Cell biology Theme 1 Flashcards
1
Q
All cells need to
A
Reproduce , Grow , Release energy , excrete waste, move and respond to the environment
2
Q
The main 2 types of cells are
A
prokaryotic and Eukaryotic
3
Q
The 2 distinct features of eukaryotic cells are
A
A nucleus and membrane bound organelles
4
Q
The nuclear envelope is continuous with the …
A
Endoplasmic reticulum
5
Q
What is the nuclear lamina ?
A
A fibrous network of filamentous proteins that provides mechanical support
6
Q
What are the function of nuclear pores ?
A
To communicate with the cytosol
7
Q
What is the nucleolus ?
A
A dense sphere in the nucleus where rRNA is formed
8
Q
What is the endoplasmic reticulum ?
A
A irregular maze of interconnected sacs that are membrane bound
9
Q
What is the function of the endoplasmic reticulum ?
A
Synthesis of many cellular components as well as secretion
10
Q
What is the function of the RER ?
A
Has ribosomes on its surface which are forced to attach if the gene has an ER signal sequence
11
Q
What is the function of the SER ?
A
The site of lipid synthesis and protein modification (eg. formation of glycoproteins)
12
Q
What is the golgi apparatus ?
A
Sacks of flattened, membrane enclosed sacs called citsternae which collectively make the golgi.
13
Q
What is the function of the golgi apparatus ?
A
Modifies and packages molecules made in the ER destined fro secretion/transportation. Usually proteins and lipids.
14
Q
How are molecules transported by golgi ?
A
They are transported from the cis to trans end of the apparatus , then to lysosomes,endosomes or secretory vesicles.
15
Q
What is the endomembrane system ?
A
A continual exchange of materials takes place between the endoplasmic reticulum , golgi apparatus , lysosomes and outside of the cell
16
Q
How can molecules be modified ?
A
Glycolisation- the attatchment of a branched oligosaccharide to lipid/protein.
17
Q
What is the function of glycoproteins ?
A
intercellular signaling, receptors and membrane integrity
18
Q
What is the function of a lysosome ?
A
intracellular digestion , they release nutrients from ingested food. They also contain hydrolytic enzymes that are active under a low pH.
19
Q
How do lysosomes maintain a low pH?
A
There is a proton pump that actively tansports H+ ions into the lysosome.
20
Q
What are peroxisomes ?
A
A small organelle present in the cytoplasm that contains the reducing enzyme catalase
21
Q
What is the function of mitochondria ?
A
Generates chemical energy for the cell through ATP production in respiration
22
Q
What is the membrane of the mitochondria like ?
A
Double membrane , the inner membrane is folded to form cristae
23
Q
What is the difference between the cytoplasm and the cytosol ?
A
The cytoplasm is the contents of the cell including the organelles whilst the cytosol is the water based gel where fundamental chemical reactions take place.
24
Q
What is the function of the plasma membrane ?
A
it maintains cell integrity , allows selective passage and has cell surface receptors
25
What is the principle of compartmentalisation and why is it useful ?
the formation of cellular compartments by membrane enclosed regions. Usually needed for isolation, efficiency and economy. Allows the separation of anabolism and catabolism
26
Why is compartmentalisation needed in mitochondria ?
Provide additional surface area , allows non-compatible reactions to occur at the same time
27
Why is compartmentalisation needed in lysosomes ?
allows the maintenance of an acidic environment and to prevent auto-digestion of organelles.
28
What is endocytosis ?
The process by which a substance is captured from the outside of the cell. Engulfing it with the cell membrane , bringing it into the cell
29
What are the 2 types of endocytosis ?
Phagocytosis and pinocytosis
30
What is the process of Phagocytosis ?
A particle binds to the phagocytic cell surface and activates a receptor. This causes sheet like projections called pseudopods to engulf the bacteria into a phagosome. The phagosome binds with a lysosome and the bacteria is destroyed.
