Cell Signalling Flashcards
1
Q
What are ligands?
A
Signalling molecules
2
Q
What do ligands do?
A
They bind onto specific receptors (other molecules)
3
Q
How does a message carried by the ligand work?
A
Leads to a change in the cell in the activity of a gene, or induce a process like cell division.
4
Q
What does cell to cell signalling involve?
A
Transmission of a signal from a sending cell to receiving cell
5
Q
What are the basic 4 categories of chemical signalling?
A
Paracrine
Autocrine
Endocrine
Signalling by direct contact
6
Q
What is paracrine signalling?
A
Cell communication over a relatively short distance
7
Q
How does paracrine signalling work?
A
Cells that are near one another communicate through release of chemical messengers;
Ligands can diffuse through the space between cells
8
Q
When does paracrine normally take place?
A
Used in different tissues and contexts, important in development (spinal cord development)
9
Q
What is the subtype of paracrine signalling?
A
Synaptic
10
Q
What is synaptic signalling?
A
Synapse process, the junction between two nerve cells where signal transmission occurs.
Ligands are called neurotransmitters which quickly cross small gap between nerve cells. When they bind onto the receptor, chemical change inside cell happens (often opening ion channel)
11
Q
What is autocrine signalling?
A
Cell signals itself releasing a ligand that binds to its own receptor
12
Q
Where can you find autocrine signalling?
A
During development, helping cells take on and reinforce heir correct identities.
Important in cancer (key role of metastasis, spread of cancer from original sight)
13
Q
What is endocrine signalling?
A
Cells need to transmit signal over a long distance.
14
Q
Which system does endocrine signalling work very closely with?
A
Cardiovascular system
15
Q
How does endocrine signalling work?
A
In long distance endocrine signalling, signals are produced by specialised cells and released into the bloodstream which carries them to target cells in distant parts of the body.
16
Q
What are these signals called which gets made at one place and travel a long distance through blood?
A
Hormones
17
Q
In humans, where are hormones released from?
A
endocrine glands like thyroid, hypothalamus, pituitary, pancreas, and gonads
18
Q
What is signalling through cell to cell contact?
A
Gap junctions, tiny channels which allow small signalling molecules called intracellular mediators to diffuse between the two cells.
19
Q
How does binding of a ligand to a receptor work?
A
Specific ligands bind to specific matching receptor which changes the shape of the receptor allowing transmit of a signal or produce a change inside the cell.
20
Q
What are the two categories of receptors?
A
Intracellular (membrane bound) receptor
Cell surface receptor
21
Q
What are intracellular receptors?
A
Found inside the cell in the cytoplasm or nucleus
22
Q
What are cell surface receptors?
A
Found in the plasma membrane anchored proteins.
23
Q
Does ligand need to cross the plasma membrane for cell surface receptors?
A
No
24
Q
What are the 3 domains of cell surface receptors?
A
Extracellular ligand binding domain
Hydrophobic domain
Intracellular domain
25
What are the three main kinds of cell surface receptors?
Ion gated channels
GPCR (G protein coupled receptor)
RTK (recpetor tyrosine kinase)
26
What are ligand gated channels?
Channels which open in response of binding of a ligand
27
How do channels form?
Receptor has a membrane spanning region of hydrophillic (love water) in the middle of the channel.
28
What does the channel do?
Lets ions cross the membrane without through hydrophobic core of the phospholipid bilayer
29
What is GCPRs?
Large family of cell surface receptors with common structure and method of signalling.
30
What do GCPRs do?
Transmit signals INSIDE the cell through a type of protein called G protein.
31
Example of GCPRs use is?
Through scent receptors
32
When a ligand is NOT present, the GCPR...
Waits at the plasma membrane in an inactive state.
33
Where do the G proteins bind to?
Onto the GPCR but bind to GTP nucleotide.
34
GTP breaks down to form...
GDP
35
When a G protein links to GTP is active/inactive?
