Week 2 Flashcards
• Outline the processes involved in DNA replication
• Enzymes that use DNA as a template move in 5’ to 3’ direction
• DNA strand opens up to form bubble, DNA polymerase comes in and forms a DNA strand from 5’ to 3’ direction toward fork (Y fork=tip where bubble ends)
• One one side it makes dna strand continuously (linking strand)and on other side it is done in pieces (lagging strand)
• Enzyme helicase opens dna strand by disccosiateidn gh bonds, primer synthesises a short piece of RNA that hydrolises onto strand of DNA to initiate synthesis as DNA polymerase needs double strand
• Primer also add hydroxyl group at 3’ as DNA polymerase can only elongate
• Exonuclause removes rna primer and DNA polymerase fills it in
DNA ligase joins -lagging strand- to form long piece of DNA
Describe the sequence of events that occur in transcription.
- Gene expression is specific to a cell type via transcription profiles
- DNA uncoils forming bubble where RNA polymerase uses DNA as a template to make complementary RNA strand
- RNA has promoter region and coding region
- Promotor region/transcription factor binding site where transcription factors bind which enables RNA polymerase to bind to TATA box start making RNA
- 3 types of RNA polymerase I-rRNA, II-mRNA, III-tRNA
- Once RNA polymerase is activated it makes a large amount
- Processing RNA starts with addition of a 5’ CAP which protects RNA from being degraded from exonuclaese and important for translational initiation and then a 3’ poly A tail polyadenylation for export into cytoplasm and RNA stability
- RNA Splicing introns are spliced out
- Alternative splicing where whole exons may be spliced out which forms smaller protein due to cell deciding a certain domain isnt needed or it needs to form an inhibitor
Describe the sequence of events that occur in translation.
○ Occurs in cytoplasm
○ 3 parts
○ Initiation
§ mRNA enters and ribosome finds 5’ CAP and reads 3 nucleotides at a time-codon
§ Every RNA molecule starts with AUG-first aa is methionine- and tRNA binds via complementary pairing
○ Elongation
§ Amino acids link together via peptide bonds
○ Termination
§ Proteins released and further modified
• Outline the processes involved in DNA damage, proofing and repair
• Environmental factors resulting in mutations
○ UV-non ionsiing
○ Cross links T-C
○ Phosphate backbone breaks and results in translocation
○ Heat stress
○ Loss of purine bases-G/A
○ Mutagenic chemicals
○ Alkylation, hydrolysis, crosslinking, oxidation
○ DNA replication
○ Nucleotide Excision Repair=whole region is cut out and new dna is formed
○ Base Excision Repair =single base is removed and new one is ligated
○ Non homologus rejoining repairs via direct ligation
Homologous recombination is where undamaged strand is template to correct damage
• Summarise four levels of protein structure (1st)
○ Primary
§ Sequence of aa
§ Sense of direction with amino terminus and end with carboxyl terminus
§ Aa can be hydrophobic, hydrophilic or non charged influnces structure
Summarise four levels of protein structure (2nd)
Secondary
Protein folding involving h bonds
Form either alpha helices or beta pleated sheets
Alpha helices forms when H of carbonyl group bonds with h of amine grop and all side chains face outwards free to interact with other proteins
Beta pleated sheets form when 2 or more segments of polypeptide line up forming a sheet-like structure forming H bonds between carbonyl and amine group of backbone while side chains are exposed on both side of polypeptide
Summarise four levels of protein structure (3rd)
Tertiary
3d spatial organisation of proteins
Formed via itneractions of side chains (R groups)
H bonds with interactions of partial positive and negative charges,
ionic bonds of interactions between opposite charged side chains,
hydrophobic interactions which include non polar side chains clusters on the inside of protein and polar clusters of side chains on the outside
Disulfide bonds (special type of bond) covalent links between sulphur groups of cystein amino acids forming strong bonds usually safety pin-like structure
Summarise four levels of protein structure (4th)
Quaternary
For proteins with multiple polypeptide
Held together by non-covalent bonds, hydrogen bonds oor Vand der Waals forces all sub units cooperate to form final shape of protein and enable activity of protein
(STRUCTURE) Define the different types of proteins according to their structure and/or function.