31
What is pinocytosis ?
Ingestion of fluid and small molecules via small pinocytic vesicles. A droplet becomes adsorbed on the cell surface and the membrane invaginates to form a vesicle in the cytoplasm.
32
What are pinocytic vesicles coated in ?
Clathrin
33
The bilayer arrangement is ?
the most energetically favourable
34
the fluidity of the lipid bilayer depends on ?
composition - ie. the nature of the phospholipid tails, the closer and more regular the packing of the tails the more viscous and less fluid the membrane
35
The shorter the chain length...
the smaller the tendency of tails to interact and the more fluid the bilayer is
36
What is cholesterol and what is its function ?
Short and rigid molecules that fill spaces and kinks created by unsaturated tails . It stiffens the bilayer making it less permeable and less fluid.
37
Why is membrane fluidity important ?
Permits lipids and proteins to diffuse from sites of synthesis to other regions. Allows molecules to distribute evenly between daughter cells.
38
What is the cytoskeleton ?
A structure that helps cells maintain their shape and allows internal organisation
39
The cytoskeleton is made of which 3 types of protein ?
Actin , Microtubules and Intermerdiate filaments
40
What is the structure of intermediate filaments ?
Rope like strands made of helicous fibrous proteins , they are the toughest
41
What is the role of intermediate filaments ?
they are the toughest filament and provide mechanical strength
42
Describe the role of Keratin
It is concentrated and anchored at the plasma membrane of cell-cell junctions in cells prone to mechanical strength
43
What are the 2 types of intermediate filaments ?
Cytoplasmic and Nuclear
44
Describe the properties of nuclear and cytoplasmic filaments
Cytoplasmic are rope like whilst nuclear are meshwork like
45
What are microtubules made of ?
tubulin - alpha and beta
46
What are the structure of microtubules ?
Heterodimers , hollow cylinders which grow from centromeres. the heterodimers add to the positive end opposite the negatively charged centromere
47
What is the function of microtubules ?
They have a role in transportation and positioning organelles. They act as tracks.
48
How do microtubules play an important role in cell division ?
Microtubules guide chromosomes to daughter cells during mitosis
49
How do Antimitotic drugs work ?
Vinca alkanoids and taxens both bind to beta tubulin disturbing the dynamics of microtubules. Vinca alkanoids prevent the polymerisation of microtubules whilst taxens stabilise pre-existing microtubules.
50
In ciliated cells where do microtubules grow out from ?
Basal bodies
51
How do microtubules act as tracks ?
The microtubules provide tracks whilst motor proteins (kinesins and dyneins) associate with the microtubule allowing cargo to be moved,
52
What is the structure of motor proteins and how do they work ?
They are diamers as they have a head and tail. The tail interacts with cargo whilst the head interacts with the microtubule. ATP dependent.
53
What is the role of actin ?
It is the thinnest and is needed for cell movement , through cell crawling. Involved in the support of microvilli and contractile bundles.
54
What is the structure of actin ?
Actin monomers pack tightly together to form 2 helices that are tightly wound,
55
What does actin associate with and why ?
different proteins which determines the function of the actin eg. a bundling protein.
56
What is the cell cortex ?
A specialised layer dense layer of actin that is cross linked, at the inner face of the membrane. It can associate with proteins that determine the shape of the cell , conferring shape.
57
What does spectrin do erythrocytes ?
Its in the cell cortex and cross links with actin providing the discoid shape of erythrocytes.
58
How do cells move using actin ?
Rearrangements of actin filaments within the cortex provide the basis for changes in cell shape and cell locomotion.
59
What is the extracellular matrix ?
A collection of extracellular molecules screted by cells to assist in the formation of tissue
60
In conenctice tissue which protein is preseent in the matrix ?
Collagen , interwoven with elastin
61
What is the structure of collagen ?
It is a rope like superhelix which consists of 3 lon polypeptide chains with glyceine at its core. There are cross linkages formed when bonds from between amino acids , making collageb fibrils. Also proline present.