Active
36
When a G protein links to GDP is active/inactive?
Inactive
37
Describe how GCPRs work
Unbound GCPR is unbound and therefore inactive
G protein is bound to GDP and enzyme is inactive too.
Signal binds to receptor and G protein binds to GTP (turns on) but enzyme is still inactive.
Activated G protein + GTP dissociates, receptor activates the enzyme to do a cellular response
G protein has GTPase activity promoting release from enzyme reverting back to resting state.
38
What is the first step of cell communication?
Reception of signal
First messenger (signal protein) binds to protein receptor
Conformational change to the receptor because of the binding
39
How does RTK work?
At rest, RTK are inactive monomers
Signal molecule (growth factor) binds to RTK, dimerises in membrane (separate monomers stick together now like magnets)
TK of one monomer phosphorylates the other monomer activating both monomers.
Each activated RTK binds to activate specific proteins and anzymes
40
Ligand gated ion channels how they work?
At rest, lgand unbound and gate is closed
Ligand is the signalling molecule and gate opens once it binds onto the channel allowing flow of ions.
Ligand comes of and gate closes back to resting state
41
Cytosollic or nuclear recpetors are what relationship with water and why?
Hyrdrophilic as they need to pass the hydrophillic plasma membrane which was made out of phospholipids, lipid soluable or small
42
What two types of cells are there?
Prokaryotic
| Eukaryotic
43
What characteristics does each cell have?
```
DNA (heritable material)
RNA (messenger intermediate)
Proteins (as the workers)
ATP (energy source)
Has a relationship between DNA, RNA and proteins
```
44
What are membrane-bound organelles?
Organelles protected by a single or double plasma membrane.
45
What is the difference between the shape of DNA in eukaryote and prokaryotes?
EU - Linear double helix
| PR - Circular
46
What do they eu and pro have in common?
Have cytoplasm enclosing them both
47
In pro, where is DNA stored?
No nucleus so it's in nuclear area (nucleoid)
48
Structure of phospholipids are
Double layer of fats called phospholipids
49
WHat is a phospholipid?
Each layer made up of a hydrophilic head and hydrophobic tail with proteins embedded in it
50
What is the function of the plasma membrane?
as a barrier to control entry and exit into the cell semipermeable
51
What 3 forms of the protein can be found in the plasma membrane?
Transmembrane
Peripheral membrane
Glycoprotein
52
Structure of phospholipids which make up the plasma membrane is?
Heads out tails in
53
What is the function of embedded proteins?
mediate movement of hydrophilic substances and intercellular communication
54
What is the structure of transmembrane protein?
Spans the entire membrane, integral protein
55
What are the 6 different functions of plasma membrane?
```
Transport
Enzyme activity
Cell-cell recognition signalling
Signal transduction
Intercellular joining
Attachment to the cytoskeleton and ECM
```
56
What is an important feature of the plasma membrane?
We have to understand the fluidity of the plasma membrane
57
Name the organelles with a double lipid bilayer
Nucleus
| Mitochondria
58
Describe the endomembrane system
Transport vesicle from the rough ER is in a transport vesicle which enters the golgi apparatus to modify entering in the cis face and exiting through the trans face and is either secrete out of the cytosol. secreted for membrane renewal or enzyme for cytosol
59
How is DNA organised and coiled within the nucleus to form a chromosome?
8 histone proteins make a nucelosome where the DNA is wrapped around the nucelosome 2x (10nm)
During early mitosis, chromatin condense to chromatin fibre which is 30nm
Fibres condense into loops which are 300nm
Finally form chromosomes held centrally at the centromere 1400nm
DNA can be divided into genes located along teh chromosome (genses codes for proteins via transcription and translation)
60
Describe what DNA is
DNA is a double helix polymer made of many monomers. These monomers are called nucleotides/
61
What does a nucelotide contain?
