Cell and Molecular Biology Flashcards
How are lysosomes formed
From endocytic vesicles and vesicles from GA
What are lysosomes
organelles responsible for waste processing and recycling in animal cells
What are vacuoles
organelles responsible for waste processing and recycling in plant, fungi and algal cells
What receptor is involved in routing of lysosomal enzymes
mannose-6-phosphate (M6P)
Name a role of M6P Receptors
Synthesis and tagging
Recognition
Transport Vesicle Formation
Delivery to Lysosome
Catalyzation of macromolecule breakdown
Name a function of Lysosomes
Endocytosis
Phagocytosis
Autophagy
ER and Golgi transport
Breakdown of macromolecules
Recycling of cellular components
Defense against pathogens
What is Endocytosis
Materials from outside the cell being engulfed by the plasma membrane forming a vesicle that fuses with a lysosome for degradation
What is phagocytosis
When large particles or cells are ingested forming phagosomes which then fuse with lysosomes
What is Autophagy
When damaged organelles or cytoplasmic materials are encapsulated in autophagosomes which fuse with lysosomes for breakdown and recycling
What is the optimum pH of lysosomal enzymes
4-5 (acidic) This is due to environment of lysosome being acidic
How is acidity maintained in lysosomes
Proton pumps transporting hydrogen ions into lysosome
Membrane permeability - as membrane is impermeable to ions so cant diffuse out
What are some differences between lysosome and vacuole
Lysosomes are only found in animal cells
Vacuoles have wider roles including storage, maintaining of turgidity
Vacuoles are larger (only one in cell compared to many lysosomes)
Define In vitro
In vitro refers to studies conducted in a controlled environment outside of a living organism e.g. test tube
Define In Vivo
In vivo refers to studies or experiments conducted in living organisms
Define Ex Vivo
Ex Vivo refers to studies conducted on tissues or organs taken from a living organism but out with the organism itself
Describe a type of in vitro model
Cell culture - primary cell culture and immortalized cell line grown under controlled conditions
Organotypic - 3D cultures that maintain some characteristics of original tissue
How are cells cultured in vitro
Isolation - cells are isolated from tissues or obtained from cell banks
Culture medium - cells are grown in a nutrient rich medium that provides the necessary growth factors, hormone and gases
Substrate - cells are often cultured on a flat substrate to which they adhere
Environmental control
What are some limitations of in vitro models
Lack of complexity, an artificial environment genetic drift and limited longevity
What are some ethical considerations of using animals in experiments
The three Rs (Replacement, Reduction, and Refinement) is a good guide. Animals need welfare and care. You need to be able to justify animal use
What are some ethical considerations of using humans in experiments
You must receive informed consent, must maintain their privacy, must insure a minimization of risk.
What are some ethical considerations of using in vitro cells in experiments
Source of cells
Consent for donated tissue
Use of embryonic stem cells
Replacement of animals /p
Name a function of membranes in eukaryotic cells
Compartmentalization
Selective permeability
Signal transduction
Energy transduction
Cell to cell communication
What is selective permeability in membranes
Membranes regulate the entry and exit of substances which maintains the internal balance of ions and molecules. Crucial in homeostasis
What is energy transduction
Membranes produce ATP in organelles like mitochondria and chloroplasts
Describe the structure of the membrane and phospholipids
Made up of a phospholipid bilayer. Phospholipids are made up of hydrophilic (polar) heads and hydrophobic (nonpolar) tails. Membranes are fluid and flexible due to unsaturated fatty acids. The arrangement of lipids forms a selective barrier
What are the polymer components of membranes
Integral and peripheral membranes
Carbohydrates (glycolipids + glycoproteins)
Lipids (other than phospholipids) such as cholesterol
How does sterols such as cholesterol affect membrane fluidity
At high temperatures they stabilize the membrane and at low temperatures make it more fluid
Name a function of proteins in membranes
Integral proteins function as channels and carriers for ions and molecules across the membrane.
Proteins act as receptors for signaling molecules
What are the functions of carbohydrates in the plasma membrane
Cell recognition - important in immune responses and tissue formation
Protect the cell surface from mechanical and chemical damage
What molecules require membrane transport proteins
Some ions due to their charge cannot diffuse through the lipid bilayer (Na+, K+, Ca2+, Cl- etc.)