62
What is the structure of elastin and how is it deposited ?
Loose unstructured polypeptides interowve with collagen. Cross linkls form between the elastin molecules allowing the formation of fibres. Fibrillin is secreted by the ECM and acts as a scaffold for the deposition of elastin. Elastin allows for arterial stretch as well as recoil.
63
What are glycosaminoglycans ?
Negatively charged polysaccharides , can be proteoglycans. Positively charged ions are attracted b, this lowers the water potential and draws water into tissue. This acts as a shock absorber by resisting compression. Present in dentine , stopping the enamel chipping. In the gingiva acts as a shock absorber
64
How is DNA found ?
DNA is highly condensed and packaged by proteins into chromatin. This is distributed among 24 diff chromosomes.
65
What are homologous chromosomes ?
Similar in length , gene position and centromere location. They contain different alleles
66
What are fundamental units ?
octamers- they are composed of 8 histone proteins which make up the nucleosome. 147 Base pairs stretcj around the nucleosome.
67
which histone proteins are present in the nuclesome ?
2 each of H2A H2B H3 and H4
68
What is a linker histone ?
A linker histone helps to pull nucleosomes together and pack them into a comapct chromatin fibre.
69
What is the structure of histone 1 ?
consists of a globular region and a pair of long tails at C and N terminal ends. The C terminal binds to chromatin allowing H1 to bind. This is because C end is larger.
70
What is heterochromatin ?
A region of the chromosome that is largely silent as the DNA is tightly wound.
71
What is euchromatin ?
It is more stretched and accessible DNA that is more likely to be expressed. (not all the time tho)
72
What are histone proteins ?
Proteins consisting of a high amount of positive amino acids ?
73
How do covalent modifications affect chromatin structure?
The amino acids in the histone have an N terminus amino acid tail that is positive and attracts modifications such as phosphate groups , acetyl groups and methyl groups.
74
How does acetyl and methyl modification work ?
Acetyl groups are negatively charged they repel negative DNA, hence the chromatin structure is unchanged. Methylation of a H3 protein is associated with gene silencing as heterochromatin forms.
75
Where does DNA start to replicate ?
At replication origins , which are usually A-T stretches of DNA .
76
What opens the double helix for replication ?
initiator proteins
77
What are replication forks ?
they form at each replication origin , 2 at each origin. the 2 forks move away from the origin in opposite directions. this is bidirectional.
78
What direction does DNA polymerase grow the new strand ?
in the 5' to 3' direction.
79
What else is required by DNA polymerase ?
An RNA primer , made by primase. This is necessary because DNA polymerase can only add new nucleotides to an existing strand of molecules.
80
What is the concept of Okazaki Fragments ?
DNA strands are anti-parallel. . the 3' to 5' strand appears to grow in the same direction as the 5' to3'. This is because in the 3' to 5' direction the new strand is made discontinuously,, in separate small fragments. The DNA polymerase moves bacjward relative to the replication fork. The fragments are joined together with ligase.
81
What is the lagging strand ?
The delay caused by ligase sticking the fragments together means that one strand lags behind the other,
82
How does torsional stress build up in a DNA molecule ?
As DNA helicase unwinds the DNA it generates a section of overwound DNA. This builds up as the chromosome is too large to rotate and relieve the stress.
83
What is the role of DNA topoisomerase ?
It relieves the stress by generating temporary nicks in the DNA. These nicks allow the chromosome to move and relieve the stress.
84
How does DNA polymerase "self-correct" ?
DNA polymerase monitors the base pairing between incoming nucleotides and the template strand. if correct the reaction is catalysed.
85
How does DNA polymerase take part in proof-reading ?
DNA polymerase checks whether the previous nucleotide pairing is correct before the creation of the next pair. Incorrect pairings are clipped off.
