1
Q
Define a cell
A
Cells are the basic unit of life
2
Q
Describe 2 types of cells and give examples
A
1) Prokaryotic cells: Contain no nucleus or membrane bound organelle eg = Bacteria and Archea
2) Eukaryotic cells: Contain a nuclues and membrane bound organelle = Animals, plants and fungi
3
Q
Do all cells haave the exact same cell chemistry
A
All cells have similar cell components however they may differ in terms of the proportion of the chemical components
4
Q
What is a polymer and a monomer
A
- Polymers are large complex subastances made up of building blocks
- Monomers are the building blocks that make up a polymer
5
Q
Major Biological macromolecules/polymer: List them and state whether they are branched or unbranched. Also state their monomers
A
1) Proteins - Unbranched
monomer = Amino Acid
Main function: Plays and important role in cell sttructure as well as carrying out necessary metabolic processes in the organism
2) Nucleic Acid - Unbranched
Monomer = Nucleotides
Plays a role in storing genetic information
3) Polysaccharides - Both branched and unbranched
Monomer = Sugars
Plays a role in energy storage and makes up the structure of DNA and RNA
6
Q
Revision on DNA
- Define DNA
- What are the names of the nucleotides in DNA
A
- Deoxyribonucleic Acid is a type of nucleic acid. It is a double helix that stores all the genetic information of all living organisms
1) Adenine (A)
2) Thymine (T)
3) Cytosine ( C )
4) Guanine (G)
7
Q
Define Genetic Code
A
Genetic code refers to a sequence of nucleotides
8
Q
Define DNA Replication and describe its process
A
DNA replication refers to templated polymerisation. Its Function is to ensure that there is an exact copy of DNA in the cell for cell devision
1) Helicase unwinds the double helix and breaks the hydrogen bonds
2) DNA polymerase collects the dna bases that are floating around and attatches them to their complementary base pair on both parent strands .
3) DNA ligase then glues the base pairs together and forms the phosphate backbone
4) The new double helices then rewind and you have ttwo identical DNA strands
9
Q
Define transcription and also discuss the difference of RNA to DNA
A
def : Transcription is the process where the genetic code is copied onto mRNA which will be carried to the ribsomes to be translated into proteins
-RNA is a type of Nucleic Acid like DNA except
- It is shorter
-Single stranded
-Contains Uracil instead of -Thymine
- Made up of Ribose sugar instead of deoxyribose
10
Q
Describe Trnascription
A
- helicase unwinds the double helix and breaks the weak hydrogen bond
- RNA polymerase will collect floating RNA nucleotides and attatch them to their complemenatry bases on one DNA strand.
- This will form a single stranded mRNA strand which will leave the nucleus via the nucleosome
11
Q
List the types of RNA and their funtion
A
- mRNA = Responsible for carrying the genetic code to the ribsome to form protein
- tRNA = Collecting amino acids in teh cytoplasm with the help of its anticodon to the ribosome to form the protein chain
- rRna = Plays a role in the formation of the ribosome and regulates the RNA process
12
Q
Describe the process of Translation
A
This is the process where the gentic code in mRNA is translated into proteins
- The tRNA uses its anticodon to collect the amino acids floating around in the cytoplasm.
- TRNA brings amino acid to the ribosome where attatch themselves to their complementary base pairs on the mRNA strand
- This forms a protein chain. The amino acids are joined by peptide bonds
- They will fold to form a specific shape = protein
13
Q
Define Gene
A
these are nucleotide sequences that code for a single protein
14
Q
Genome
A
This refers to the total DNA in a cell
15
Q
Do all cells have the same DNA ?