A phosphate group
Nitrogenous Base
Sugar (deoxyribose)
62
How is the DNA stabilsied? What bonds
Hydrogen bonds (at the bases attachment) and phosphodiester bonds at the chain
63
What would go wrong if there was an issue with lysosome?
Loss of autophagy, autolysis + cellular digestion
64
What would go wrong if there was an issue with mitochondira?
RIP powerhouse of the cell
65
What would go wrong if there was an issue with golgi appararatus
Inability to modify MEMBRANE, ORGANELLE and SECRETED PROTEINS + effect on lysosomes
66
What would go wrong if there was an issue with smooth ER?
Can’t produce carbohydrates and lipids + tissue specific effects i.e. loss of detoxifying enzymes in the liver/loss of calcium stores in muscle
67
Is a glucose a source of energy?
no it isnt the SOLE source of energy
68
What do complex molecules do?
The store energy
69
What are the steps for gene expression?
DNA (transcription)
Pre-mRNA (mRNA processing)
Mature mRNA (transition)
Protein (folding post transition modifications)
70
What are the sub types of transcription?
Initiation
Elongation
Termination
71
What are the steps of mRNA maturation?
5' cap
Poly A tail
mRNA splicing
72
What are the subtypes of translation?
Initiation
Elongation
Termination
73
What is happening in transcription?
RNA copy segment of DNA
74
What is happening in maturation of mRNA?
Also called mRNA processing
75
What is happening in translation?
Protein production using mRNA template
76
What is the first step of initiation in transcription?
DNA is double stranded (5 to 3 on one strand and 3 - 5 on the other, only ONE will be the template strand)
77
What is the 2step of initiation in transcription?
Upstream (3 to 5) of the gene. is the promoter which usually includes the TATA box with sequence 5- TATAAAA 3)
78
What is the 3step of initiation in transcription?
Transcription factors bind to the promoter specifiaclly to the TATA box
79
What is the 4step of initiation in transcription?
RNA II polymerase is then able to bind to the transcription factors and the START CODON on the DNA
80
What is the 5step of initiation in transcription?
RNA II polymerase undertakes transcription moving from 3 to 5 along template strand and manufacturing the mRNA in 5 to 4 direction
81
what is the 6step of initiation in transcription?
Transcription includes both translate and non translated sequences of
82
Which direction do proteins work in?
5 to 3 direction
83
What is the nucleus lined by?
Nuclear lamina
84
How do substances enter and exit the nucleus?
through the nuclear pore
85
What is the primary function of the nucleus?
House and store DNA
86
What is the other function of the nucleus?
rRNA and ribosome production
87
What is the cytoplasm?
Any part of the cell interior to the plasma membrane
88
What is the cytoplasm surrounded by?
Cytosol a jelly-like substance
89
What can be found in the cytoplasm?
```
Nucleus
Ribosomes
Lysosomes
Mitochondria
ER (smooth and rough)
Golgi complex
Cytoskeleton
```
90
Where is DNA found?
Nucleus
91
What is the structure of DNA?
Made up of nucleotides
92
What kind of bonds found between the bases?
H bonds
93
What is a chromosome?
A piece of DNA many genes
94
What is a gene?
Section of DNA with known function
95
What is the levels of the appearance of DNA?
DNA wrapped 2x around 8 histones = 1 nucleosome 10nm
Many nucleosomes = chromatin
Chromatin condenses further into chromatin fibre 30nm
Chromatin fibre condense coiled up even more to become chromatid 300nm
2 chromatids become a chromosome 1400nm
96
What are pyrimidines?
One ring
Cytosine
Thymine
Uracil
97
What are purines?
2 rings
Adenine
Guanine
98
What types of sugars are there?
Deoxyribose (DNA)
| Ribose (RNA)
99
What is the structure of ribosomes?
Small and large subunit
100
Where can ribosomes be produced?
Nucleolus
101
How are ribosomes made?
Made with rRNA proteins from RNA
102
What is the function of ribosomes?