Large polar molecules due to size and polarity (e.g. glucose, amino acids)
Water can diffuse through to an extent aquaporins facilitate its transport to make it faster
Define Membrane potential
The voltage difference across a membrane resulting from the unequal distribution of ions across the cell membrane. This potential energy influences the movement of charged substance across the membrane.
Define electrochemical gradient
The combined effect of both the concentration gradient and the electric potential gradient on the movement of ions across membranes. It dictates the direction ions will move.
Define what a channel is
Channels allow molecules to pass through by diffusion acting as pores that can open or close
Define what a transporter is
They bind to specific molecules on one side of the membrane and change shape to release them on the other side
Define what passive transport is
Transport that does not require energy allowing substances to move according to concentration gradient
Define active transport
transport that requires energy to move substances against concentration gradients
Define coupled transport
Transport that involves the simultaneous transport of two different molecules where the movement of one is directly coupled with the movement of another.
Define uncoupled transport
transport of a single molecule without the direct coupling to the transport of another molecule
Define the cytoskeleton
A complex network of protein filaments that plays a vital role in both plant and animal cells. It is also integral to the structure and function of plant cell walls
What are the functions of the cytoskeleton in animal cells
Support/shape - Provides mechanical support and maintains cell integrity and shape
Intracellular transport - serves as tracks for the transport of neurotransmitters and other molecules between the cell body and synaptic terminals
Cell division - mitotic spindle ensures accurate chromosome segregation
Cell movement - actin filaments and myosin motor proteins facilitate muscle contraction
Signal transduction - cytoskeletal elements participate in signal transduction pathways that control cell growth differentiation and apoptosis
What are the functions of the cytoskeleton in plant cells
Support/shape - directs the desposition of cellulose fibres to cell wall synthesis
Cell Division - for the preprophase band and later phragmoplast
Signal transduction - plays a role in growth, development and stress response
The cytoskeleton is also vital in integration of cell wall components
Name the three principal components of the cytoskeleton
Actin filaments, Microtubules, intermediate filaments
Define Actin Filaments
Thinnest filament (7nm diameter), primarily involved in cell shape and movement. Found just beneath the cell membrane and in areas requiring strength or movement and composed of actin monomers.
Define Microtubules
Thickest filament (25nm in diameter), crucial for cell division, intracellular transport and cell structure. THey radiate from the cell centre. Composed of alpha and beta tubulin.
define Intermediate filaments
Intermediate thickness (10nm in diameter), providing mechanical support and resilience against stress. Found throughout the cell often surrounding the nucleus and made of various proteins
What circumstances require cell death
Damaged DNA
Infection
Developmental processes
Maintaining homeostasis
Disease prevention
Define Apoptosis
Programmed cell death, characterized by cell shrinkage, DNA fragmentation
Define necrosis
Accidental cell death resulting from external factors like trauma or infection leading to swelling and rupture
Define Autophagy
A process where cells degrade their own components through lysosomal machinery often as a survival mechanism
Define Proptosis
A form of programmed cell death associated with inflammation, involving cell swelling and lysis to release pro-inflammatory mediators
Define Ferroptosis
AN iron dependent form of cell death characterized by the accumulation of lipid peroxides
Name the 3 stages of apoptosis
Initiation phase, execution phase phagocytosis
Define Phagocytosis
The cell beaks apart into apoptotic bodies and then phagocytosed and digested by neighboring cells
Name the 4 stages of necrosis
Onset, Cell swelling, organelle swelling and dysfunction, rupture
What are the consequences of uncontrolled cell death
Tissue damage, autoimmune disease, cancer (insufficient cell death), degenerative disease
Define anoikis
a form of apoptosis that is induced when cells lose their attachment to the extracellular matrix
Define contact-depended signalling
Signalling that requires direct physical contact between cells through membrane bound receptors and ligands
Define paracrine signalling
Signalling molecules released by a cell that affect nearby cells