A
Yes however different cells express different genes hence they will have different functions
16
Q
Define mutation and how has that been the cause of evolution
A
Mutation : Mutation refers to any change in the genetic make up of an individual
- Some mutations can be harmful but others are actually beneficial
- With beneficial mutations it can allow an organsims to adapt to various chnaging environments hence they are favored by natural selection
17
Q
List the 3 major groups in the tree of life
A
1) Bacteria
2) Archea
3) Eukaryotes
18
Q
describe the component of water in the cell
A
70 percent : Makes up most of the cell hence most reactions occur in aqeous solution
19
Q
List the forces found in the cell
A
1) Covalent bond : This is teh equal sharing of electrons
2) Ionic Bond: This is the transfer of electrons and subsequent elctrostatic forces of attraction
3) Hydrogen Bond : This is the partial sharing of Hydrogen atoms
4) Van der Waals Forces : These are weak dipole- dipole interactions
5) Hydrophobic Forces : These are forces with atoms that repel water
20
Q
Covalent Bonds list the properties
A
- They are extremely strong
- Bonds cannot be broken via heat but only by enzyme-controlled reactions
21
Q
Noncovalent Bonds list the properties
A
- They are weaker than covalent bonds
- They are more flexible than covalent bonds
- They play and important role in the folding of proteins
-They allow for molecular recognition and enzyme specificity
22
Q
How do noncovalent bonds play a role in protein folding
A
- amino acids combine to form a protein chain
- the noncovalent bonds will then initiate the folding
- Amino acids contain carboxyl groups and amino groups which contain dofferent polarities
- There are electrostatic forces of attraction in the side chains and backbone
- hydrogen bonds in the backbone
- hydrophobic forces and Van der waals by the side chains
23
Q
Discuss the importance of water and pH
A
- When water hydrolises it changes the pH of the water
- Any change to the pH of the water will denature the porteinas it will break the noncovalent bonds in the protein
- Same applies with temperarure noncovalent bonds easliy break with high temp
24
Q
List the two main portein structures
A
1) Alpha helix
2) Beta sheet
25
How many levels of proteins are there and describe these levels
4 levels
1) Primary level:
This is the polypeptide chain
This determines the higher structure
2) Secondary Level :
This is where the polypeptide chain conforms into an alpha helix or beta sheet
alpha = spiral
beta = zig-zag flat sheet
The structure is stablaised by hydrogen forces
3) Tertiary Level:
This is the full 3D conformation of the protein
- Includes alpha helices, beta sheets and folds
- Stablised by noncovalent bonds
4) Quaternary Structure :
This inlcudes the addition of polypeptide chains
26
Define Protein Domain and what are their purposes
A protein domain is a segment of a polypeptide chain that folds individually and has a specific function
- Protein domains provide specialised functionality
- They promote evolutionary modification
27
Give examples of Protein Domains
1) Src Protein Kinase : Signals pathways in verterbrate cells
2) SH2 and SH3 : Have regulatory roles
3) c- terminal - forms protein kinase enzymes
28
Define proetin families and give an example
Protein Families refer to proteins that have the similar amino acid sequences and similar 3D structure.
Example : Serine Proteases : Protein cleaving enzyme
29
What is a subunit, how are they structured and give an example
A subunit is a polypeptide chain found in a large polymer.
Each subunit contains a binding site that enables them to bind with other subunits
example: Haemolglobin
30
What is an unstructred polypeptide chain and give examples
An unstructured polypeptide chain is a polypeptide chain that has not fully folded.
They are secreted outside the cell in the extracellular matrix.
1) Collagen = this is a triple helix and provides strength
2) Elastin = These are disorderd polypeptide chains and they form elastic fibres.
31
What are Covalent Cross- linkages and give an example
These are bonds that reinforce the protein structure
Example = Disulphide Bonds
They are formed between Cysteine side chains
- Cross- linkages onlu happen outside the cell
- They are broken by reducing agents
32
What is the function of a protein
A proteins unique functions depends on the molecule that it binds to.
The binding molecule = Lingand
33
What does protein binding depend on
1) Shape complementarity
2) Chemical compatibility
34
Give an example of 2 very important proteins
1) Antibodies
2) Enzymes
35
Define an antibody and describe its structure and function
An antibody is a protein that is produced in response to an antigen
Basic Structure :
- Y shaped
- Contains 4 polypeptide chains: 2 heavy 2 light
- The heavy chains are held together by disulphide bonds
- Contains 2 identical binding sites which recognise the epitope of the antigen
36
Application of antibodies : Recognising and producing antibodies EXPLAIN
- Antigens can be injected into an animal to produce antibodies
- There are a variety of antibodies
eg ) anti A antibodies = polyclonal antibodies which are released into the bloodtsream.
eg) B cell line antibodies = monoclonal antibodies
We can use antibodies as molecular tags to recognise other proteins
37
Define an enzyme and state its 3 key factors
An enzyme is a biological catalyst that binds with a substrate in order to create a product.
