Week 2 Flashcards
What is the plasma membrane important in?
- Separates intracellular from extracellular environment
- Controls internal conditions of cell
- Important in communication between cells
What comprises the phospholipid (draw + label)
- Hydrophilic head (glycerol and phosphate)
- Hydrophobic tail (two fatty acids, one unsaturated)+
Looks like RC body pin
Draw the cell membrane. Why is it oriented like this?
- Phospholipid bilayer
- Hydrophobic tails face away from aqueous environment, hydrophilic heads face out
What structures/substances are in the plasma membrane?
- Cholesterol
- Glycoproteins/Glycolipids
- Integral proteins
- Peripheral proteins
What is the function of cholesterol in the cell membrane?
Adds rigidity and structural integrity
What is the function of glycoproteins/glycolipids
Cell-cell communication, anchoring, adhesion
What is the structure of integral proteins?
Called integral because they cannot be removed. Transmembrane proteins, act as channels.
What is the function of peripheral proteins?
Can be removed (peripheral)
(e.g. Useful in enzymatic activity)
What are the six classifications of surface proteins?
- Cell-cell recognition
- Anchoring
- Adhesion
- Receptor
- Channel
- Enzymatic activity
What characteristics affect the permeability of a cell membrane (including the substance and the membrane itself)?
Substance: size, lipid solubility, charge
Membrane: presence/arrangement of lipids and proteins
From most easily to least easily, which kinds of substances can cross the cell membrane?
- Hydrophobic molecules
- Small polar molecules
- Large polar molecules
- Ions (can’t without transport protein assistance)
How do non-polar, uncharged molecules cross the cell membrane?
Simple diffusion
How do small/medium charged molecules and macromolecules cross the cell membrane? (passive transport)
Facilitated diffusion
How does water cross the cell membrane
Osmosis
What are the three types of passive transport?
- Diffusion
- Facilitated Diffusion
- Osmosis
What are the types of active transport?
- Primary
- Secondary
- Vesicular transport
Describe primary active transport
- ATP is used to transport a substance across the plasma membrane against the conc gradient
Describe secondary active transport
The energy of one substance moving along its concentration gradient is used to facilitate the movement of another molecule against its concentration gradient (e.g. sodium glucose pump)
What are the three types of endocytosis?
- Pinocytosis
- Phagocytosis
- Receptor-mediated endocytosis
What is the name given to cytoplasmic extensions during phagocytosis?
Pseudopodia
Approximately how many genes in the human genome?
25,000
How do you differentiate between peptides and proteins?
Peptide: <50 amino acids
Protein: >50 amino acids
How can you relate the joining of amino acids back to Greenslade’s chemistry class?
Amino acids are joined by peptide/amide bonds, just like we learned last year:
Recall the four levels of protein organisation
- Primary
- Secondary
- Tertriary
- Quaternary
Which terminus does the polypeptide structure begin an end?
Begins at amino terminus, ends at carboxy terminus (think: alphabet, a before c)
Interestingly, the same alphabet logic applies to afferent vs efferent signals
Why do post-translational protein modification affect the function of a protein?
They affect the strcture of the protein, and therefore the function is altered
What do structural proteins form?
Muscle, bone, skin, connective tissue and the cytoskeleton
What are some examples of structural proteins?
- Muscle Proteins
- Collagens
- Cytoskeletal Proteins
- DNA-Associated proteins (e.g. histones)
What is the most abundant protein in the human body?
Collagen (25%)
What are the three steps of haemostasis?
- Vasoconstriction
- Temporary plug
- Blood coagulation, resulting in a fibrin clot
What are the most important coagulation proteins?
- Thrombin
- Fibrinogen
What is the function of anticoagulation Proteins
Prevents blood clots
What are the two types of coagulation disorders?
- Bleeding disorders (not enough coagulation)
- Thrombotic disorders (too much coagulation)
How can enzymes act as biomarkers?
Tissue destruction due to pathology results in enzyme release into the bloodstream. Pathologists can use this information to detect diseases.
What is another name for signalling proteins?
Ligands
What is the function of cell adhesion molecules?
Hold cells and tissues together.
What three domains do cell adhesion molecules consist of?
- Intracellular domain: interacts with the cytoskeleton
- Transmembrane domain: inserted in membrane
- Extracellular domain: interacts with other molecules outside of the cell
What are the three stages of the central dogma?
DNA → RNA → Protein
What is DNA replication important for?
Development, growth, tissue repair and maintenance
What are the phases of cell replication, and when does DNA replication occur?