§ Structural proteins
□ Make framework for cell shape and structure
□ Muscle proteins
® Form thick and thin filaments
® Their interaction form basis of contraction in presence of calcium and ATP
® Actin and myosin proteins important for contracting and relaxing
® Actin has helical secondary structures
® Trypomyosin (helicals structure forming a coiled domain) assists in actin contractions and troponin b
® Inds to tropomyosin and can form helical structures
(COLLAGEN) Define the different types of proteins according to their structure and/or function.
® Main structural proteins in Extracellular matrix
® 25% of toal protein
® Provide strength support and shape to tissues
® Mineralised as bone or non-mineralsied as cartilage or tendons
® 3 polypeptide chains forming triple superhelix structure stabilsied by hydrogen bonding
® More than 1000 mutations associated with disease
Eg osteogenesis imperfect (weak bones, irregular connective tissue)
(Cytoskeletal proteins) Define the different types of proteins according to their structure and/or function.
® Cytoskeleton, cilia, flagella
® Continually changing dynamic polymer structure
® Assmebles and disassmbles
® Important for cytokinesis, cell protection, motility, transport molecules, cell division, give cell shape, organelle organisation
® 3 types of main proteins actin filaments, microtubules, intermediate filaments
◊ Microfilaments made of actin monoers in doble helice structure
} In charge of movement, cell chape, transport, cytokinesis
◊ Intermediate filaments intermediate size
} In charge of cell shape, anchor organelles, nuclear lamina, cell-cell junctions
◊ Microtubule are largest of the filaments
} Made of tubilin
in charge of cell division, centrosomes transport of organelles and chromosomes and formation of flagella and cillia
(Histone in nucleus) Define the different types of proteins according to their structure and/or function.
Basic proteins rich in ammonia acids and arginine
Histone 2a and histone 2b link and H3 and H4 link forming a tetramers structure
In cells 2 tetramers structures get together and form an octamer structure
Around an octamer is 146 bases of DNA forming the nucleosome
Nucleosomes fold onto one another to form highly compact chromatin structure which folds again to form chromosome
2m of DNA in each cell
Histones maintain a + charge and basic, as DNA has - charge the electrostatic force attraction enables formation of nucleosome
Important for all DNA processes
Histones have the helix-turn-helix which is essential for binding to DNA
(immunity proteins) Define the different types of proteins according to their structure and/or function.
◊ Immunity proteins ◊ Anitgens } Polypeptide, protein, polysaccharatides } Essential to activate antibody response } Types include (exogenous from outside, endogenous from inside due to metabolism or infection, autoantigen is self hurting-autoimmune tumour antigen and native antigen that is not processed) ◊ Complement } Over 30 proteins } Involved in clearing invading pathogens } Activation cascade forming membrane attack complex } Results in cell lisis ◊ Anitbodies } Identify and neutralise foriegn particles } 2 polpeptide chains form Y protein } Has carbohydrate attached } Trunk portion never changes but tip is variable that binds to antigen } Vairable part has beta sheet structure } Different class of antibodies had different function (IgG, IgM, IgA, IgD and IgE) ◊ Cytokines } Small proteins/peptides } Regulate immunity and inflammation and haemopoiesis } Made by helpatitit cells and macrophages } Generally act by binding to receptors } Associated with cancer and arthritis
(Transcription factors) Define the different types of proteins according to their structure and/or function.
◊ Sequence-specific DNA binding proteins that control transcription
◊ 1600 proteins for transcription factors
◊ Control activation or repression of genes
◊ As a dna binding domain and an activation domain that interacts with co factors that assist bringing rna polymerase to the dna repssors stop rna polymerase from coming
◊ All different shapes and sizes mostly helical structures
◊ Zinc finger structure-speicifc protein fold that has a finger like shape held via a Zn ion
◊ Many mutations in transcription factors eg diabetes, developmental disease and cancer
(coagulation proteins) Define the different types of proteins according to their structure and/or function.
