Module 2: Inside the Cell Flashcards
What is the structure of the cell membrane?
Two rows of molecules with glycerol heads (facing outwards and hydrophilic) and two glycerol tails (facing inwards and hydrophobic). The chain is also imbedded with proteins and changes depending on what must be transferred in and out of the cell
What is the function of DNA?
Forms inherited genetic material
What is the function of RNA?
Relays instructions from genes to guide synthesis of proteins from amino acids
What is DNA made of?
Nucleotides consisting of a nitrogenous base (ATCG), phosphate group and a pentose sugar.
What is the fluid mosaic model?
A model of the plasma membrane where the PM is a sea of fluid lipids with floating (iceberg) proteins.
What are the two classes of membrane protein?
Integral (extends into/through the membrane. Most are transmembrane)
Peripheral (not firmly embedded, attached to polar heads)
What are the stabilizing bonds in DNA?
Phosphodiester bonds (links sugar to phosphate) H bonds (links opposing nucleotides together)
What are the six different types of membrane proteins?
Ion channels, carriers, receptors, enzymes, linkers, cell identity markers
What are ion channels?
Form a pore which specific ions can cross. Most have several for different ions (integral)
What are carrier proteins?
Transport substances across membrane by changing shape. Requires ATP/ Allows polar substances through the membrane or against diffusion gradient. (integral)
What are receptors?
Serve as recognition sites. They relay information to cell interior, usually a ‘signal cascade’. They bind to a specific molecule called a ligand (integral)
What are enzymes?
Catalyse reactions in or outside cell. (integral and peripheral).
What are linkers?
Anchor filaments inside and outside the cell to gives stability and shape. Can also bond to proteins of PMs in neighbouring cells to link together. They bond to intermediate filaments in the extracellular matrix (integral and peripheral.
What are cell identity markers?
Also known as glycoproteins. They allow cells to recognize each other during tissue formation, or by recognizing foreign bodies. (This cell is ME, this cell is NOT ME)
What are the benefits of membrane fluidity?
Allow mobility and structure, self repair if punctured
What is an electrical gradient?
Difference in electrical charge between two areas. Across the membrane this is called membrane potential.
Describe prokaryotic cells
cytoplasm with PM, no nucleus or membrane bound organelles, have ribosomes, DNA is in circular chromosomes,
Describe eukaryotic cells
Cytoplasm with PM, nucleus and membrane bound organelles, ribosomes, Linear DNA
What is the structure of the nucleus?
Enclosed by a double lipid bilayer (nuclear envelope) and lined with nuclear lamina. Continuous with rough ER. Has nuclear pores for materials entry/exit. Dark centre is the nucleolus
What is the function of the nucleus?
House/protect DNA. RNA/ribosome production. Allow molecules to be separated where necessary- eg enzymes and substrates
What is the structure of the ribosmes?
Two subunits (large and small). Made of RNA and rRNA. They are made separately in the nucleolus and can be attached to ER or free.
What is the function of the ribosome?
On ER = make proteins for secretion, insertion into membrane or specific organelles.
Free = make proteins used in cytosol
What is the structure of rough Er?
Continuous with the nuclear membrane. Folded into flattened sacs. Studded with ribosomes
What is the function of Rough ER?
Site of protein synthesis
What is the structure of smooth Er?
Extends from the rough ER in a network of tubules. No ribosomes.
What is the function of smooth Er?
Synthesis of lipids and steroids. In the liver, enzymes of SER detox drugs etc. Houses tissue specific proteins and enzymes
What is the structure of the golgi complex?
Made of cisternae containing different enzymes for different functions. Entry (cis) cisternae receive proteins, medial modify them, and trans finish then package final proteins
What is the function of the golgi complex?
Protein modification, packaging and transport
What is the structure of the lysosome?
Surrounded by plasma membrane. Contains powerful digestive enzymes
What is the function of the lysosome?
Membrane actively pumps H+ for acidic medium (good for enzymes). Recycles worn out structures and entire cells. Also used in extracellular digestion (eg. sperm)
What is the structure of the mitochondria?
Outer and inner membrane, cristae (folds), and matrix. New mitochondrion are formed from existing ones
What is the function of the mitochondria?
Site of cellular respiration, production of ATP and apoptois.
What is the structure of microfilaments?
Thin, comprised of actin and myosin. They surround the inner edge of the cell.
What is the function of microfilaments?