Define synaptic signalling
signalling where neurotransmitters released from neurons cross synaptic gaps to target cells
Define endocrine signalling
hormones released into the bloodstream affecting distant target cells
Define what a receptor is
A protein molecule on the cell surface or inside a cell that binds to a specific ligand to initiate a cellular response
What is a ligand
A molecule that binds specifically to a receptor to trigger a signal transduction pathway or cellular response
Define, intercellular, intracellular and extracellular
Intercellular - occurring between cells
Intracellular - occurring within a cell
Extracellular - occurring outside a cell(s)
What are the main cell surface receptors
Ion Channel-linked receptors
G-Protein-Linked Receptors
Enzyme Linked Receptors
How does an Ion Channel linked receptor work
Opens or closes in response to ligand binding allowing ions to pass through membrane
How does a G Protein linked receptor work
They activate G proteins which in turn activate other intracellular signalling pathways
How does an enzyme linked receptor work
They function as enzymes or re associated with enzymes that are activated upon ligand binding
What is autocrine signalling
Signalling molecules that interact with receptors on same cell
What is paracrine signalling
When signalling molecules interact with receptors on nearby cells
What are gap junctions
Direct cytoplasmic connections between cells that allow molecules and ions to pass directly from one cell to another
What are second messengers
Second messengers are produced in response to the activation of cell surface receptors. These amplifications lead to the activation of multiple signalling proteins which creates a cascade effect
What are kinases
Enzymes that transfer phosphate groups from atp to specific substrates, often activating or deactivating target proteins
What is phosphatase
Phosphatase removes phosphate groups from proteins, often reversing action of kinases
What does the balance between kinase and phosphatase effect
The balance of activities regulates many processes including cell growth, differentiation and apoptosis
Why do cells need to divide
Growth, repair and regeneration, reproduction, maintenance
Describe the structure of chromosomes
a long DNA molecule with part or all of the genetic material of an organism. DNA wraps around histones which makes the structure chromatin which condenses to form chromosomes
Describe the function of chromosomes
they carry genes
How many chromosomes are in the human body
In humans there is 23 pairs (46). Varies between organisms
What are the phases of the cell cycle
G1 phase - cell grows and works as normal. Decision to divide occurs at G1 checkpoint
S phase - synthesis phase where DNA replication occurs
G2 phase - cell continues to grow and prepare for division. Integrity of DNA checked here
M phase - mitosis, cell divides its duplicated DNA into two sets of chromosomes which are separated into two daughter cells
Define mitosis
the process by which a cell divides its nucleus and duplicated chromosomes into two nuclei each with an identical set of chromosomes
Describe the phases of mitosis
Prophase - chromosomes condense and become visible, nuclear envelope breaks done, mitotic spindle begins to form
Metaphase - chromosomes align at the cell equator, the spindle fibres attach to centromere of each chromosome
Anaphase - sister chromatids separated and pulled to opposite poles.
Telophase 0 chromatids arrive at opposite poles. nuclear envelop reform around each set of chromosomes which begin to decondense
Define cytokinesis
the process of dividing the cells cytoplasm into two daughter cell following mitosis
What is the role of cyclins
Proteins that act as regulatory subunits that activate CDKs with different cyclins being synthesized and degraded at specific stages of the cell cycle
What is the role of Cyclin-Dependent Kinases
CDKs are serine/threonine protein kinases that when activated by binding to cyclins, phosphorylate specific target proteins to regulate cell cycle progression. Their activation is essential for the cell to transition from one phase to the next in cell cycle
What do cyclin-CDK complexes effect
They ensure that cell cycle does not proceed if the conditions are not favorable or if errors are detected. They are tightly regulated by phosphorylation and dephosphorylation.
What is thought to be the origin of mitochondria
a symbiotic relationship between eukaryotic cell and proteobacterium
What is thought to be the origin of chloroplast
endosymbiotic engulfment of photosynthetic cyanobacterium by a eukaryotic cell
Describe the permeability of outer mitochondrial membrane
The OMM is highly permeable to small molecules and ions due to presence of porin protein channels.