Protein production
103
Where can ribosomes be found?
Free in cytoplasm
| Attached in the ER (rough)
104
How are these proteins modified?
In the cytoplasm
105
What is the function of bound ER ribosomes?
Production of membrane protein or rotein for use in specific organelles secrete proteins
106
How are these proteins from the ER modified?
In the golgi apparatus
107
Where is cholestrol found?
In the hydrophobic tails
108
Why do we need cholesterol ?
To hold membrane together
109
What happens when a membrane is heated up?
Cholestrol holds it togehter
110
What happens when we cool the membrane?
Fluidity of membrane is altered by aount of cholestrerol
111
Where is cholesterol made?
In the liver
112
What is phosphatdylcholine?
Choline, phosphate 4 glycerol
Found outside cell
Chraged area
113
What is programmed cell death?
Apoptosis
Phosphatidylcholine folds in 4 the layer underneath it (phosphatidylserine) end up on the outside
Annexin 5 binds to increase and the cell dies
114
Where does apoptosis happen?
In the liver
115
Where does apoptosis not happen?
Stem cells
| Female germline eg. ovaries
116
What are 2dry functions of the nucleus?
rRNA and ribosome prod
| Compartmentalisation so molecules can be segregated
117
What is the function of histones (nucleosome?
Uncoiled DNA for transcription and translation carry epigenetic marks
118
Epigenetics is used for?
predict dis-eases
119
How often do cells divide?
Most cells every 12 hours
Early embryos every 24 hours
Some cells do not divide like neural stem cell
120
What causes skin cancer?
Formation of thymine dimers in DNA when exposed to UV light
121
When are ribosomes mature?
Can be used after pushed out from the nuclear pore
122
What happens if lysosome bursts?
cell dies
123
How does lysosome digest?
Autophagy vesicle and lysosome fuse
124
What is the structure of the ER?
An extensive network of tubules and tubules
125
Where is the rough ER?
Stretch out from the nuclear membrane
126
Where is the smooth ER
extends out from the rough ER
127
What is the function of the rough ER
processing packaging sorting
128
What kinds of proteins enter the rough ER?
secreted proteins
membrane proteins
proteins due to work in specific organelles
129
What do the proteins look like after it has been in the ER rough?
Has a vescile surrounding it goes to golgi
130
What is the function of the smooth ?
Housing unit for tissure specidc proteins and enzymes site of production of lipids and carbs in cell
131
What can stored enzymes proteins be used for?
In the liver to detox ify drugs or harmul substances
132
What is the structure of golgi?
A number of flattened membranous cisternae all stacked on top of each other in a c wifi shape
133
What is the function of golgi?
Modify sort package and transport proteins from the rough ER
134
What do the sacs of cisternae contain?
Diff enzymes of diff function
135
What is the role of medial cisternae?
Modify proteins for function or destination
136
What is the role of cis face?
Vesicle from rough ER is enter over here
137
What is the role of trans face?
exit cisternae modifies if neccessary package the protein to its destination
138
What is the structure of the lysosomes?
Vesicles (bubble) formed from golgi complex
139
What does lysosome contain
Digestive enzymes and hydrolytic powerful enzymes
140
What is lysosomes surrounded by
plasma membrane of the plasma membrane of golgi
141
What is the function of the proteins found inside of the plasma membrane
pumps H+ inside from cytoplasm
| allows enzymes to function in the lysosome
142
What is the function of lysosome?
```
Digestion of
substances that enter a cell
broken down organelles autophagy
entire cells autolysis
any extracellular digestion
```
143
What happens after lysosomes have finished digesting the contents?
Recycle stuff
144
What is the structure of mitochondria?
Outer and inner mitochondrial membrane
double phospholipid bilayer
fluid filled interior cavity mitochondiral matrix
145
Function of mitochondira?