86
Where are the origins of replication in a chromosome ?
the centromere and the 2 telomeres
87
Where are telomeres ?
at the end of chromosomes
88
What do telomeres do ?
they attract telomerase which adds repeated short fragments allowing the lagging strand to continue.
89
What is phylogeny ?
The study of evolutionary relationships between organisms
90
When did modern eukaryotes first evolve ?
About 2 bn years ago
91
What is the average size of a bacterial cell ?
1-5 microns
92
What is the average size of the human cell ?
50-100 microns
93
How can we determine the evolutionary relationships between different bacteria ?
Isolate DNA from each bacterium
Locate and isolate the rRNA gene
Amplify the gene using PCR
Sequence the DNA and look for differences.
94
What are 4 different bacterial shapes ?
Cocci , rods , spirilla and spirochetes
95
How can bacteria be classified ?
```
Whether or not they retain the gram stain -
Gram positive (purple) and gram negative (pink)
```
96
What are the two types of membranes ?
outer membrane and cytoplasmic membrane
97
What is the periplasm ?
A space in gram negative bacteria between the outer and cytoplasmic membrane.
98
What are pilli ?
Strands which protrude off the bacterial surface and are used for adhesion and DNA transfer
99
What is the role of the capsule ?
protects from dessication or immune attack
100
What is the outer membrane made of ?
Peptidoglycan , thick in gram positive and thin in gram negative
101
What is the mitochondrial genome like and how is energy released ?
the DNA is free and circular and they release energy via oxidative phosphorylation
102
What is the role of the bacterial cytoskeleton ?
It acts as scaffolding that directs cell shape producing the different morphologies.
103
What is the bacterial cytoskeleton made of ?
homologues of actin and tubulin
104
What is MreB and what does it do ?
a homologue of actin that froms the cytoskelton by making patch-like filaments around the inside of the cell.
105
What is FtsZ ?
a homologue of tubulin , it assembles into a ring that is used in cell division
106
What is the structure of the bacterial cytoplasmic membrane ?
A phospholipid bilayer embedded with proteins
107
What are hopanoids ?
sterol like molecules that strengthen the cytoplasmic membrane in bacteria
108
What is peptidoglycan ?
A rigid polysaccharide that provides structural strength found in all bacteria
109
What is the structure of peptidoglycan ?
made of 2 glucose residues and D isomers of amino acids. It is synthesised to form a sheet and individual strands are connected by peptide cross links
110
Why are bacteria subject to attack by lysosomes ?
They contain lysozymes that can cleave the peptide cross links leading to cell lysis
111
What is an unusual feature of peptidoglycan ?
there are 2 amino acids present of the D stereoisomer
112
What is the single layer of peptidoglycan bacteria are covered in called ?
the murein sacculus
113
What is the structure of the gram positive cell wall ?
A thick peptidoglycan cell wall made of several cables which are cross linked. covalently bonded to the cell wall are teichoic acids and lipotechoic acids. These provide mechanical strength and impermebility to the cell wall.
114
in gram negative bacteria what does most of the cell wall consist of ?
an outer membrane which also contains polysaccharide, specifically lipopolysaccharide. It is of moderate strength. It makes the outer membrane impermeable.
115
What is the periplasm and what does it do ?
The space between the outer and cytoplasmic membrane. It stops proteins from diffusing away and contains many transport proteins and hydrolytic enzymes.
116
How does the antibiotic Bacitracin work ?
It blocks cell wall formation by forming a complex with the molecule that acts as a carrier in the transfer of polysaccharides to synthesise peptidoglycan. Therefore cell wall formation is stunted.
117
How does Polymixin B work ?
Causes cell membrane permeability so that water is uptaken leading to cell death
118
how does Penicillin work ?
Inhibits DD-transpeptidases that form peptide cross links in peptidoglycan
119
What are archea ?
An intermediate microoranism of bacterian and eukaryotes. There is no nucleus or organelles inside. They are single celled and have a complex RNA polymerase rather than a complex one. Their membranes have glycerol ethers rather than glycerol esters.