Describe the permeability of inner mitochondrial membrane
The IMM is selectively permeable with a tight barrier to most ions/molecules. Transport requires transport proteins
Describe the electron transport chain
The ETC is a series of complexes that transfer electrons from electron donors to acceptors via redox reaction. This produces an electrochemical gradient that ATP synthase uses to produce ATP
Describe oxidative phosphorylation
Synthesis of ATP from ADP and inorganic phosphate driven by ETC
Describe Krebs cycle (citric acid cycle)
a series of reactions that oxidize acetyl-CoA to CO2 generating NADH and FADH2 which are used in electron transport chain
What processes occur in IMM
Electron transport chain and oxidative phosphorylation
What processes occur in Mitochondrial Matrix
Citric acid cycle
Define cellulose
long chain polysaccharide that forms microfibrils providing tensile strength
define Hemicellulose
a matrix of polysaccharides that bind to cellulose contributing to wall flexibility
Define pectin
a group of polysaccharides that are rich in galacturonic acid contributing to porosity and hydration of the wall
define the cell wall
a complex dynamic structure that surrounds the plasma membrane of the cell
what are the function of the cell wall
It provides support, protection and acts as a filtering mechanism.
Define the extracellular matrix
a network of extracellular components that provides structural and biochemical support to the surrounding cells in animal tissue
Name the key components of extracellular matrix
Collagen, elastin, proteoglycans, fibronectin and laminin
What are some similarities between the cell wall and ECM
Both provide structural support
both offer protection against pathogens, mechanical stress and osmotic pressure changes
both play roles in regulating external environments
What are some differences between the cell wall and ECM
They are made of different things
their functionality is different
the EMC is more involved in regulation of biochemical environment
How does the ECM interact with integrins
Integrins are transmembrane receptors that facilitate cell-EMC adhesion acting as a critical mediators of cell signalling and mechanical transduction.
What triggers anoikis
the loss of cell-EMC interactions (especially ones mediated by integrins
Define immunology
the branch of biology that studies the immune system its functions, disorders and mechanisms in protecting the body
Define viruses
intracellular pathogen that hijack the host cellular machinery to replicate
Define prions
Misfolded proteins that can induce other proteins to misfold
Define adaptive immunity
Characterized by specificity and memory. It adapts its response to specific pathogens and improves upon repeated exposure
What are B cells
Cells that produce antibodies that neutralize pathogens
Define T cells
Cytotoxic T cells kill infected cells
Helper T cells coordinate the immune response
Define innate immunity
First defense, providing immediate but non specific responses to pathogen. Includes physical barriers, phagocytic cells and NK cells
What are the tasks of the immune system
Detection and elimination, Discrimination, regulation, memory
Where do immune cells originate from
All immune cells originate from hematopoietic stem cells in the bone marrow
What are progenitors
Lymphoid progenitors give rise to B, T, and NK cells
Myeloid progenitors develop into granulocytes, monocytes and other cells involved in innate immune response
What are the cell types of the innate immune system
Macrophages
Neutrophils
Dendritic cells
NK cells
Eosinophils and Basophils
How do Macrophages work
Engulf and digest pathogens, present antigens to T cells
What do neutrophils do
Phagocytose bacteria and fungi
What do dendritic cells
present antigens to T cells linking innate to adaptive immunity
WHat do NK cells do
Kill virus infected cells and tumor cells
What are eosinophils and basophils involved in
allergic reactions and parasitic infection
What are the responses to an infectious agent
Recognition, activation, elimination and resolution
Define Cytokine
small proteins important in cell signalling in the immune system. THey modulate balance between humoral and cell based responses
Define chemokine
type of cytokine that specifically induces chemotaxis in nearby responsive cells. THis directs immune cells
Define chemotaxis
The movement of an organism or cell along a chemical gradient toward higher concentration (often towards site of infection/injury)
What are neutrophils
primary responders to infection. Phagocytose pathogens and release antimicrobial peptides and enzymes
What are eosinophils
mainly involved in parasitic infection they contribute to dealing with allergic reactions
They release cytotoxic granules and inflammatory mediators to kill parasites and modulate inflammation
Define basophils
involved in allergic reactions and parasitic infections. They release histamine and other mediators that contribute to inflammation and allergic reaction
What are the types of granules in neutrophils
Azurophilic (primary) granules
Specific (secondary) Granules
Gelatinase (tertiary) granules
Define monocytes
Monocytes circulate in the blood and migrate into tissue to differentiate into macrophages and dendritic cells
Define Macrophages
Macrophages phagocytose pathogens and dead cells
How do immune cells activate
Immune cells are activated by recognition of pathogens or by cytokines and chemokines produced by other immune cells
What are the key characteristics of the adaptive immune response
Specificity
Diversity
Memory
Self-nonself recognition (ability to distinguish own cells to foreign cells
What cell types are responsible for adaptive immune response
B cells
T cells
What are the key features of immunological memory
Longevity, rapid response, enhanced affinity
What is MHC class I
Presented by all nucleated cells allowing cytotoxic T cells to monitor for pathogens
What is MHC class II
Presented by professional antigen presenting cells (dendric cells, mactophages etc.)