ATP prod through cell resp
146
Inner mitochondiral matrix contain
cristae (folds)
147
What is ATP cycle
ADP + P arrows touch top bottom of ATP (and)
148
What are the three types of cytoskeleton filaments
Intermediate filaments 8- 12 nm
Microtubles 25nm
Microfilaments 7nm
149
structure of microfilaments
made from actin molecules assembles in Q long hains twited around each other
150
microfilaments function
bear tension and weight promote motility if required
151
microfilaments found
in all eukaryotic cells around periphery and lining at the interior of microvilli
152
function of microfilaments
muscle contraction
cell division
cytoplasmic streaming
153
How does microfilament do the function?
Anchoring cytoskeleton to plasma membrane proteins
154
Is microfilaments permanent?
most permanent of cytosketon
155
structure of microtubles
tubulin dimers twisted into coil to form a tube
156
function of microtubules
support cell shape and size
scaffold or guide for movement of organelles
support cilia and flagella
157
is microtubles permanent?
no
158
function of microfilaments and intermediate filaments
bear tension and weigh in cell trough cell anchoring
159
transcription occurs where?
in nucleus
160
why is the template strand 3 to 5
because all proteins work and need to be manufactured in the 5 to 3
161
what is the TATA sequence
5-TATAAAA - 3
162
What doe RNA polymerase II bind to?
transcritpion factors and start codon
163
intitation steps into 3
transcription factors bind to TATA box in promoter region of strands
RNA polymerase II binds to transcription factors and start codon of DNA
RNA polymerase II undertakes transcription moving 3 to 5 the template strand and the new mRNA is 5 to 3 opp
164
Elongating include?
Elongating the growing mRNA strand
unwinding the DNA and rewinding after it has finsihed copying
165
Hoe long does RNA polyermase II inwinnd DNA double helix?
10-20bpm at a time
166
Where are the nucetides added as the mRNA gorws?
at the 3 end
167
transcription rate in eukaryot?
40 nucelotide per sec
168
elongationn step s
RNA polymerase II moves along DNA elongating the mRNA strand
mRNAstrand grows and comes out of DNA
DNA helix rewinds after it
169
What happens in termination stage?
polyadenyoation signals is added after stop codon mRNA transcripts released
170
How much does the polyadenylation signal is the mRNA trnascript?
10 - 35 downstrea
171
sequence of adenylation signal
5-AAUAAA-3
172
termination process steps
RNA poly reaches the stop codon
RNA poly transcribes a polyadenylation signal in the DNA
mRNA transcrpt is no 5-AAUAAA-3
10-35 downstrea, of the polyadenylation signal mRNA transcripts excised from the RNA poly
173
Will only one codon code for an amino acid?
No! More than one codon will code for an amino acid
174
What does that mean?
Each amino acid codon sequence will usually the same 2 bases and different 3 base
175
Why?
Because there are only 20 amino acids where they differ are their side chains
176
What are the three stop codons?
UUA
UAG
UGA
177
What is the common thread?
Gene expression involves making proteins using a DNA template and RNA intermediary in order to fulfil a function need
178
What does the sequence of DNA govern /
The sequence of mRNA which governs the sequence of the final protein
179
What does the protein govern made from the DNA and mRNA?
The final shape and structure
| As structure determines the function the DNA sequence is likely to determine the ability of the protein to function
180
How does the sequence of the final protein link to the shape and structure?
Through the amino acid side chains and how they interact with each other
181
What are amino acids
building blocks which make proteins
182
When are amino acids reactive?
When they are in solution and are ionised
183
How do proteins have different properties?
Size of protein
The content of amino acid
The sequence of amino acid
184
How are amino acids numbered
N and C terminus
185
What joins amino acids together?
A peptide bond (forms polypeptide)
186
What are 3 features of a polypeptide?
Side chains stick out of the backbone
Directional N terminus and C terminus
It is flexible
187
What is the classification for peptide
Less than 50 amino acids oligopeptide
188
What is the classification of a polypeptide?