G1: Growth - Preparation for DNA synthesis
S: Synthesis - DNA Replication occurs here
G2: Growth - Preparation for mitosis (new organelles)
M: Mitosis (Prophase, metaphase, anaphase, telophase)
True or false: DNA replication occurs from one end to the other.
False, DNA replication occurs in bubbles, which expand into one another until two strands are formed.
Think of this as like two forks of replication moving away from one another.
Which end of DNA strands does DNA replication start and finish?
From 5’ to 3’
What are fragments of the lagging strands called?
Okazaki fragments
What is the role of primase?
Adds a 3’ group for polymerase to start from (binds to hydroxyl group of second nucleotide)
What is the name of the enzyme that ‘unzips’ DNA?
DNA Helicase
What is the role of DNA polymerase?
Adds complementary nucleotides to unzipped original DNA strand
List some external factors that can damage DNA
- UV light
- Thermal damage
- Mutagens
List some internal factors that can damage DNA
- Mistakes in polymerase
- Reactive oxygen species
What are the four types of DNA damage?
- Break (double/single stranded)
- Bond between neighbouring nucleotides
- Nucleotide modification
- ‘Rung’ linkage
MNRB (___ are bad -> damaging)
What occurs during nucleotide excision repair?
Enzyme excises a long piece of DNA that spans a damaged nucleotide. Polymerase then fills in right sequence. Ligation.
What is base excision repair?
Damaged base is removed. Polymerase adds in right one, and ligation occurs.
What is the difference between NER and BER?
BER only acts on one damaged base, whereas NER can act on a section of DNA.
What occurs during mismatch repair?
- Enzyme makes a ‘nick’ upstream
- exonuclease removes the section including the mismatched base
- polymerase and ligase
What occurs during non-homologous end joining?
Ligase simply joins two broken ends
What is non-homologous end joining?
Homologous chromosome is used as a template for repairing the damaged chromosome
Which type of RNA does RNA polymerase 1 make?
rRNA
Which type of RNA does RNA polymerase 2 make?
mRNA
Which type of RNA does RNA polymerase 3 make?
tRNA
Exons vs Introns
Exons: Code for protein
Introns: Don’t code for protein
What is the 5’ cap during post-transcriptional processing?
Modified guanine added to 5’ end for molecular stability and to help it attach to the ribosome.
What is polyadenylation, where does it occur, and why?
Occurs on 3’ end to add molecular stability and helps it get exported to the cytosol. (It’s painful, so at the end it shouts AAAAAAAAAAA!)
Which is the first codon that signals the beginning of translation?
AUG methionine (Cam Chau)
What are the three steps in translation?
- Initiation: mRNA binds to ribosome and tRNA deliver first amino acid
- Elongation: Amino acids are linked by peptide bonds
- Termination: Proteins are released for further modification
What are the three pockets on a ribosome:
APE
A: Amino acid
P: Peptide
E: Exit
Moves from A to E
Which histones pair up?
H2A and H2B, H3 and H4
What happens when two pairs of histones join together?
Tetramer unit is formed
What happens when two tetramer units combine?
Octamer unit is formed
___ Base pairs wrap around an octamer structure to for a _____
146 base pairs to form a nucleosome
What does The Programmed Theory State?
Ageing has an internal clock
What does Error Theory state?
Ageing is a result of the accumulation of errors in vital cellular molecules.
What is cellular senescence?
A permanent block block in proliferation of a cell.
What are some useful applications of senescent cells?
- Immunity (stop viruses from propagating)
- Tumor suppression
- Wound healing (inflammation)
What are some detrimental consequences of senescent cells over time?
- Chronic inflammation
- Tissue degeneration
What is the name given to the type of drugs that can destroy senescent cells?
Senolytics
What is the name given to the type of drugs that can destroy senescent cells?
Senolytics
What are the caps on the end of chromosomes called?
Telomeres
Why do the telomeres of adult cells decrease with age
- Enzyme telomerase is responsible for maintaining telomere length.
- Telmoerase is not present in adult cells
- With each cell division, telomeres of adult cells shorten
What happens when telomeres are completely gone from a chromosome?
Senescence kicks in, and the cell stops dividing
How are reactive oxygen species produced and what do they do?
- Formed during ATP metabolism
- Oxidize macromolecules (including DNA: internal factor of harm)
What are a cell’s three options if its DNA is damaged?
- Senescence
- Apoptosis
- Altered function
What is epigenetics?
A change in gene expression that is NOT dependent on DNA sequence
What are the consequences of hypomethylation that comes with age?
Chromatin is more open -> genetic instability -> DNA damage…
What factors can lead to hypomethylation?
Diet, stress, chemicals
What is the function of stem cells?