Where do B cells mature
Bone marrow
Where do T cells mature
the thymus
Define the nuclear envelope
A double-layered membrane that encloses the nucleus, separating its contents from the cytoplasm
Define nuclear pores
Openings in the nuclear envelope that allow for the exchange of materials
(like RNA and proteins) between the nucleus and cytoplasm
define nucleoplasm
The gel-like substance within the nucleus, containing the chromatin and
nucleolus
Define chromatin
complex of DNA and histones
What is the nucleolus
dense region within nucleus where rRNA is synthesised
What are the functions of the nucleus
Genetic info storage, gene expression regulation, ribosome assembly
define semi-conservative replication
Each new DNA molecule consists of one original strand and
one newly synthesized strand
define Conservative Replication
The original DNA molecule is conserved, and an entirely new
molecule is synthesized
define dispersive replication
Both strands of the new DNA molecules are a mix of old and new
DNA
What is the function of DNA polymerase
Removes RNA primers from the fragments and replaces them with DNA
nucleotides
What is the replication fork
A Y-shaped region where the DNA double helix is unwound into two single
strands for replication to occur.
What is the continuous strand
Synthesized continuously towards the replication fork
because the DNA polymerase can add nucleotides in the direction of unwinding
what is the fragmented strand
Synthesized discontinuously away from the replication
fork in short segments known as Okazaki fragments, because DNA polymerase can only
synthesize DNA in one direction (5’ to 3’), necessitating this backstitching process.
What are some examples of DNA proofreading
Exonuclease activity, mismatch repair, post-replication repair
What is the DNA helicase
enzyme that unwinds DNA double helix
what is gene mutation
permanent alteration in DNA sequence
Describe what base pair substitution is and what the types are
Type of mutation where one nucleotide is replaced by another
Silent mutations, missense mutations, nonsense mutations
What is frame shift
caused by addition or subtraction of base leads to entire reading frame being off causing wrong codons and potential early termination
What are induced mutations
mutations caused by exposure to mutagens (physical - UV or xray, chemical - alkylating agents, biological agents - viruses)
What is transcription
copying a sequence of DNA into RNA
define translation
process in which mRNA is used to synthesis protein
What is the central dogma
Describes flow of genetic information
DNA->RNA->Protein
describe mRNA
single stranded, serves as template for protein synthesis during translation
describe tRNA
cloverleaf structure with a anticodon arm and amino acid attachment site. Transfers amino acid to growing polypeptide chain
describe splicing
removal on non coding introns anf joining of coding exons
what is tRNA synthase
enzyme that provides tRNA with the correct amino acid
what are the 3 stages of translation
Initation - ribosome assembles around target mRNA. First tRNA is attached at start codon
Elongation - ribosome continues to translate each codon in turn adding amino acid to growing peptide chain
termination - process ends when a stop codon is reached
What are the functions of the A, P and E sites of ribosomes
A (aminoacyl) site is the entry site for the aminoacyl tRNA
P (peptidyl) site holds tRNA carrying the growing polypeptide chain
E (exit) site is where tRNA no longer bound to amino acid leaves ribosome
Describe rough ER
characterized by presense of ribosomes
primarily involved in synthesis of proteins
Describe Smooth ER
lacks attach ribosomes
involved in lipid synthesis, carbohydrate metabolism, ion storage and other functiona
Describe the GA
an essential organelle. Plays role in modifying sorting and packaging protein and lipids for secretion and delivery