Generate movement and provide mechanical support (eg for microvilli)
What is the structure of the intermediate filaments?
Thicker than micros, smaller than tubules. Made of proteins (eg keratin) so strong.
What is the function of intermediate filaments?
Stabilize and hold organelles in place. Used in cell junctions
What is the structure of microtubules?
Largest component of cytoskeleton. Long, unbranched and hollow
What is the function of microtubules?
Determine cell shape, convey secretory vesicles, move projections (eg flagella)
What is the structure of centrosomes?
Cylindrical and made of tubules
What is the function of centrosomes?
Cell division, production of tubules
What is the structure of cilia?
Thin, hair like projections
What is the function of cilia?
Move extracellular objects
What is the structure of flagella?
Long, hair like projection
What is the function of flagella?
Move entire cell
What are the three steps of protein synthesis?
Transcription, mRNA maturation, Translation
Why is protein synthesis important?
It allows a cell to function as proteins are the functional component of the cell. It also allows the cell to produce proteins needed for a specific purpose within or out of the cell. Finally, it is crucial for cellular communication.
What is the difference between mRNA and DNA?
mRNA is single stranded, with ribose sugars and the base Uracil instead of Thymine.
What are the three steps of transcription?
Initiation, elongation, termination.
How do cells initiate protein synthesis?
The promoter sequence consists of the TATA box and the start sequence. First, transcription factors bind to the promoter region. An enzyme (RNA polymerase) is able to bind to the transcription factors. This allows elongation to begin
What is elongation in transcription?
The RNA polymerase enzyme unwinds small portions of the DNA double helix at a time. This allows complimentary nucleotides from the nucleolus to move in and form an mRNA strand complementary to the DNA template.
What is termination in transcription?
The enzyme moves from the promoter region to the polyadenylation signal, where it slows and stops. The enzyme and transcription factors then detach, and the mRNA strand is free to move.
What is added to the mRNA strand during mRNA maturation?
Firstly, a 5’ cap is added to the 5’ untranslated region (UTR). This provides the strand stability and prevents enzymes from degrading the mRNA. A Poly-A tail is added to the 3-prime end, to slow the action of enzymes and allow the mRNA to be used multiple times. Note: The poly-a length is determined by the adenylation signal.
What is mRNA splicing?
snRNPs and a spliceosome join to the part of the mRNA (intron) which they want to remove. The spliceosome cuts up the mRNA, and the snRNPs are complimentary to each cut site, binding the two pieces back together. After this, the mRNA leaves the nucleus through the nuclear pores
Why is splicing important?
Introns have no function for the particular protein being formed (but may be functional for others). Therefore they are not useful for translation and would only form an altered chain. Therefore they must be removed.
How is translation initiated?
The small subunit of the ribosome binds to the aminoacyl tRNA- this one always matches the start sequence- AUG (met) The subunit-tRNA complex binds to the 5’ cap on the mRNA and runs along the promoter until it reaches the start codon. The large subunit then binds.
What is elongation in translation?
The original (met) tRNA is in the P site of the ribosome, and a ribosome with an anticodon complementary to the next mRNA codon arrives in the a site. The ribosome catalyzes a peptide bond between the two amino acids, stripping the p-site tRNA of its acid. The mRNA then shifts, knocking the p-site tRNA through the exit site, and the A site to the P-site. The next tRNA then arrives, and the process continues until the stop codon is reached.
How is translation terminated?
When a stop codon is reached, a complementary release factor binds into the A site. The ribosome cannot catalyze a peptide bond between the tRNA and release factor, so the polypeptide is released, the ribosome breaks up and the mRNA is broken up or re-translated for more proteins.
What are the 4 groups of an amino acid?
H group, Carbonyl group, Amino group, Side chain.
What is primary structure?
The sequence of amino acids bonded in a polypeptide
What is secondary structure?
Alpha helixes or beta plated-sheets when the chain begins to fold or curl together. There are H bonds between the backbones of the amino acids.
What is needed for primary structure to become secondary structure?
Hydrogen bonding
What is tertiary structure?
The protein becomes more globular, smaller and collapses into itself by tightly coiling. It contains H bonds between side chains. The protein may be fully functional at tertiary stage of development
What is needed for secondary structure to become tertiary structure?
Hydrophobic collapse from inside the protein. Van der Waals forces between non-polar side chains, H bonds between polar side chains, ionic bonds between charged side chains. Disulphide bonds between cytosine molecules
What is quaternary structure?