Increases the reaction by 10 ^ 6 - 10 ^12 times
1) They have an active site
2) They are highly specific
3) They lower the activation energy
38
Define protein machine and give an example
A proetein machine is a biological structure that produces multi - protein assemblies
example = Ribsosomes
The movement of protein is driven by atp - gtp hydrolysis
39
Name 3 processes of cell purification
1) Centrifugation
2) Cell chromatograpghy
3) Gel electrophoresis
40
Name 3 processes of shape determination
1) Mass spectrometry
2) NMR spectrometry
3) X-Ray crystallagraphy
41
What is the plasma membrane and list its functions
The plasma membrane is a structure that encloses the cell.
Eukaryotes only have a plasma membrane
Prokaryotes have a plasma membrane and internal membrane
1) Acts as a selective barrier
2) Provides signal sensing
3) Privides mechanical flexibility
42
Describe the structure of a plasma membrane
Plasma membranes consist of a lipid bilayer and proteins found between the layers.
- The lipid bilayer: Inner layer is hydrophobic ( head) and outer layer is hydrophylic ( tail )
The proteins perform the primary functions of the membrane
43
What are the monomers of phospholipids
1) Fatty acids
2) Glycerol
44
Describe the fluidity of membrane and why it is important
The lipids in the membrane move laterally. The do not flip up and and down
1) Membrane fluidity enables for the membrane proteins to diffuse quickly into the lipid bilayer which is crucial for cell signalling.
2) Membrane fluidity allows for membranes to fuse with one another
3) The fluidity also ensures that the molecules are distributed evenly for cell diffusion
45
List the factors that affect Fluidity
1) Hydrocarbon Tail :
A shorter tail = more fluid
2) Double bonds :
Unsaturated = more fluid
3) Temperature
Low = Gel structure
High = Fluidity
4) Cholestrol
- It buffers fluidity
46
Describe the symmetry of the lipid bilayer
1) The lipid bilayer is asymmetrical due to the different membrane proteins
47
List the different membrane proteins
1) Transmembrane
2) Monolayer linked ( Cytoplasm side)
3) Lipid anchored ( the leaflet sides )
4) Protein attatched
48
List the function of membrane proteins
1) They transport ions and molecules
2) They anchor the membrane to the cytoskeleton and the ECM
3) They act as receptors
4) Thye function as enzymes
49
Define membrane transport proteins and why they are important
Name the two types
Membrane transport proteins are proteins that are responsible for transporting ions or charged polar molecules through the membrane.
This is important because the membrane only allows nonpolar molecules to pass through
Transporters
Channels
50
Discuss how the membrane protein transporters function
The transporters have a specific binding site that complements the shape of the molecule. They bind to the molecule and undergo a transformational change and transport the molecule
Channels only allow molecules of a specific charge and size to pass through .