Clotting factors=inactive zymogens
They are serine proteases that become activated and catalyse the next reaction in the cascate resulting in fibrin plug containing lots of enzymes with calcium
Coagulation protein types
Thrombin
Fibrinogen
Anticoagulations-prevent blood clots
Given to patients pron to clots and thus pron to strokes and heart attacks
These include warfarin, heparin and thrombin inhibitors
Coagulation and anticoagulation maintain homeostasis
CARRIER Describe the structure and list the functions of the cell membrane
Carrier protein
Only open to one side of membrane at once and move against concentration gradient using energy to change shape
It binds to substrate and undergoes reversible confromational change opening up to one side of cell to transport the molecule out
Channel protein-opens up hole of the membrane so it mayu transverse through membrane and enable a continuous opening
They allow polar molecules and lines to travel
They are gated and open in response to electrochemical gradient changes
ALBUMIN Describe the structure and list the functions of the cell membrane
Albumin is a transporter protein that maintains oncotic pressure (form of osmotic pressure) of plasma
Key carrier protein in the serum and most abundant in blood
It carries negative charge and combined cations and hydrophobic molecules such as steriod hormones and fatty acids
Has 3 large domains held together by disulfide bonds that from heart shape and mainly comprised of alpha helicals structures
CHANNEL Describe the structure and list the functions of the cell membrane
Channel protein-opens up hole of the membrane so it mayu transverse through membrane and enable a continuous opening
They allow polar molecules and lines to travel
They are gated and open in response to electrochemical gradient changes
PASSIVE Describe the active and passive processes that transport substances across the cell membrane.
• Passive transport-no ATP
○ Follow concentration gradient
○ Facilitated (carrier mediated)
○ The natural tendency of substances to move from high concentration to low concentration to maintain equal distributiuon
○ Simple Diffusion
§ Molecules pass through plasma membrane
§ Membrane has no influence of direction
§ Concentration gradient detect this
○ Facilitated diffusion
§ Large or charged molecules moved via membrane channel (water, water soluble molecules, ions) or carrier molecule (hydrophillic molecules, large molecules)
§ Concentration gradient determines the direction
§ No energy required
○ Osmosis
§ Diffusion of water across membrane
§ Maintain similar solute concentrations in ICF and ECF
§ Can simply diffuse or enter via aquaporins
Can pass at very high speeds up to 100,000,000 molecules per second in single file
ACTIVE Describe the active and passive processes that transport substances across the cell membrane.
○ Carrier mediated
○ Against concentration gradient
○ Primary active transport
○ Against concentration gradient
§ Phagocytosis (large particles engulfed)
Pinocytosis (ECF engulfed)
§ Exocytosis
Endocytosis (receptor mediated sometimes)
§ Transmembrane pumps using ATP to transport substances against concentration gradient
§ Eg proton pumps that moves protons against concentration gradient for ATP synthesis and Na+/K+ pump which drives action potential formation in nervous system
○ Secondary active transport
§ Not requiring ATP
§ Concentration gradient of one molecule provides energy for the transport of another against its concentration gradient
§ Transports 2 different molecules at once
§ Na/glucose cotransporter-transports free glucose in kidney
□ Exocytosis
® Release of digestive enzymes by the pancreas
® Movement of substances out of cell
® Transport vesicles in the cell migrate to the membrane, fuse with it and release contents to ECF
Examples include the release of neurotransmitters, secretion of enzymes and hormones and secretion of antibodies from plasma cells
Describe the events and processes of cell cycle in somatic cells.