Two or more tertiary structure interact to form a functional complex
What are 7 possible steps in post-translation protein modification?
- Phosphorylation (add a P group)
- Methylation (Add an Me group)
- Acetylation (Add an acetyl group)
- Biotinylation (Add a biotin group)
- Carboxylation (Add a carboxylic acid group)
- Carbohydrate addition (Specifically for membrane bound proteins)
- Cleavage (Cut into smaller parts)
Why is post translation modification important?
The addition or removal of groups can mean protein is given or loses functionality. As a result, the protein’s function can be regulated, and it is no longer necessary to break up a protein and reform it when you want to stop or start its activity.
How are cytosolic proteins processed?
They are made by free ribosomes and modified by other free proteins in the cytosol
What is the process of modification for organelle/membrane bound and secretory proteins?
The beginning of the polypeptide chain contains a signal peptide, which a signal recognition particle (SRP) recognizes. The SRP attaches to the ribosome and transport the entire complex to the rough ER. From there, the polypeptide will be formed directly into the rough ER, where it is put into a transfer vacuole and moved to the golgi body. The golgi body then modifies the protein with a series of enzymes in its cisternae, before putting it into a membrane vesicle, transport vesicle or secretory vesicle depending on its function.
What is the purpose of cell communication?
To co-ordinate local and global responses in the body
What is the definition of communication in terms of the body?
Sending molecules or chemicals, either locally or widely, to elicit a response
What are the three steps of cell communication?
Reception, transduction and response
What are the four types of receptors?
G- Protein coupled receptors, Receptor Tyrosine Kinases, Ligand gated channels and intra-cellular receptors
Where are receptors located?
They are proteins located within the cell membrane.
What is the process of reception?
Ligand (specific chemical/protein) binds to the receptor site, and causes a shape or chemical change within the protein to allow it to begin transduction
How does reception work with G-protein coupled receptors?
The ligand binds to and activates the receptor, changing its shape and allowing a g-protein to bind to it. The G-protein loses a GDP and gains a GTP, and moves along the cell membrane to an enzyme. It binds to the enzyme, causing it to become activated and initiate a cellular response via a phosphorylation cascade or a secondary messenger. Eventually the G protein loses a P atom, returning its GTP to GDP
How does reception work with Receptor Tyrosine Kinases?
Binding of the ligand to two RTKs cause them to dimerise. This process starts cross-phosphorylation, where, 6ATP are converted to 6ADP and a phosphate is added to each of the dimer’s 6 Tyrosine groups. This allows enzymes to bond to their specific groups, and can catalyse many different reactions.
How does reception work with Ligand Gated channels?
These are water filled pores with gates only able to be opened by a particular ligand (primary messenger). When the ligand binds to the gate, it opens, allowing ions to pass through. These act to initiate the cell response due to their electrical signals.
How do intracellular receptors work?
If the ligand can cross the plasma membrane it can be picked up by a receptor protein in the cytoplasm. The two form a hormone-receptor complex and are able to move to the nucleus to elicit a cellular response
What is transduction?
The receptor activates the enzyme or secondary messengers, which create a signal transduction pathway (most commonly with phosphorylation).
How is transduction completed? (without ions)
The active enzyme (or relay molecule) passes a P to an inactive protein kinase, activating it. This then passes the P to a second inactive kinase, therefore activating it. This continues on from protein kinase to protein kinase until one activates a protein to initiate cellular response. Note that multiple kinases can be activated by a single active kinase, so the signal is amplified.
How is transduction completed? (with ions)
After the ligand gated channel opens, the ions flow freely into the cell. The change in the electrical environment activates proteins to initiate cellular response
What are secondary messengers (+ examples)
small molecules which transfer the signal from an enzyme to the cascade or a gate. Examples are cAMP and IP3.
How does cAMP act as a secondary messenger?
The enzyme activated converts ATP into cAMP, which goes on to activate protein kinases. The signal progresses from there.
How does IP3 act as a secondary messenger?
Initially, Ca2+ ions are actively pumped into the ER so that their concentration is low in the cytosol (this is to ensure that the appearance of Ca2+ is enough of a change to cause a reaction). When the primary messenger causes an enzyme (phospholipase c) to be activated, breaking PIP2 into DAG and IP3. IP3 then travels to the IP3-gated channel in the ER, where it causes the gate to shift and allows Ca2+ into the cytosol. The Ca2+ causes a change in the electricity of the cell, resulting in activation of proteins.
