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Ecology & Conservation Year 1 > APS138 Molecular and Cell Biology > Flashcards

APS138 Molecular and Cell Biology Flashcards

1
Q

How is DNA packed in the nucleus?

A
  • DNA is wrapped around histones to create chromatin

- Density of this varies and acts as a regulator

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2
Q

Tightly packed chromatin

A

HETEROCHROMATIN

  • Prevents RNA Pol binding
  • Therefore is ‘silent’
  • Characterised by +ve histone tails
  • Allows tighter binding of histones to DNA
  • Associated with Methylated DNA which is inaccessible
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3
Q

Lightly packed chromatin

A

EUCHROMATIN

  • Decondensed by active regulatory mechanisms that allow transcriptional machinery to access DNA
  • Associated with unmethylated DNA and is accessible
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4
Q

What enzymes condense chromatin?

A

Histone Deacetylase
Histone Demythylase
(Modify the histone tails)

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5
Q

What enzymes decondense chromatin?

A

Histone acetyl transferases
Histone methyl transferases
(Neutralise +ve charges)

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6
Q

DEFINITION: Epigenetic Trait

A

A trait that can be passed on by meiosis

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7
Q

Inactive RNA Pol 2

A
  • RNA Pol has a tail that is not phosphorylated
  • It is not bound to a promotor
  • Gene & Promotor are typically cytosine-methylated and associated with tightly packed chromatin
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8
Q

Paused/ Stalled State of RNA Pol 2

A
  • Gene is almost ready to be transcribed
  • Transcription factor is bound to the promotor (could also be sat on gene body)
  • RNA Pol 2 is phosphorylated at Serine 5 but remains inactive
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9
Q

Elongation/ Active State of RNA Pol 2

A
  • More transcription factors bind to regulatory elements in the promotor
  • RNA Pol 2 gets phosphorylated at Serine 2 and 5 which triggers the transcription progress
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10
Q

RNA Processing- Splicing and Alteration of mRNA ends

A
  1. 5’ & 3’ ends are capped
    3’ end is also subjected to polyadenylation
  2. Introns are spliced out by the spliceosome
    Alternative splicing provides more regulation
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11
Q

DEFINITION: Ubiquitous Regulators

A

Small RNAs that exist everywhere and throughout cells regulating gene expression
Double stranded and roughly 19-30 nucleotides long

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12
Q

3 Examples of Ubiquitous Regulators

A
  1. microRNA (miRNA)
  2. small interfering RNA (siRNA)
  3. piwi interacting RNA (piRNA)
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13
Q

Post Transcriptional Gene Silencing- Small RNAs

A
  1. Repression of gene translation - miRNA

2. Promote mRNA degradation - miRNA & siRNA

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14
Q

Transcriptional Gene Silencing- Small RNAs

A
  1. Repression of gene transcription via chromatin remodelling and DNA methylation (recompensed) - siRNA from double stranded RNA or piRNA from single stranded RNA
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15
Q

miRNA Basics

A
  • Come from non coding genes
  • The genes have complimentary sequences to a coding gene elsewhere in the genome
  • This produces a tertiary structure that resembles hair pins
  • These are recognised by RNA induced gene silencing complex
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16
Q

How miRNA works

A
  • Once recognised by a gene silencing complex the larger pre miRNA is chopped up by enzymes
  • They’re downloaded one strand at a time onto Argonaute proteins which protect them
  • Helps them bind onto the gene that needs silencing
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17
Q

DEFINITION: Ubiquitin

A
  • A small protein that regulates the turnover of proteins
  • Addition of ubiquitin targets a protein for degradation
  • Form of gene regulation after synthesis
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18
Q

DEFINITION: Glycosome

A

Peroxisome involved in glycogen storage and metabolism

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19
Q

DEFINITION: Coenocytic Structure

A

A multinucleate structure

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20
Q

Reasons for compartmentalisation

A
  1. Maintain different environments
  2. Metabolic Regulation
  3. Sequestrion of toxic substances
  4. Cells secrete and internalise large numbers of proteins
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21
Q

Uses for Protein Filaments

A
  • form 3D mesh which creates a rigid shape and structure
  • for movement, forms trackways
  • almost exclusive for animal cells and associated with location and translocation of the nucleus
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22
Q

DEFINITION: Actin

A
  • Fibres 3-6nm diameter
  • Used for gliding, contraction and cleavage
  • With myosin responsible for muscle contraction
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23
Q

DEFINITION: Microtubules

A
  • Determine cell shape
  • Provide a trackway for movement of cell organelles and vesicles
  • Form spindle fibres in mitosis
  • Inside the flagella and cilia
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24
Q