Cell cycle • Interphase (¾ of cycle) ○ Cell mainly exists here ○ This is where it performs normal function ○ Prepares if it wants to divide ○ Can be indefinite ○ Not actively focused on division • G1 ○ STEP BETWEEN DIVISION AND S phase ○ Normal cell function ○ Generates organelles ○ 8-12 hours • S ○ Duplication ○ Dna rpelication ○ Histones and nuclear proteins ○ 6-8 hours • G2 phase ○ 2-5 hours ○ Final protein synthesis ○ Centriole replicates • G0 ○ Normal cell function ○ Not prepping for division • Mitosis • Prophase ○ Early-DNA condolences, nuclaer membranes disapper ○ Late-centrosome migrate to ends of cell • Metaphase ○ Chromosomes align in centre ○ Attach to microtubules by cetrosome • Anaphase ○ Mucrotubules pull sister chromatids apart • Twlophase ○ Nuclear membrane reform ○ DNA uncoils • Cytokinesis ○ Cytoplasmic division of daughter cells • Checkpoints ○ G1-is DNA intact G2-is replication of DNA properly Ana and metaphase-spindle fibres properly attached
• Describe the events and processes of cell division in somatic cells MEIOSIS
• Meiosis 1
○ Prophase 1
§ Leptonema: diploid chromosome condense forming long thin threads, attach to nuclear envelope and individual chromatids not visiple
§ Zygonema: synapsis occurs as mother and father DNA line up and zip together to form tetrad
§ Pachynema: all chromosomes align and recombination of non sister chromatids align and exchanged material
§ Diplonema sister chromatids move away from each another and visible
§ Diakinesis: condense chromosome, nuclear membrane detached, nuclear envoelpe disintregreates, sister chromatids join at centromere, non sister chromatids join at chiasmate ○ Metaphase 1 § Spindle fiblres form § Tertads line up on spindles on metaphase plate § Centromeres from homolgous chrosms on opposite ends § Random assortment iintroduces diversity (random ordered line up) ○ Anaphase 1 § Chromosomes pulled apared § Each cell has 1 of a pair of chromosomes with crossed material ○ Telophase 1 § Nuclear division § Cytoplasmic division § Males it is equal § Femal what larger cell becomes egg the smaller is a polar body and then is disintegrates ○ Prophase 11 § Envelop disintegrages ○ Metaphase 11 § Spindle fibres line up to chromosomes at plate ○ Anaphase11 § Centroemeres split § Sister chromatids pulled to opposite pulses § Daughters not identical ○ Telophase11 § Nuclear membrane forms around each set § Ends with males-haploid cells with 22 chromosomes and X or Y § Females 22 chromosomes and X and X
outline the processes of cell cycle regulation.
• Cyclins
○ Cyclin D levels increase at transcription so more protein is made
○ It triggers transition from G0 to G1
○ Cyclin E triggers S phase
○ Cyclin A increase from S to G2
○ Cyclin B increase from G2 TO M
○ Degrade after phase
○ Bind to cyclin dependent kinase to activate it
○ Levels of cyclin dependent kinase is constant but cyclin levels that bind to it that fluctuate
○ Cyclin dependent kinase inhibitors bind to kinases and stop cell division if something is wrong with cell to give it time to repair
○ Lots of deletions of these inhibitors in cancers that means problematic cells keep dividing eg p16 and p21 genes
• P53-protein 53 kiladotans
• Transcription factor that activate transcription
• Found to be produced by DNA damage
• It scans DNA and if it sees issues it tries to repair it
• Causes cell cycle arrest by activating p21 which inhibits CDK2 and CDK4
• Activates repair pathway to maintain genomic stability
• If too many errors it cativates apoptosis which is cell suicide
• It inhibits angiogensis (forming new blood vessels)
Outline the differences between embryonic and adult stem cells
Embryonic stem cells (ESCs) result from the early divisions of a fertilized egg. These undifferentiated cells. ESCs are pluripotent, meaning they
have the potential to generate any of the more than 200 cell types in
the body
Adult stem cell usually multipotent-can only make cells type related to mother cell type
Explain the mechanism of cell differentiation.