120
Explain the process of binary fission
bacteria replicate their DNA and elongate to twice their length
FtsZ accumulates at the centre to form the Z ring.
the FtsZ ring contracts and leads to the formation of a septum which is an invagination in the membrane.
The cell divides downwards from the septum
(In e-coli the mreB cytoskeleton divides down the septum)
121
What are the 4 phases of the bacterial growth curve ?
lag , exponential , stationary and death
122
Why is there a lag phase ?
to allow cells to adapt to the agar and express the appropriate genes
123
What are the 2 ways of quantifying the numbers of microroganisms ?
Viable count and optical density
124
How does viable count work ?
bacteria re grown in a solution , diluted down to form colonies and the dilution factor is used to calculate how many were originally in the sample.
125
How does optical density work ?
a spectrophometer is used to measure the measure the density of light that passes through a solution. the bacteria form a cloudy solution which will block the light. However a problems arises in that dead cells will also block the light.
126
What is the equation for generation time ?
time/number of generations
127
What is the equation for N (number of bacteria after a specific time)
N=N0 X 2^n
128
What is the equation for n ?
n= 3.3(logN-logN0)
129
What nutrients do bacteria require ?
oxygen , carbon , inorganic ions , organic nutrients
130
What are obligate aerobes ?
cannot respire anaerobically so they require constant oxygen
131
What are obligate anaerobes ?
they respire anaerobically as they are poisoned by oxygen , found in low oxygen concentrations.
132
What are facultive anaerobes ?
they can switch between either respiration type.
133
What are autotrophs ?
they were earlier organisms that used c02 to make molecules
134
What are heterotrops ?
they are capable of using complex organic substances to obtain carbon.
135
What are inorganic ions ?
nitrogen , sulphur , phosphate and magnesium
136
What are organic nutrients ?
carbohydrates and amino acids
137
How can analysis of bacterial metabolism of substrates aid us ?
analysis of metabolism aids bacterial identification.
eg. E-coli and salmonella are identical however using a lactose agar we can distinguish between them. E-coli use lactose and turn pink. Salmonella dont and turn yellow.
138
What is chemotaxis ?
Movement of a motile cell in a direction towards a particular chemical
139
What is phototaxis ?
Bacteria that use light as their energy source , colonies will move towards light.
140
How can bacteria move towards certain stimuli ?
they have directional sensing and motility (swimming via flagellum)
141
What are flagella ?
Rotating helical structures that enable motility and are tethered to the cell envelope.
142
What is the structure of flagella ?
consists of a basal body and a tail supported by microtubules.
143
How does the flagellum move ?
The protein rings are associated with a motor protein that is driven by ATP hydrolysis - allowing a spinning motion.
144
Are bacterial cells haploid or diploid ?
haploid
145
What is the genetic material like in bacteria ?
one circular chromosome consisting of 0.75-10 megabases
146
What are plasmids ?
extra circular chromosomes, these are able to move easily and are associated with antibiotic resistance and viralence
147
How is the bacterial genome represented ?
a circle where each gene is an arrow , the DNA is double stranded so each direction represents a different strand. it is colour coded to predict the role of the protein product.
148
Why doesnt mRNA from prokaryotes under go splicing ?
bacterial DNA has no introns
149
What is vertical gene transfer
transfer of DNA from parent to offspring
150
What is transformation ?
DNA uptake from the environment
151
What is transduction ?
when a bacteriophage picks up DNA and deposits it in a cell
152
What is conjugation ?
this is pilus mediated , usually a sex pilus.
153
What is a biofilm ?
Communities of microorganisms associated with extracellular material found at interfaces,
154
What are planktonic cells ?
Single cells suspended freely in water
155
What is the capsule ?
Extracellular polysaccharides secreted to retain water and nutrients and protect against immune system attack.