What body process uses Ca2+ ions as secondary messengers?
Muscle contraction
What disease affects the cAMP messenger?
Cholera
Why is it important that there are multiple steps in the signal cascade?
This allows greater control over individual steps, so that other cascades can interact and meet together, and stop and start and various points along the cascade to control which responses are being generated. Also, it allows greater amplification of the signal as more kinases can activate more kinases.
How long do signals last and why?
Only a short time to ensure homeostasis is maintained.
What are some examples of cellular responses?
Gene expression Altering protein function Open/close ion channels Alter cellular metabolism Regulate organelles or organization Combinations of these
How does signalling end?
The start of cellular response causes the original signal cascade to stop.
What is cellular response?
An activity or function of the cell that meets the need or requirement that initiated the signalling event in the first place.
What role does insulin play in the body?`
Insulin ‘shoves’ glucose into cells to remove it from the blood. This means that there is more glucose for cellular respiration, and increased protein synthesis. It also means they can be stored as glycogen and the adipose tissue can produce more triglycerides
What role does glucagon play in the body?
It breaks glycogen down to glucose from the skeletal muscle and liver. This increases the concentration of glucose in the blood. In the liver, it also increases the synthesis and release of glucose.
What is diabetes mellitus?
In type 1: Pancreas does not produce insulin. Type 2: Cells do not recognize or accept insulin. As a consequence of both, the cells cannot easily uptake glucose, meaning the blood glucose level is high. Therefore, the blood thickens, becoming viscous and making it difficult for O2 to be transported around.
What are the four steps of cellular respiration?
Glycolysis, conversion to Acetyl Co-enzyme A, the Krebs cycle and the Electron Transport Chain
What occurs during glycolysis?
Glucose is oxidised to 2 pyruvic acids, 2 (net) ATP and 2 NADH. (NADH are formed by NAD+ accepting an H-). This is anaerobic and occurs in the cytoplasm
What occurs during conversion to Acetyle Co-Enzyme A?
A pyruvic acid molecule is converted. Each glucose (2 P acids) produces 2 ACEAs, 2NADH and 2CO2(waste). It requires oxygen.
What occurs during the krebs cycle?
The CoA undergoes a series of reactions where the product of one is the substrate of the next. Each CoA produces 1 ATP, 2CO2, 1FADH2 and 3NADH. It occurs in the matrix and requires Oxygen. If no oxygen is present, lactic acid is produced.
What happens during the Electron transfer chain? (Not chemiosmosis)
This occurs in the cristae of the mitochondria. It is aerobic. NADH and FADH2 donate 1-2 e- each int electron carrier complexes (protein channels in the inner membrane). The inner membrane has 4 channels. The electrons are moved between channels, and each time it moves, an H+ ion is actively pumped into the intermembranal space. The last channel of four converts e- +O2 into H2O,
What happens during chemiosmosis?
The H+ ions are allowed to flow down a specific ion channel containing ATP synthase. The passage of H+ ions spins this enzyme, giving it energy to convert ADP to ATP, thus producing energy. It occurs on a mass scale.
How many ATP are produced per mole of glucose?
30-32 (as not all NADH/FADH2 give one or two electrons consistently).
How is cellular respiration controlled?
Feedback mechanisms target enzymes involved in respiration. EG. if not enough citrate (in krebs cycle) is being converted it builds up, inhibiting phosphofructokinase (in glycolysis) from producing more. Excess ATP in the cell gives the same effect.
Why does the Electron Transfer chain produce so much ATP?
It has oxidative phosphorisation rather than substrate level, and it is on a production line, so more can be done in a short time.
How much ATP does each step generate?
Glycolysis: 2ATP. ACoA- 0ATP. Krebs Cycle: 2ATP. ETC: 26/28ATP.
What is the aim of cell division?
To produce two daughter cells genetically and functionally identical to the parent cells
What are the different parts of the cell cycle called?
G1, S, G2 and M
What is G0?
When a cell has opted out of the cell cycle. Could be that it hasn’t entered yet (eg stem cells) or that it has divided enough already (eg neural cells).
What is G1?
When the cell is metabolically active. Cell functions occur (eg filtration of blood in kidneys). At the end of G1, all cellular organelles are replicated.