DEFINITION: Intermediate Filaments

A
  • 8-12nm diameter
  • Give cell flexibility
  • Anchor and position the nucleus
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25
Q

Two types of motor protein involved in the movement of molecules and vesicles

A
  1. Kinesin

2. Dynein

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26
Q

DEFINITION: Kinesin

A
  • Motor protein
  • Travels towards the plus end
  • Away from the nucleus
  • Requires ATP
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27
Q

DEFINITION: Dynein

A
  • Motor protein
  • Travels towards the minus end
  • Towards the nucleus
  • Requires ATP
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28
Q

DEFINITION: Melanocytes

A
  • Specialised cells containing melanosomes which allow fish such as cephalopods to change colour
  • Motor proteins transport these along microtubule/ actin tracts
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29
Q

Function of Cortisol microtubules

A
  • Form a template for the deposition of cellulose in bands
  • Leads to turgor driver cell growth which is constrained along the X axis
  • Move in parallel with cellulose synthase complexes
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30
Q

Rough Endoplasmic Reticulum

A
  • Processes folding and assembly of proteins
  • Protein translocates via translocation pores
  • N-Terminal Signal Peptide is removed whilst Nascent Polypeptide emerges into lumen
  • Lumen is specialised for folding, assembly, modification, quality control and recycling
  • Proteins undergo glycosylation and disulphide bond formation
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31
Q

What makes Endoplasmic Reticulum Dynamic in Plant and Animal Cells

A

Plant Cells: Movement depends on actin/ myosin

Animal Cells: Movement relies on microtubules

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32
Q

The Golgi Apparatus

A
  • Distribution, shipping and manufacturing department of cells chemical products
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33
Q

Role of Endoplasmic Reticulum & Golgi in milk secretion

A
  1. Transport of ions & water across membrane into the lumen
  2. Smooth ER forms cytoplasmic lipid vesicles & lipid secretion
  3. Rough ER synthesises milk protein (casein) modified in the lumen, then delivered to Golgi where lactose is synthesised
  4. Vesicular movement of immunoglobulins protect from diseases
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34
Q

Ricin in Castor Beans

A
  • The beans contain ricin which is a cytotoxin that inhibits protein synthesis and is for anti herbivory
  • When seeds germinate its rapidly degraded
  • Initially synthesised as proricin and is not catalytically active until proteolytically cleaved within protein bodies so it doesn’t poison itself
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35
Q

DEFINITION: Chaperones

A

Proteins that assist correct intracellular folding and polypeptide assembly

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36
Q

Quality Control in the ER

A
  • Mutant proteins which have been incompletely or incorrectly folded are retained in the ER and degraded by lysosomes and proteosomes
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37
Q

ER Quality Control and Cystic Fibrosis

A
  • Cystic Fibrosis transmembrane conductance regulator (CFTR) is a chloride ABC Transporter
  • Mutated version of the channel protein still works but is identified and degraded
  • Not enough channels in the epithelial lining so fail to take up enough Cl- from the lumen
  • Causes yucas accumulation
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38
Q

Roles of Vacuoles/ Lysosomes

A
  • Storage of carbohydrates, organic acids, anthocyanin, seed storage proteins
  • Isolate toxic substances
  • Anti herbivory, produces tannins, ricin
  • Maintain internal hydrostatic pressure
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39
Q

Cyanogenesis in plants

A
  • Method for anti herbivory
  • Plants containing high levels of cyanide
  • If consumed too much can cause chronic cyanide poisoning
  • Cyanide ions interfere with ion containing respiratory enzymes
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40
Q

Cyanogenesis in animals

A
  • Larvae of the Burnet Wasp can sequester cyanogenic glucosides
  • Stored in viscous droplets in cuticle cavities in the integument
  • Adults then release it as a pheromone to attract males
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41
Q

Endosymbiotic Theory

A

Concept that ancestral eukaryotes encorperated with aerobic bacteria to become more efficient, became the mitochondria
Also occurred for the chloroplast

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42
Q

Secondary Endosymbiosis

A
  • Plastids contains multiple membrane envelopes which suggests multiple endosymbiosis events occurred
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43
Q

Repeated Endosymbiosis

A
  • Termed as the driver of plant/algal diversity
  • Believed through multiple endosymbiosis all higher plants evolved from algae
  • Multiple membranes support the theory
  • Different types of chlorophyll also support this; red and green chlorophyll from green lineage and others form red lineage
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44
Q

