sex chromosomes
39
other than the nucleus, where can DNA be found?
mitochondria
40
why is human genome bigger than expected for small number of genes?
- junk DNA
- retroviral integration
- pseudogenes
- VNTRs
41
synteny
- DNA sequences on chromosome is present across different species
- occurs between closely related species (e.g. chimp/human) and non-closely related species (human/mouse)
42
example of synteny
human chromosome 2 = chimp chromosome 12 + 13
43
junk DNA
non-functional sequences of DNA
44
how do retroviruses affect DNA?
- retroviruses insert DNA copy into cells
- viral DNA integrated into host cell
- mutations can cause non-productive copy to be integrated which remains in DNA and is passed down cell generations
45
pseudogenes
sequences of DNA that resemble functional genes but are non-functional
46
how many pseudogenes in the human genome?
20,000
47
how are pseudogenes formed?
gene duplication - duplicate genes has mutation that renders inactive
reverse transcription - mRNA lacks introns/regulatory sequences, reverse transcribed into DNA, lacks promoter regions/introns so not active gene
48
VNTRs
variable number tandem repeats - multiple copies of same short sequence of bases
49
how are VNTRs used for testing?
- amplified through PCR
| - DNA fingerprinting for forensic/paternity testing (VNTRs inherited from mother/father different)
50
what does polymerase slippage cause?
extra/missing copies of bases - creates sections of DNA that can no longer code/function
51
SNPs
single nucleotide polymorphisms -base substituted in genome and substitution in at least 1% of population
52
what effects can SNPs have?
- no effect
- subtle effect e.g. phenotypic change
- disease
53
GWAS
genetic wide association studies - provide sequence/location of SNPs
54
role of TATA boxes
- short run of T/A bases 25-35bps away from start of transcription
- T/A lowest energy base pairs so easiest to unwind
- transcription factors bind
- RNA polymerase II can bind to transcription factors
55
what % of mammalian genes has a TATA box?
10-15%
56
role of CpG islands
- stretches of DNA where multiple points of C-G bases upstream of start site
- if CpG island methylated, gene coding switches off
57
how does DNA transcription occur?
1. transcription factors bind to promoter region causing DNA strand to unwind
2. RNA polymerase II binds to transcription complex
3. polymerase moves down antisense/template DNA strand in 3' -> 5' direction
4. polymerase add complementary RNA nucleotides onto 3' end of mRNA strand in 5' -> 3' direction
5. mRNA strand is released, undergoes modification and leaves nucleus through nuclear pores
58
how is eukaryotic mRNA modified after transcription?
methyl capping - methyl g cap added to 5' end to stablise/protect against degradation
polyadenylation - sequence downstream of mature RNA cut off and polyA tail added to 3' end to stabilise/protect against degradation
59
polycistronic
prokaryotic mRNA that can encode for more than one protein
60
lac operon
gene system whose operator gene and three structural genes control lactose metabolism in E. coli
61
splicing
removing introns and reconnecting exons in mRNA
62
introns
noncoding sequences of DNA
63
exons
coding sequences of DNA
64
what structure removes introns during splicing?
spliceosome
65
how can different proteins be produced from same mRNA?
alternative splicing leads to inclusion of different exons
66
enhancer sequences
sequences far upstream/downstream of genes that regulate level of transcription of genes when proteins being
67
how do enhancer sequences function over large distances?
- dna between enhancer and promoter region loops out
| - allows enhancer proteins to come into contact with RNA polymerase
68
trans-acting factors
regulatory RNA that act across DNA strand by diffusing from enhancer region
69
what is the function of trans-acting factors in gene transcription?
regulate transcription activity by enhancing or silencing it
70
regulatory RNA
non-coding RNA molecules that play a role in controlling gene expression
71
barr body
inactivated X chromosome in females
72
why do men not have a barr body?
only occurs in XX cells as have 2 copies of XX (men have XY in cells)
73
why is the barr body inactivated?
regulated amount of X-linked genes transcribed
74
what RNA causes the barr body to become inactivated?
Xist
| X inactivation specific transcript (regulatory RNA)
75
how is genetic code degenerate?
more than one triplet codon codes for same amino acid
76
how is genetic code triplet?
amino acids coded by three codons
77
what is the start codon?
AUG (methionine)
78
what are the stop codons?
UAA, UAG, UGA
79
what is the start codon in bacteria?
N-formyl methionine
80
structure of tRNA
- tightly packed clover shaped
| - anticodon complementary to the mRNA opposite where amino acid esterified
81
how are tRNAs protected from degradation by RNAses?