What is S?
Synthesis of DNA. The helix is unwound and okazaki fragments (new nucleotides) move in to the exposed bases and pair. This occurs from the 5’ to 3’ direction until all DNA is duplicated. Due to the fact that one original strand is used in each of the two replications, this process is called semi-conservative.
Why is DNA replication important?
It is important so that future proteins formed from gene expression can occur normally.
What is G2 phase?
Ensures DNA synthesis is complete and correct, and prepares for M phase by producing enzymes, proteinis and gathering reactants for replication. Centrosomes are replicated.
When do the cell checkpoints occur?
Between the G1/S phases and the G2/M phases.
What is checked in G1/S?
Cell decides whether to divide. It checks that its biochemical functions have been fulfilled.
What is checked in G2/M?
It’s the last chance to stop division. It makes sure that the cell should divide at this point in time. It also makes sure that the cell is healthy and all duplication is complete.
Why are these checkpoints important?
If there is a problem with the cell, it doesn’t copy. This would mean there are two dysfunctional cells instead of just one. (more difficult to fix).
What happens if the cell fails the checkpoints?
The cell cycle is paused so that the cell can repair itself. Otherwise, the cell commits suicide.
How does the G2/M checkpoint occur?
CDK is a molecule which is always in the cell, but normally in an inactive state. When active, it gains a quaternary structure and develops an enzymatic function. In the late S phase and early G2 phases, the protein cyclin is produced. When cyclin attaches to CDK it activates it, so that it is now MPF. MPF gives rise to the rapid onset of mitosis. After mitosis is initiated, the cyclin is degraded and MPF reverts back to CDK to be recycled.
How does a cell fail the G2/M checkpoint?
If there is a problem with the cell, ie it has a mutation etc, the production of cyclin will be delayed or canceled until the cell repairs or dies.
Why must cyclin be degraded after the onset of mitosis?
So that it doesn’t continuously promote cell division.
What is M phase?
Mitosis, where the cell duplicates itself. This is made up of 5 stages:
Prophase: The chromatin condenses to chromosomes held together by centromeres. The mitotic spindle forms and the nuclear membrane dissolves
Metaphase: Microtubules attach to centromeres and arrange them at the cell equator
Anaphase: The microtubules contract, dragging one copy of each chromosome to opposite poles of the cell
Telophase: Chromosome reverts to chromatin and the Nucelar membrane reforms
Cytokinesis: The cytosol splits, and the plasma membrane pinches off, enclosing two new identical cells.
What protein normally promotes cell division?
Proto-oncogene
What protein normally inhibits cell division?
Tumor suppressor gene
What is cancer defined as?
The loss of control of the cell cycle
What occurs when cancer develops?
G1 phase gets shorter and the cell focusses only on division
What is required for cancer to occur?
Mutations in both proto-oncogenes and tumor suppressor genes.
Proto-oncogenes become oncogenes and tumor suppressor genes become mutated tumor suppressor genes.
What sort of mutation must occur to make cancer develop?
It must change the shape and function of both proteins. If it only codes for multiple copies of a protein or a same-sense/mis-sense mutation, this will not affect the cell cycle.
What happens to the proto-oncogene when it mutates to an oncogene? (+example)
It becomes hyperactive. This means it constantly promotes cell division. Eg. ras (g-protein) mutation means it stays in an active state, continuing to activate a signal cascade to produce promoter proteins. All feedback mechanisms are overruled.
What happens when a tumor suppressor gene mutates to a mutated tumor suppressor gene?
Causes a non functional protein. There is no longer an ability to tell the cell to stop dividing as the protein is under active. It also stops checks to determine whether the cell should/is ready to divide. Eg. P53 gene
What is the regulatory process of healthy cell division?
If a cell has a problem, P53 is up-regulated. Extra protein is formed to act as a transcription factor for this protein. It inhibits the cell cycle until the cell is repaired or dead.
What is the regulatory process of unhealthy cell division?
Up-regulated P53 produced to fix cell, but this is non functional. Therefore, division goes ahead with the mutation copied into daughter cells.
What defence does the cell have against cancer occurring?
There are different proto-oncogenes and tumor supporessor proteins coded for by different genes, operating at different parts of the cell cycle. This produces redundancy. As a result, mutations would have to occur in all of these for control over cell division to be lost.
How does cancer spread?
It metastases using the blood and lymph systems as carriers.