Endosymbiotic Zooxanthellae in Coral Polyps

A
  • Have a mutualistic relationship with dinoflagellates (unicellular algae)
  • The polyps protect the algae from predators and the algae provides energy
  • High water temps trigger the polyps to expel the zooxanthellae
  • Coral Bleaching
45
Q

Result of symbiosis on cell autonomy

A
  • After the organelle DNA has been transferred the cells loses autonomy and has an increased nuclear complexity
  • This process in continuous so overtime genome in chloroplast for example will be reducing
46
Q

How protein signals reach the chloroplast lumen

A
  1. Chloroplast signal sequences attach to the receptor
  2. TIC TOC complexes are protein translators that pass through the two membranes
  3. Chloroplast signal is cleaved off to reveal a thylakoid signal
  4. Four different pathways into the lumen
47
Q

DEFINITION: Etioplast

A

Chloroplasts that have not been exposed to light, found in flowering plants grown in the dark

48
Q

DEFINITION: Chromoplast

A

A coloured plastid usually red or orange which is produced when plants ripen.
Not a chloroplast

49
Q

DEFINITION: Leucoplast

A

A plastid used for storage of lipids, starch and protein

50
Q

Apicomplexa

A
  • Parasite derived from red algae which switched to be heterotrophic so lost plastids
  • Retains some of its plastid genome
  • Has four membranes and is suitable for drug treatments
    Eg. Plasmodium
51
Q

Advantages for the introduction of mitochondria and chloroplasts

A
  • Enabled a 200,000 fold rise in genome size in eukaryotes as allowed oxidative phosphorylation across large internal membrane
  • Allowed multicellular life
52
Q

What was Watson able to deduce about DNA after Franklin first photographed DNA using X ray diffraction

A
  • DNA was helical
  • The spacing between nitrogenous bases
  • Width of the helix
  • That DNA was a double helix
53
Q

Structure of the DNA polymer

A
  • Polynucleotide strands were directional
  • 5’ end was always a phosphate
  • 3’ end was always an OH
54
Q

Base Pairs Rules

A 
Adenine to Thymine (2 H Bonds) 
Guanine to Cytosine (3 H Bonds) 
Purines has 2 organic rings 
Pyrimidines have a single ring 
Strands run antiparallel
55
Q

Semi Conservative model of replication

A
  • Two strands are complementary
  • Each strand acts as a template for new strand
  • In replication parent molecule unwinds an two daughter strands are built based on base pairing rules
56
Q

Adding Nucleotides to DNA

A
  • Process called DNA polymerisation
  • Uses nucleotide triphosphate, phosphate energy for addition
  • DNA strands elongate in the 5’ to 3’ direction
57
Q

DNA Replication in Prokaryotes

A
  • Fast and accurate

- Only used DNA polymerase 3 and 1 §

58
Q

DNA Replication in Eukaryotes

A
  • Accurate but slower than prokaryotes
  • Will take a few hours
  • Lots of different enzymes and proteins take part, at least 11 different DNA polymerases
59
Q

DNA Replication in E. coli

A
  1. Begins at the ‘ Origin of Replication’
  2. In the circular chromosomes there is only one origin which is a short stretch of DNA with a particular base sequence
  3. Parental strands separate and form a replication bubble
  4. This bubble has a fork at each end
  5. Replication proceeds in both directions until the forks meet resulting in two daughter cells
60
Q

DNA Replication in Eukaryotic Cells

A
  • Linear chromosomes have many origins of replication
  • Parental strands separate to form replication bubbles
  • These fork at either end and expand as replication proceeds in both directions
  • Eventually bubbles fuse resulting in the synthesis of two daughter molecules
61
Q

Enzymes involved in DNA Replication in Eukaryotes

A
  1. Topoisomerase > Prevents breakage
  2. Helicases > Unzip the DNA
  3. Primase > Synthesises short RNA primers using parental DNA as template
62
Q

Synthesis of the Leading Strand

A

CONTINUOUS

  • Along template strand DNA polymerase 3 synthesises a complementary strand continuously by elongating DNA in the 5’ to 3’ direction
  • DNA Pol 3 remains in the replication fork continuously adding nucleotides
63
Q

Synthesis of the Lagging Strand

A

DISCONTINUOUS

  • Primase synthesises short RNA primers
  • DNA Pol 3 synthesises at the 3’ end of the primer and continues in the 5’ to 3 direction until it reaches a fragment ahead
  • DNA Pol 1 replaces the RNA Primer with DNA nucleotides
  • DNA ligase joins the Okazaki fragments together
64
Q