- tightly packed structure
| - modified bases
82
what is wobble base-pairing?
- first base of tRNA anticodon can pair with different third bases on mRNA codon
- more economical as reduces number of tRNA molecules required as some can recognise more than one codon
83
what is the role of aminoacyl tRNA synthetases?
esterify correct amino acid to tRNA
84
how does translation occur?
1. small ribosome subunit binds to 5' region and moves down mRNA until reaches appropriate AUG codon in good position
2. large ribosome subunit binds
3. initiator met-tRNA binds to methionine and is recognised by initiation factors on small subunit
4. ribosome moves along mRNA sequence, adding correct amino acids to polypeptide chain for mRNA using tRNA
5. ribosome dissociates once stop codon reached
85
polysome
polysome
86
what is the effect of nonsense mutations?
- mutation results in premature stop codon
- causes ribosome to dissociate early
- mRNA after stop codon not translated
- exposed mRNA region digested by RNAses (nonsense mediated decay)
87
E site of ribosome
exit site, empty tRNA ejected from ribosome
88
P site of ribosome
peptidyl tRNA binding site, tRNA attaches when adding amino acid to polypeptide chain
89
A site of ribosome
aminoacyl tRNA site, tRNA enters ribosome
90
what are the differences between eukaryotic and prokaryotic ribosomes?
eukaryotic - larger, 80S, attached to outer surface of nucleus/ER
prokaryotic - smaller, 70S, free floating in cytosol, targeted by antibiotics
91
endosymbiogenesis hypothesis
eukaryotic mitochondria arose from invading bacteria at some point during evolution
92
how are secretory proteins imported into ER?
- signal sequence (first stretch of 20 hydrophobic amino acids) recognised
- ribosome docks to ER
- protein fed through membrane into lumen
- signal sequence cut off
93
how are transmembrane proteins imported into ER?
- ribosome docks to ER
- transmembrane domain (first stretch of 20 hydrophobic amino acids) produced and enters lumen
- translocation stops
- c terminus (chan after transmembrane domain) remains in cytosol
94
how are transmembrane proteins exported from ER?
- transmembrane domain now extends out of ER after modification
- domain anchors protein into lipid bilayer
- tail extends into cytosol
- part of domain extends extracellularly
95
what modifications are proteins subjected to inside ER?
- folding
- glycosylation
- disulphide bond formation
96
glycosylation
addition of a carbohydrate group
97
disulfide bridge formation
cystine contains thiol group -> forms S-S cross link with cystine further down peptide chain to loop it or on separate peptide chain to join together
98
what happens to proteins in Golgi apparatus?
- some ER sugars are trimmed or replaced
| - package proteins into vesicles and direct proteins depending of signals on protein
99
what are the compartments of the Golgi apparatus?
cis, medial, trans
100
what is the difference between sugar side chains of proteins in humans and microorganisms?
human - end in salic acid
microorganism - more mannose rich (recognised as foreign in humans)
101
how does prenylation result in proteins anchored to inner leaflet of membrane?
- G proteins synthesised as cytosolic protein (doesn't pass through rER of Golgi apparatus)
- at C terminus of protein, cut and lipid tail added
- protein unstable with lipid tail in cytosol so integrated into inner plasma membrane
102
how is biologically active insulin produced?
- single gene codes for long protein
- signal peptide sent to ER
- signal sequence cleaved in ER
- disulphide bonds form between end + C terminus
- connecting loop cut out by proteases
103
is insulin glycosylated?
insulin is not glycosylated - no carbon chains
104
recombinant DNA
DNA produced by combining DNA from different sources
105
how commercial recombinant insulin produced?
- fusion protein used to trick yeast to produce insulin
- cleavage recognition site engineered into fusion protein allows protease to cut off yeast section and leave insulin region ready to fold
106
pharming
production of pharmaceutical products from farm animals
107
what is an example of pharming?
production of insulin from mammary glands of cows/goats
108
cancer
disease caused by uncontrolled growth/division of cells
109
neoplasia
new growth of cells not physiologically contained
110
malignant neoplasia
cancerous growth which is able to metastasise
111
benign neoplasia
growth of cells localised so cannot metastasise
112
dysplasia
abnormal cell with some features of cancerous cell but not fully malignant
113
metastasis
the development of malignant growths away from primary site of cancer (spread of cancer)
114
8 hallmarks of cancer
1. tissue invasion/metastasis
2. sustained angiogenesis
3. activated growth signalling
4. evade cell death/senescence
5. limitless replicative potential
6. evade immune surveillance
7. handle metabolic stress
8. DNA damage and genetic instability
115
how does sustained angiogenesis contribute to cancer?