Replace aged cells in the tissues and organs of the body
What happens to stem cells with ageing?
- Reduced potential to differentiate (what does this mean?)
- Reduced potential to proliferate (what does this mean?)
- All stem cells may differentiate, leaving none left
What causes the release of Insulin Like Growth Factor 1? How does this result in aging?
- Eating foods, glucose increases
- Anterior pituitary secretes growth hormone
- Liver cells produce IGF-1, causing glucose to be taken up
- As this rate of cell division and metabolism increases, so does the wear and tear on the body. This results in aging
In terms of the immune system, explain why inflammation increases with age
With age, the adaptive immune system decreases and the innate immune system increases. This leads to an increase in inflammatory cytokines, which leads to chronic inflammation
What diseases has inflammation been linked to?
- Cancer
- Cardiovascular disease
- Diabetes
What are some functions of mitochondria (other than respiration)?
- Intracellular signalling
- Regulation of innate immunity
- Apoptosis regulation
What are some consequences of decline in mitochondrial function?
- Decrease in respiration
- Fatigue
Does apoptosis result in inflammation?
No. none.
What two enzymes are involved in apoptosis?
Caspases: control apoptosis
Phagocytes: Clean up debris
Which of necrosis and apoptosis is planned/unplanned
Necrosis: unplanned
apoptosis: planned
What happens during necrosis?
Cells swell up and burst, causing leakage into the extracellular environment. This causes neighbouring immune cells to be activated, leading to inflammation.
What should happen to a cell that is irreparably mutated?
It should be deleted via apoptosis
What happens if the genes associated with apoptosis are damaged?
Controlled cell death is impaired, which can lead to tumor growth and cancer
Intrinsic apoptosis pathway
- Internal DNA damage/cell stress
- Mitochondrial membrane is disrupted, prompting the release of apoptotic inducing molecules.
- These molecules form the apoptotic complex, activating caspase, which cleave proteins in the cell to induce its death
Extrinsic apoptosis pathway
- Ligands bind to death receptors
- Apoptotic complex is activating, causing caspase to initiate cell death
Steps of apoptosis
- Cell shrinkage
- Blebbing of membrane
- Apoptotic bodys formed
- Phagocytes engulf apoptotic bodies
Explain the interaction between pro- and antiapoptotic proteins
Apoptosis is in a constant balance. When apoptosis is induced, proapoptotic proteins cancel out anti-apoptotic proteins, which causes apoptosis.
What happens when cytocrome C enters the cytoplasm?
The apoptotic complex is formed
What causes necrosis?
Lack of blood and oxygen to the tissue
What are some real-life examples of things that can cause necrosis? (Read: hazards)
- Chemicals
- Infection
- Burns
- Radiation
Summarise the process of necrosis
- Cell swells as ions and water enter it
- Membrane undergoes blebbing
- The whole cell ruptures
- Inflammation occurs as neighboring immune cells are recruited
What happens when a ligand binds to an extracellular receptor? How is this interpreted?
The cell converts this external input into intracellular processes via intracelluar signal transduction. This results in a cellular response.
Is receptor-ligand binding irreversible?
Not necessarily. It depends on the strength of the chemical bonds that hold the two structures together.
Receptor Agonist vs Receptor Antagonist
Agonist: Causes cellular response (intended effect)
Antagonist: Inhibits receptor agonist => no response
What are some examples of lipid-soluble ligands that can bind with intracellular receptors?
Steroid hormones, derived from cholesterol:
Sex Steroids: Oestrogens, androgens
Corticosteroids: Cortisol
This is why taking steroids is such a bad idea; they can literally enter your cells and make changes to DNA.
How are hydrophobic ligands transported through the bloodstream? Why does this make sense?
- Transported by carrier/transporter proteins
- Plasma is largely composed of water, so it makes sense that these hydrophobic ligands cannot travel through the aqueous bloodstream unassisted.
What are some examples of water-soluble ligands? Where do they bind?
- Cytokines, growth factors, insulin, HGH, serotonin, melatonin
-They bind to extracellular receptors, since they are not lipid soluble and cannot cross the plasma membrane
What are some other types of molecules that can act as ligands?
- Neurotransmitters
- Gases
- Ions
- Drugs
What regulatory proteins do drugs tend to target?
- Enzymes
- Carrier proteins
- Ion channels
- Receptors
List the four superfamilies of cellular receptors
- Ligand-Gated Ion Channel (Ionotropic receptors)
- Enzyme-Linked Receptor (Kinase-Linked)
- G Protein-Coupled Receptor
- Intracellular Receptor
Draw and label an intracellular receptor (incl. before and after the ligand has bound to the receptor)
Receptor: Binding Doman + Zinc Finger (DNA-Binding Domain)
Before: Attached to protein to form a domplex
After: Detached from complex
Where can intracellular receptors reside?