Limitation to replicating the ends of linear chromosomes

A
  • DNA Pol can only add to the 3’ end of pre existing nucleotides so there is no way to complete the 5’ end of DNA daughter strands
  • Repeated rounds of replication over time produce shorter DNA molecules with uneven ends
65
Q

DEFINITION: Telomeres

A
  • Special nucleotide sequences at the end of eukaryotic chromosomes
  • They don’t contain genes and the DNA consists of multiple repetitions of one short nucleotide sequence
  • Prevents shortening of DNA molecules and postpones erosion of genes near the end of DNA
66
Q

1st Level of chromatin packing

A
  • Histone proteins are responsible

- Nucleosome consists of DNA wound twice around a protein core of 2 molecules, of each of the four main histone types

67
Q

2nd Level of chromatin packing

A
  • Results from interactions between the histone tails of one nucleosome, the linker DNA and nucleosomes on either side
  • Interactions cause fibre to coil forming chromatin which is 30nm thick
68
Q

3rd Level of chromatin packing

A
  • The 30nm fibres form loops called looped domains which attach to a chromosome scaffold made of proteins thus making a 300nm fibre
  • In mitotic chromosomes the looped domains coil themselves compacting the chromatin to produce a characteristic metaphase chromosome 700nm
69
Q

DEFINITION: Gene expression

A

The process by which DNA directs protein synthesis, consisting of two sections transcription and translation

70
Q

Differences between RNA and DNA

A
  • Contains ribose sugar not deoxyribose
  • Substitutes Uracil for thymine
  • RNA is usually single stranded
71
Q

T & T in Prokaryotes

A
  • Bacteria lack a nuclei and DNA is not segregated, this means translation and transcription are coupled
  • Ribosomes attach to the leading end of mRNA during transcription
72
Q

DEFINITION: Central Dogma

A

Refers to the molecular chain of command in a cell which has a directional flow of genetic information
DNA > RNA > Protein

73
Q

DEFINITION: Initiation

A
  • RNA Polymerase binds to the promoter

- DNA strands unwind and the Pol initiates RNA synthesis at the start point on the template strand

74
Q

DEFINITION: Elongation

A

Polymerase moves down stream unwinding DNA and elongating RNA in the 5’ to 3’ direction
- DNA helix reforms

75
Q

DEFINITION: Termination

A
  • RNA transcript is released and polymerase detaches from DNA
76
Q

Initiation in prokaryotes

A
  • Promoters signal the start point and usually extend several dozen nucleotides
  • RNA Pol binds in precise location and orientation determining which strand is the template and start point
  • RNA pol recognises and binds independently
77
Q

Initiation in eukaryotes

A
  • Transcription factors mediate RNA Pol binding and initiation
  • A transcription factor must recognise a TATA box and must bind to DNA before RNA pol can
  • Transcription factors and RNA pol 2 make up the transcription initiation complex
  • The DNA helix unwinds and RNA synthesis begins at the start point on the template strand
78
Q

Termination of transcription in Prokaryotes

A
  • Polymerase stops transcription at the end of a specific RNA sequence known as the terminator
  • mRNA can be translated with further modifications
79
Q

Termination of transcription in Eukaryotes

A
  • RNA Pol 2 transcripts polyadenylation signal sequences
  • 10 to 30 nucleotides past this enzyme cut the RNA from the polymerase
  • This releases pre mRNA which undergoes processing
80
Q

Modification of mRNA ends

A
  • 5’ end receives a modified nucleotide 5’ cap

- 3’ end gets a poly- A tail

81
Q

Function of mRNA modification

A
  • facilitate the export of mRNA to cytoplasm
  • protect mRNA from hydrolytic enzymes
  • help ribosomes attach to the 5’ end
82
Q

RNA splicing

A
  • Non coding regions called introns need removing from RNA transcripts
  • Spliceosomes carry out the splicing
  • They consist of small nuclear ribonucleoproteins and they base pair with nucleotides
  • The spliceosome cuts the pre mRNA releasing the intron for degradation and joins the exons
  • Finally the spliceosome comes apart releasing the modified mRNA
83
Q

Intron Functions

A
  • Regulate gene expression
  • can encode multiple polypeptides based on which segments are exons (alternative splicing)
  • Number of possible proteins is greater than number of possible genes
84
Q

DEFINITION: tRNA

A

Aids with translating mRNA message into a protein, transfer amino acids to the growing polypeptide chain in the ribosome.
Each one has a specific amino acid and anti codon on each end, anti codon is complementary to mRNA