156
Binding sites are complementary to what ?
their ligands shape
157
What are the non-covalent bonds between the ligands and the protein
van der Waals , Hydrogen bonds and electrostatic forces
158
What is the structure of an antibody ?
2 heavy + 2 light polypeptide chains
| 2 binding sites allow 2 molecules to bind per antibody
159
What is the specificity of antibodies ?
sequence variaition means that different shaped antigens will bind to different shaped binding sites. Different antibodies therefore recognise different antibodies.
160
What produces antibodies ?
B-lymphocytes
161
How can we make antibodies ?
Injecting the antigen into an animal , the blood of the animal will contain antibodies complementary to the antigen,
162
how can we detect the presence of a protein in a blood sample ?
using enzyme linked antibodies
add antibodies to the blood sample and wash to remove unbound antibodies
add a secondary antibody (which has the enzyme bound) and wash
add the substrate of the enzyme and the intensity of the colour of the precipitate will indicate the quantity of protein in the blood sample.
163
why do we use secondary antibodies ?
allows more antibodies to bind to the primary antibody, creating a darker ppt.
164
What is the ELISA test ?
it is used to quantify the amount of protein in a sample , the amount of enzyme product is proportional to the amount of antigen in the sample.
165
What is immunoblotting (western blotting) and what is it used for ?
used to estimate protein size
proteins can be extracted from a cell and separated via gel electrophoresis ( when an electric current is applied to proteins covered in detergent to give them a negative charge) the proteins migrate towards the anode. the bigger the protein the less it will migrate. add antibodies to detect the position of the protein
166
What is DAPI and what does it do ?
it binds to the minor groove in DNA and then fluoresces blue. it can be used to locate the position of the nucleus.
167
Why do we want to detect nucleic acid sequences ?
to look for gene mutations
| Identify chromosome rearrangements/deletions
168
How can we detect nucleic acid sequences ?
DNA hybridisation
169
What is the process of DNA hybridisation ?
An oligonucleotide probe is prepared synthetically
it is labelled with a fluorophore/enzyme
The DNA is 'melted' , the temperature is reduced and the probe is added in excess , it will bind to its complementary target sequence in DNA
It will fluoresce or the substrate of the enzyme can be added
170
What is a chromosome spread ?
they are used to observe chromosomes specifically deletions when part of the chromosome is missing
171
What is the genetic abnormality in chromosome 22 ?
In leukaemia cancer cells , the philadelphia translocation lead to the formation of an oncogene.
172
Why do we use restriction enzymes on chromosomes prior to analysis ?
to digest the chromosomes as they are usually quite large.
173
What are major components of the ECM ?
```
collagen
elastin
integrin
fibronectin
fibroblasts
glycosaminoglycans
```
174
By what process do fibroblasts secrete collagen
exocytosis
175
What is collagen 1 ?
it is present as long fibrils
| present as skin , tendon , bone , ligaments , dentine and interstitial tissues
176
What is collagen II ?
present as long fibrils in cartilage and vitreous humour
177
What is collagen III ?
long fibrils associated with type 1 and found in muscle and red blood cells
178
What is collagen IV ?
sheet forming collagen found in basal lamina of epithelial cells
179
What is collagen V ?
long fibrils associated with type 1 and present in foetal membranes , skin , bone and placenta .
180
Which amino acid is found uniquely in collagen ?
Hydroxyproline
181
What are collagenases and how can they be used in treatment ?
collgane has to be romdelled in growth and repair and macrophages have to get through the collagen - collagenases can be used. they can be used in the treatment of burns.
182
What is the relationship between collagen , integrin and fibronectin ?
collagen fibrils are connected to fibronectin , a glycoprotein. via integrin dimers - these are connected to actin filaments and allow cells to crawl through the ECM.
183
Which amino acid is the precursor of the hormone thyroxine
tyrosine
184
Which amino acid provides the positive charge for histones ?
arginine
185
Which RNA molecule is covalently bonded to amino acids ?
tRNA