More than 50 amino acids
189
How are proteins arranged?
Single polypeptides or multiple polypeptide bonded together
190
How are theree different proteins?
Vary in shape according to function due to sequence of amino acids
191
4 common types of proetins adn their shape?
TATA box binding protein: Butterfly shaped
Porin = doughnut shaped
Trypsin= globular
collagen= long fiber
192
what do ribosomes contain?
both protein and ribosomal RNA (rRNA)
193
What is the role of the large sub unit?
form peptide bonds
194
Small subunit?
Hold mRNA in place
195
What are the three site of tRNA are found in rbosomes?
A P E site
196
A site?
Acceptor site for aminoacyl tRNA binds to mRNA codon
197
P site?
peptide bond forms that adds an amino acid to the grwoing polypeptide chain
198
E site
where tRNAs no longer bounded to an amino acid and exit the ribosome
199
What is the ribsome described as?
A molecular machine that synthesises prteins
200
Were are ribsomes assembled and what happens?
Assembled in the nucleolus and transported to the cytosol
201
What is the 3 step sequence?
An aminoacyl tRNA carrying the correct anticodon for the mRNA codon enters the A sit
A polypeptide bond forms between the amino acid on the aminoacyl tRNA in the A site and the growing polypeptide chain on the tRNA in the p site
The ribosome makes ahead three bases and all 3 tRNAs move down one position and the tRNA in E site exits
202
What is nascent polypeptide chain?
The chain that emerges from ribosome unstructured and non-functional chain
203
What occurs when the nascent peptide chain leaves the ribosome?
It begins to fold into a 3D conformation due to polar non polar environment
204
What is the definition of a polypeptide?
Unbranched polymers of the 20 amino acids held together by peptide bonds
205
What is a protein?
3D structured functional chain
| Unbranced polymers of 20 amino acids held by peptide bonds with a specific 3D shape or function
206
What are the building blocls of protein?
Amino acids linked though a peptide bond
207
What are the 4 types structures of polypeptide?
Primary
Secondary
Tertiary
Quartenary
208
What is primary structure?
linear order of the amino acids determined by order of codons of mRNA
209
Secondarystructure?
By maximising the hydrogen bonding between parts of the polypeptide backbone (segments of polypeptide chain)
210
When does polypeptied bcome a protein?
Tertiary, 3D
211
What are the 2 subtypes of secondary structure?
Alpha helix
| Beta sheet
212
How is alpha formed?
The primary chains is coiled to form spiral structure which is stabilised by H bonds
213
Beta sheet fomed?
The primary chain zig zags back and forth forming a pleated sheet. Adjacent strands are held together by H bonds
214
What is the transition from 1 to 2 structure?
O from C=O form H bond with H from N-H
215
How do 3 structures arise?
From interaction between amino acids side chains groups
216
WHat interactions for 3 to arise?
H bonds between polar side chains
Hydrophobic interaction collapse(tdd between non polar side chains)
Ionic bonds between charged amino acids side chains
disulphide bridges between cystine molecules
217
What is the strongest interactiona nd why
Disulphide bridges as it is covalently bonded (reinforce shape)
218
WHy is here hydrophobic interactions
Hydrophobic groups will pack closely together at the core of the protein to get away from water and cytosol
219
What is 3 structure?
Superimposed on 2 structure alpha helix and/or beta sheet are folded up to form compact globular molecule held together by intramolecular bonds
220
Example of 3 structured proetin?
Prealbumin (transthrytin) transports the thyroid hormone throxine in serum and cerospinal fluid (CSF)
221
What is 4 structure
2+ oligomerise polypeptide chains each with their own 3 structure aggregated to form a larger macromolecular complex (to achive full functionality)
222
example of 4 strcutre and how it oligomerises
2 identical prealbumin subunits join together head to tail to form dimer
223
What determines how a protein will function?
The intricate structure or the complex as it has a specific shape