85
Q

tRNA Structure

A
  • A single strand with around 80 nucleotides folded on itself
  • Includes a loop containing the anticodon and an attachment site at the 3’ end for the amino acid
  • H bonds cause it to twist and fold into a 3D molecule
86
Q

tRNA Recycling

A
  • tRNA are used repeatedly

- After depositing the amino acid at the ribosome it is released back into the cytosol to pick up another amino acid

87
Q

DEFINITION: Aminoacyl- tRNA Synthetase

A

Enzyme that connects the correct amino acid to tRNA
Each amino acid has a specific active site and the enzyme catalyses the covalent bonds with a process driven by ATP hydrolysis
Results in aminoacyl-tRNA or a charged amino acid

88
Q

3 Ribosome Binding Sites

A

P Site: holds tRNA that carries the growing polypeptide
A Site: Holds the tRNA that carries the next amino acid to be added to the chain
E Site: the exit site where discharged tRNAs leave the ribosome

89
Q

Where does binding of initiator tRNA occur in eukaryotes and prokaryotes

A

Eukaryotes: Small subunit with the initiator tRNA already bound to the 5’ cap of mRNA
Prokaryotes: Occurs at a specific RNA sequence, upstream from the start codon

90
Q

3 Steps to elongation of a polypeptide chain in the ribosome

A
  1. Codon recognition
  2. Peptide bond forming
  3. Translocation
91
Q

Termination of Translation

A
  • Occurs when a stop code reaches the A site of a ribosome
  • A release factor binds to the stop codon and causes hydrolysis of the bond between polypeptide and its tRNA P site
  • Polypeptide is released through the exit tunnel
  • Translation complex disassembles
  • Requires the hydrolysis of 2 or more GTP molecules
92
Q

DEFINITION: Polyribosomes

A

Single mRNA can be used to make many copies of a polypeptide simultaneously as multiple ribosomes trail along the same mRNA

93
Q

Polypeptide modification examples

A
  • Some are activated by enzymes that cleave them, could be to remove loops
  • Multiple subunits m)
94
Q

Name consequences of misfolded proteins

A

Allergies, neurogenerative diseases

95
Q

Protein Targeting

A

Free Ribosomes synthesise proteins that function in the cytosol
Bound Ribosomes make proteins of the endomembrane system and proteins secreted out of the cell. Polypeptides for the ER or secretion will be marked by a signal peptide

96
Q

Polypeptide Synthesis Process

A
  1. Starts in the cytosol
  2. Signal repetition protein (SRP) binds to signal peptide of a PP momentarily stopping translation
  3. Ribosome binds to the ER
  4. SRP leaves and PP synthesis resumes with simultaneous translocation pf PP across membrane
97
Q

DEFINITION: Genome

A

All hereditary information of an organism encoded in its DNA. This includes both the genes and the non coding sequences of DNA

98
Q

DEFINITION: Comparative genomics

A

Analysis and comparison of genomes

99
Q

What is the Genome Bottleneck?

A

We are now able to generate data for genomes really quickly however it still takes time to annotate genomes, computational and bioinformatic analysis lags behind our ability to generate data

100
Q

What is the relationship between genome size and phenotypes

A

There is no systematic relationship between genome size and phenotypes.
Single celled amoeba have a larger genome than humans
A larger genome also does not mean it can code more proteins due to alternative splicing

101
Q

DEFINITION: Gene Density

A

The number of genes present in a given length of DNA

Eukaryotes have more non coding DNA than prokaryotes

102
Q

DEFINITION: Pseudogenes

A

Are former genes that have mutated and are non functional

103
Q

DEFINITION: Transposable Elements

A

DNA sequences that move around the genome causing mutations by inserting functional genes or regulatory regions

104
Q

Comparative Analysis allows us to

A
  1. Gain better understanding of how species evolved
  2. Explain how evolution of development leads to morphological diversity
  3. Determine the function of genes and non coding regions in the genome
105
Q

DEFINITION: Ortholog

A

Genes in different species that evolved from a common ancestral gene by speciation, retain the same function

106
Q

DEFINITION: Paralogs

A

Genes with in a species that evolved from a common ancestral gene by duplications, have related but different functions

107
Q

Positive Regulation of genes

A

Activator protein binds onto the operator sequence which triggers the RNA Pol, rate of expression can be regulated by stability of activator protein

108
Q

Negative Regulation of genes

A

Involves repressor genes, if enough repressor proteins are present then it binds to the operator and blocks RNA Pol

Ecology & Conservation Year 1 (4 decks)

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