51
Describe the difference between passive and active transport
1) Passive transport:
The molecules move through concentration gradient. Region of high concentration to a region of low concentration
- Requires no energy
- Occurs through diffusion or facilitated diffusion (transporter)
2) Active Transport
Molecules move against the concentration gradient
Region of low to high concnetration
- this requires energy
- Pumps are used
eg) ATP pumps or channles /ion pumps
52
Describe the membrane potential and the importance of it
The cell maintains different ion concentration
- Inside of the cell ( Cytosol) = negative
- This results in a voltage across the membrane = membrane potential
- ion movement
- cell signalling
- Hameostatis
53
Describe the passive transport of Na ions and K ions
Na ion has a high concnetration outside if the cell. Because the cytosol is negatively charged the Na ion will move from a region of high concnetration to a region of low concentration inside the cell
K ion is high inside the cell but because the outside of the cell is more positively charged it is unable to diffuse through the membrane
54
List the 3 mechanisms of active transport
1) Coupled transport : Pumps molecules out and in the cell simultaneoulsy
2) Atp- driven pumps
3) Light driven pumps
55
What is cell signalling and give another name for it
Cell signalling is the conversion of information from one form to another
Signal transduction
- Cells convert extracellular signals into intracellular repsonses
56
List the 4 types of cell signalling
1) Endocrine signalling
- Hormones are released into the bloodstream where they act on target cells
2) Paracrine signalling
The signalling molecules act as local mediators and diffuse through extracellular fluid
3) Neuronal signalling
Neuron cells deliver electrical signals over a distance and chemical signals through synapses
4) Contact dependent signalling
Signals molecule on one cell and receptor on an adjascent cell
57
Describe the general principles of cell signalling
1) Cells are exposed to many signals simultaneouly
2) The response type depends on:
- Cell type
- Cell history
- current state
3) same signal can produce different outcomes
4) Responses can be fast ( movement and diffusion ) or slow ( gene expression , cell division )
58
State the two classes of receptors
1) cell surface receptor
2) intracellular receptor
59
Describe the cell surface receptor
These receptors are located outside of the cell
- They bind to hydrophyllic signal molecules
- The molecules do not enter the cell
- Signal is relayed through intracellular pathways
Example:
60
Describe intracellular receptors and give an example
These receptors are located inside the cell
- The signals are small and hydrophobic
- The signals can diffuse through the membrane
1) Steriod hormone: They bind to nuclear receptors and they regulate transcription
2) Nitric oxide ( N0)
- Diffuses freely
- It relaxes and smoothes muscles in blood vessels
- Regulates intracellular proteins
61
What is the intracellular signalling pathway also known as and describe the process
- Relay cascade
1) First messenger = Extracellular signal: Binds to cell surface receptor
- Go through a relay
2) Second messenger = small intracellular molecules
3) Effector proteins = They generate a response
62
What are the two types of molecular switches in intracellular pathway signalling
1) Phosphorylation switches
2) GTP - Binding
63
How do phosphorylation switches work ?
1) Protein kinases adds phsophate
2) Protein phosphates removes phophate
64
How do GTP binding switches work
Hydrolysis of GTP to GDP
65
List the different cell surface recpetors ( cell surface recptor families )
1) Ion - channel coupled receptors : They convert chemical signals into electrical signals
2) G- protein coupled receptors
Largest cell receptor family
- Targeted by 50 % of drugs
- They are a single polypeptide chain
- They have 7 transmembrane helices
* The GPCR binds to the ligand
*GPCR undergoes a conformational change
* Releases G protein which activates target enzymes
66
Describe the structure of G - proteins
G - proteins contains 3 subunits
1) Alpha
2) Beta
3) Gamma
The alpha and beta subunits are anchored to the membrane by lipid tails
67
Describe how G proteins switch on and off
G protein is inactive when alpha subunit is bound to GDP
- When a ligand binds to GPCR G protein is released
- This causes the GDP binded to alpha subunit to leave
- GTP replaces GDP
- Switch turns on
68
Describe Enzyme coupled receptors and their function
- These are transmembrane proteins that bind to the ligand on the outside of the cell surface.
The cystolic domain is either an enzyme itself or associated with an enzyme
The control :
Cell growth
Differnetaition
Survival
Cytoskelton reorganisation
Cell movement
69
Are cell signals highly connected ?
Yes they are highly connected and there are many different signalling pathways.
This forms a large network called = cross talk
Engineering in Biology 2
flashcards
Decks in class (24)
# Cards
-
Proteins69
-
Cell adhesion48
-
Cell migration21
-
Cell division19
-
Extracellular matrix20
-
Cell- cell interaction13
-
Cell- ECM interaction11
-
Transcient cell interaction6
-
Cell- material interaction7
-
Blood lecture 113
-
Blood lecture 215
-
Blood lecture 317
-
Blood lecture 412
-
Blood lecture 511
-
Drug delivery lecture 1( part 1 and 2 )30
-
Drug delivery lecture 232
-
Drug delivery lecture 35
-
Applied statistical mechanics lecture 14
-
Biomechanics lecture 127
-
Biomechanics lecture 224
-
Biomechanics lecture 314
-
Medical imaging lecture 147
-
Medical imaging lecture 228