- triggers growth of new blood vessels
- bring cancer cells nutrients allowing for growth
- help metastasise
116
how does activated growth signalling contribute to cancer?
constantly signals for cells to divide
117
senescence
deterioration of cells with age e.g. loss of ability to grow/divide
118
how do cancer cells have limitless replicative potential and how does contribute to cancer?
- telomeres (short repeating units of DNA at end of chromosome) shorten over cell division until cannot shorten more
- cell recognises short telomeres and stops division
- cancerous cells fuel growth of telomeres so do not shorten
119
how do cancerous cells evade immune surveillance?
- despite genetic changes, immune system struggles to recognise cancerous cells
- immune system can act on small amounts of malignant cells
in established cancers:
- immune system overwhelmed
- develop protective mechanism
120
what does the Wahlberg/reverse-Warburg effect allow cancerous cells to do?
metabolise and continue dividing if cells far from blood stream
121
carcinoma
cancer of epithelial cells/surface tissue
122
adenocarcinoma
cancer of glandular cells
123
how are cancers named?
site + histopathology + extent of spread
124
what does histopathology tell us about cancers?
cellular origin of cancer
125
schema cell carcinoma (SCC)
cancer of skin cells
126
haematological cancer
cancer of blood
127
myeloma
cancer of plasma cells from bone marrow
128
leukaemia
cancer of white blood cells from bone marrow
129
lymphoma
cancer of lymphatic glands/nodes
130
sarcoma
cancer of mesenchymal cells/connective tissue
131
osteosarcoma
cancer of bone
132
myosarcoma
cancer of muscle
133
leiomyosarcoma
cancer of smooth muscle
134
rhabdomyosarcoma
cancer of skeletal muscle
135
how does increasing genetic instability contribute to cancer?
if instability reaches certain threshold, cell can become cancerous
136
how does chromothripsis contribute to cancer?
- shattering of chromosome due to ionising radiation
- cell rearranges in wrong order so incorrect synthesis of proteins
- increases genetic instability
137
how does translocation contribute to cancer?
- rearrangement of chromosome
- genes shifted cross-chromosomes
- genes in different chromosomes may have different promoters = triggered incorrectly
- increases genetic instability
138
how does genomic amplification contribute to cancer?
- repeats of same gene = more copies of protein synthesised
| - protein can help with development/growth = rapid cell division
139
how do point mutations contribute to cancer?
- substitution, indels, frameshift
- alter triplet makeup = different amino acids produced = different protein structure/function
- protein can help with development/growth = rapid cell division
140
how does serial clone expansion contribute to cancer?
- mutationed cell divides to produce clone with same mutation
- new mutations added with each cell division
- increases genetic instability
141
oncogenes
cancer promoting genes
142
proto-oncogenes
genes involved in regulating cell growth and differentiation (not cancerous yet)
143
how do proto-oncogenes/oncogenes contribute to cancer?
- mutation in growth gene means permanently turned on/activated so growth uncontrolled
- only need one mutation (dominant effect)
144
tumour suppressor genes
- genes which protect against cancer
| - control cell cycle e.g. slow cell division, repair DNA errors and signal cell death
145
how can tumour suppressor genes contribute to cancer?
loss of function (e.g. mutation of both alleles)
146
Knudson's two hit hypothesis
both copies of allele have to be defective in same cell to allow tumor to develop
147
how does Knudson's two hit hypothesis relate to retinoblastoma?
- RB gene stops cell cycle occuring when inappropriate e.g. cell damaged
- some born with germline mutation in RB gene
- only need one more mutation to inactivate gene = retinoblastoma cancer
148
how does Knudson's two hit hypothesis relate to tumour suppressor genes?
both alleles in tumour suppressor gene must be mutated before cancer occurs
149
how can epigenetics contribute to cancer?
- tumour suppressor gene inactivation
| - methylation of promoter factors = gene inactivated as transcription factors cannot bind
150
epigenetics
changes in gene expression caused by mechanisms other than changes in the DNA sequence
151
germline mutations
mutation in germ cells (cells give rise to gametes)
152
how are germline mutations linked to familial adenomatous polyposis coli?
germline mutation inactivates APC (tumour suppressor) gene = FAPC
153
why are cancer levels higher in older population?
- long period for genetic instability to increase
| - more exposure to environmental factors
154
what environmental factors can contribute to cancer?
- tobacco smoking
- excess body weight
- alcohol
- UV light
- poor diet
- cancer-causing pathogens e.g. HPV
- physical inactivity