- Cytoplasm
- Nucleus
Mechanism of ionotropic receptors
Ligand binds with receptor, changing its shape to allow ions into the intracellular environment. This is a fast-acting process, and alters the intracellular composition and activity of the cell.
Mechanism of kinase-linked receptors
When ligand binds to receptor, the receptor changes shape, causing phosphorylation of the receptor. This activates other enzymes and proteins, causing a cellular response.
What is the role of tyrosine phosphatase?
Dephosphorylation of tyrosines on intracellular proteins and transmembrane receptors.
Which three amino acids can be phosphorylated?
Serine, threonine, tyrosine
What are somatic cells?
Body cells that are not involved in sexual reproduction
What is cell division important for?
- Repair
- Growth
- Regeneration
Do all cells have the same rate of division?
No. They are often very different
Why do cells replicate at different rates?
- Cells that are more exposed get damaged easily
- Therefore, there is a higher rate of turnover
Diploid vs Haploid
Diploid: One chromosome from each parent (2n)
Haploid: One set of chromosomes (n)
How do you count the number of chromosomes?
Number of centromeres
What are the phases in the cell cycle (from G0)
G0, G1, S, G2, M
Which phase of cell division do cells spend the most time in?
Interphase (regular function, but preparing for replication)
What occurs during the G1 phase?
- Generating new organelles
- Making a lot of proteins in case of division
What occurs during the S phase
- DNA replication
- HIstone production
What occurs during G2 phase
- New DNA is checked
- Centriole replication
- Final protein synthesis
What happens during early prophase
- DNA coils and condenses of rigidity
- Nuclear membrane dissolves
What happens during late metaphase?
- Centrosomes migrate to opposite poles of the cell
What happens during metaphase?
- Chromosomes align on metaphase plate, and are attached to microtubules held by centrosomes
What happens during anaphase
- Sister Chromatids pulled apart
What happens during cytokinesis?
Physical separation of daughter cells.
WHat are the phases of cell division in order?
- Interphase
- Mitosis (prophase, metaphase, anaphase, telophase)
- Cytokinesis
What are the three checkpoints of the cell cycle?
G1/S: Is DNA intact?
G2/M: Have you completed DNA replication
Metaphase: Are all of your chromosomes align on the equator
Remember: All have to do with DNA (why does this make sense for efficiency?)
What is the role of cyclin D?
Moves the cell from G0-G1 and G1-S
What is the role of cyclin E?
S Phase DNA replication
What is the role of cyclin A?
S phase DNA replication (same as E)
What is the role of cyclin B?
Mitotic Spindle Formation
What are cyclin dependent kinases?
- Bind to cyclins
- Phosphorylate proteins
- Regulate the cell cycle
What is the role of CDK inhibitors?
- Inhibit the cell cycle
- Allows the cell to fix its issue
- Then its levels go down
What does p53 do?
Arrests cell growth by inducing the expression of p21, a CDK inhibitor. Inhibits angiogenesis, disallowing the blood flow that cancer cells require to propagate.
What phase does p53 alter the cell cycle at, and what does it do?
G1/S phase, activates DNA repair
If there is too much damage in the cell, what does p53 do in a cell?
- Activates transcriptional expression of apoptosis pathways
In terms of mechanism, how does p53 inhibit the cell cycle
- It binds to genes involving the cell cycle and inhibits them.
- It can also promote other genes (e.g. apoptosis)
During what phase does crossing over of homologous chromosomes occur during meiosis?
Metaphase 1
What are the five phases of Prophase 1?
- Leptonema
- Zygonema
- Pachynema
- Dyplonema
- Diakinesis
What is the driving force behind cellular differentiation?
- Gene expression (turning on/off of genes)
What happens when stem cells divide?
- One daughter cell remains a stem cell, the other specialises.
Think: how does this relate to aging?
What are the four types of stem cells?
- Totipotent: can give rise to any type of cell (zygote)
- Pluripotent: All cell types except germ cells
- Multipotent: Can form cell types within a specific organ
- Unipotent: Capable of turning into one cell type
(TUMP)
What are induced pluripotent stem cells?
- De-differentiation of cells back into stem cells
- Requires specific genes
(How could this be useful in drug screening for a specific patients?)
What are the three main types of multipotent stem cells?