○ Stem cells in development-zygote-forms blastocyst that forms embryo that can be 3 types ectoderm, mesoderm, endoderm
○ Changes in size, shape membrane potential, metabolic activity
Describe the molecular and cellular hallmarks of ageing cellular changes that occur with ageing.
- Cell senescence-proliferation block
- telomere shortening-telomerase caps that stop chromosomes breaking get smaller
- epigenetic drift-
- stem cell exhaustion-low amount of STEM cells available to maintain tissue
- inflammaging-Innate immunity increases increasing pro inflammatory cytokines, low grade chronic inflammation and natural killer cells
- DNA damage to genome-errors in DNA code due to UV, chemicals, pollution, infection etc, more low density nucleosome structures meaning to more DNA exposed
- mitochondrial dysfunction-less respiration more Reactive O2 Species increase apoptosis, changed metabolites that change chromatin
- Deregulated nutrient sensing-stimulate Gfs increasing proliferation and cell damage
• Compare and contrast the processes of apoptosis and necrosis within a cell.
• Apoptosis
○ Programmed cell death
○ Suicide by coordinated intraceelular processes
○ No inflammation
○ Enzymes (caspcases) and phagocytes do this
○ Cell membrane blebbing
○ Cell becomes fragmented forming apoptici bodies Phagocytes eat the bodies
• NECROSIS • Death on large scale • Due to Mechanical, chemical, infection, immune response, injury • Cell swells as it cannot keep homeostasis due ti influx of water and ions leading to cytoplasmic vacuoles forming • Nucleus shrinks • Cell ruptures and contents spew out ot ECF • Leads to recruitment and inflammation of neighbouring immune cells and causes destruction and inflammation to surrounding tissues UNCONTROLLED
Describe the main categories of cell surface and intracellular receptors that are the targets of chemical signalling molecules.
• Modes of signalling
○ Contact dependent signalling-direct communication usually via adjacent cells talk with molecules on surface of call-juxtaicrine signalling
○ Autocrine signalling- cell releases molecules that bind to receptor expressed by same cell that results in signal transduction and response within came cell
○ Paracrine signalling-signals another cell locally and mediates physiological response
○ Endocrine signalling-signal released from cell, enter circulatory system and bind to another receptor in a cell in another area or tissue to instigate a physiological response
(hydrophobic ligand) Define the different types of ligands and their mechanisms of action.
• Hydrophobic ligand
○ Lipid soluble
○ Cross membrane
○ Mainly sex steroids (oestrogen, andorgens progesterone), corticosteroids (aldosterone, cortisol) eicosanoid hormones (prostaglandins, leukotrienes)
○ Transported through circulation bound to carrier or transport proteins
○ When released they can diffuse via capillaries and bind to receptor on surface or target cell
(Water soluble) Define the different types of ligands and their mechanisms of action.
• Water soluble ligand
○ React with ECF receptors
○ Peptides and small proteins
○ Cytokines (peptides), growth factors (proteins)
○ ECM components
○ Integrin receptors interact with cohesion complexes that result in intracellular signal transduction
Intracellular receptors-Explain how membrane receptors and downstream pathways can produce amplification of a signal.
Intracellular receptors
SLOW
receptors binds lipid soluble ligands-can diffuse through membrane to bind in cell form a receptor ligand complex, and it moves into the nucleus, and then binds to DNA, interacting with the hormone response elements or zinc fingers. Interaction then
influences gene transcription, either enhancing or inhibiting gene transcription and translation into a protein
receptor ion channels-Explain how membrane receptors and downstream pathways can produce amplification of a signal.
Receptor ion channel
FAST
cell surface receptors have a specific site where a ligand can bind-the N-terminal- and when the ligand binds to the binding site, this changes the shape of that ion channel.
The ion channel is now able to open and the ion-specific for that channel is able to move through the water-filled pore from this extracellular space into the cytosol, where it’s then able to alter the intracellular response and the activity of the cell.