- Ectoderm (Neurons, epithelial cells)
- Mesoderm (Red blood cells, cardiomyocytes)
- Endoderm (Liver cells, Pancreas cells)
What occurs during leptonema?
Chromosomes condense and attach to the nuclear envelope
What occurs during zygonema?
Homologous regions of two chromosomes join together, and tetrads are formed (4 chromatids)
What occurs during Pachynema?
Crossing over
What occurs during Dyplonema?
Homologous chromosomes separate a little bit
What occurs during Diakinesis?
Chromosomes detach from nuclear membrane, and condense.
What are the five adaptations that cells can make in response to stress?
- Hyperplasia
- Atrophy
- Metaplasia
- Hypertrophy
- Dysplasia
(trophy: size, plasia: number)
What is atrophy and what causes it?
What?: A decrease in cell size and protein content, “shrinking” of tissue. Reduction in organelle content.
Why?: Poor nourishment, deregulation of hormones, loss of nerve supply, lack of exercise
What is hypertrophy and what causes it?
What?: Increase in cell size and protein content
Why?: Mechanical (exercise), Pathological (hypertrophic cardiomyopathy)
What is hyperplasia and what causes it?
What?: Increased cell number and tissue size
Why?: Increase in demand, inflammatory state, development
What is metaplasia and what causes it?
What?: Cell changes to another cell type in response to stress
Why?: Response to changes in tissue environment. Reversible if original environment is restored
What is dysplasia?
- Disordered growth of cells
- More immature cells
- Pre-cancerous state
What is neoplasia? What is unique about this response to stress?
- Uncontrolled cell proliferation
- Loss of initial function
- Impaired differentiation
- Can be benign (localised) or malignant (invasive)
- Cannot undergo apoptosis
Unique: Irreversible
In terms of stress responses, how does cancer progress?
Normal -> hyperplasia -> dysplasia -> cancer (neoplasia)
What are oncogenes?
Mutated forms of proto-oncogenes. Can lead to cancer in cells.
Mutations in which genes can lead to cancer?
- DNA repair genes
- p53
How can changes in receptor levels lead to cancer?
- Receptors can be activated without ligand binding
- Mutations that promote progression through the cell cycle
- Higher amounts of receptors for growth factors
- Autocrine stimulation
How does enhanced telomerase expression lead to cancer?
- Telomere length is maintained
- Cells can divide indefinitely -> cancer
How does inflammation lead to cancer?
Provision of growth factors and other factors that promote proliferation
Which two cell types are activated when tumor antigens are detected? What do they do?
- Cytotoxic T-Cells
- Helper T-Cells
They produce cytotoxins and interferons to kill cancer cells
How do tumor cells promote angiogenesis?
They secrete factors to neighbouring blood vessels, thereby increasing their ability to proliferate
Why is glycolysis preferred for cancer cells?
- ATP produced faster
- Intermediate compounds promote proliferation
What is the function of the basement membrane?
Provides blood flow (therefore nutrients, oxygen, and waste)
What causes metastasis of cancer cells?
Downregulation of adhesion molecules. Upregulation of migration molecules.
What is the typical relationship between the strength of a signal and the concentration of a chemical/ligand
As the concentration of the chemical/ligand increases, the strength of the signal increases
Why does it matter that receptors exist in families?
One chemical (e.g. serotonin) may have different effects when binding at receptors in different areas of the body (e.g. gut vs brain). This is part of how adverse reactions can occur.
What is the typical shape of an effect/concentration graph called?
Sigmoid
What is the definition of drug efficacy?
Efficacy/Emax is the maximum effect that a drug can be expected to have.
What is meant by drug potency?
The potency of the drug is the concentration that produces 50% of the effect. (Higher concentration needed = less potent)
What is a partial agonist?
Drugs that bind to and active a given receptor, but have only partial efficacy compared to full agonists
What is potentiation?
Drug B may potentiate drug A by increasing the receptors affinity for A.
What is noncompetitive antagonism?
The full effect of drug A cannot be restored no matter how high the concentration.
What is competitive antagonism?
Competes with drug, meaning efficacy is same but potency is lower (conc must be higher).
What occurs during an allergic reaction to a drug?
The body mounts an immunological reaction against a drug.
How can toxicity occur with a drug?
- Binds to right receptor in wrong place
- Binds to wrong receptor in right place
Which type of protein does contact dependent signalling occur between?
Transmembrane protein (extracellular and intracellular)
What is juxtacrine signalling?
Ligand expressed on the surface of one cell, and receptor expressed on the other. Cells come together to create downstream signalling events.
Describe communication through tight junctions and adhesion molecules.
- Transmembrane proteins fuse cells together at various points.
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