Module 1 and 2 Flashcards
Bacteria engulfed to form chloroplasts
Cyanobacteria
Bacteria engulfed to form mitochondria
Proteobacteria
Theory of origin of eukaryotes
Endosymbiont theory
3 domains of life
Eukarya, archaea, bacteria
Bacteria
Prokaryotic microorganisms typically having cell walls of peptidoglycan
Chloroplast
Eukaryotic organism not an animal, plant or fungi
Eukaryote
Organism with membrane-enclosed nucleus and organelles
Fungi
Eukaryotic organisms with cells walls and that obtain food from other organisms
Peptidoglycan
Polymer in bacterial cell walls consisting of modified sugars cross-linked by short polypeptides
Prokaryote
Organism with cells that lack a membrane-enclosed nucleus and organelles
Protist
Any eukaryote that is not a plant, animal or fungus (most unicellular)
Types of monosaccharides
Hexose (6C), pentose (5C)
What are lipids made of
Combinations of glycerol, fatty acids and hydrocarbon rings
Deoxyribose vs ribose sugar
C2 is bonded to H in deoxyribose, OH in ribose (DEOXY ribose)
Plant energy macromolecule
Amylose, amylopectin (starch) (carbohydrate)
Plant structure macromolecule
Cellulose (carbohydrate)
Animal energy molecule
Glycogen (carbohydrate)
Amino acid structure
NH2CHRCOOH (R branch differs between them)
Nucleobase structures
A, G (purines, 2 rings), C, T, U (pyrimidines, 1 ring)
Simple carbohydrates
Monosaccharides (hexose, 6C, pentose, 5C)
Protein functions
Structural, regulatory, contractile, transport, storage, protective, catalytic, toxic
Function of complex carbohydrates
Recognition (cell membrane: pathogens, other cells), energy, structure
Function of lipids
Structural (phospho and glycolipids), regulatory (cholesterol), energy (fat: triacylglycerol)
Biomolecule
A molecule or ion involved in the biological processes of living organisms
Carbohydrate
A sugar (monosaccharide), double sugar (disaccharide) or polysaccharide
Cellulose
Structural polysaccharide of plant cell walls, consisting of glucose monomers joint by β glycosidic linkages
DNA function
Carries the genetic instructions for all cellular processes (growth, development, function and reproduction)
Heterogeneous
Diverse in structure, and/or composed of different biological molecules
Macromolecule
A very large molecule formed by the joining of smaller molecules
RNA function
Protein synthesis, gene regulation, genome for some viruses
Which lipid stabilises membrane fluidity
Cholesterol
Membrane protein functions
Signal transduction, cell recognition, intercellular joining, linking cytoskeleton and extracellular matrix, membrane transport
What enables cell recognition
Glycoproteins in the cell membrane
Water channel proteins name
Aquaporins
Organelle functions
Special conditions for specific processes, keep incompatible processes apart, allow specific substances to be concentrated, form concentration gradients, package substances for transport/export
Carrier protein definition
Membrane bound protein that transports solutes across membrane by binding to solute on one side of membrane and undergoing a structural change to transfer solute to other side
Cell definition
Smallest collection of matter that perform all activities required for life
Channel protein definition
Membrane bound protein that forms a hydrophilic channel through which solutes can pass without any change to structure or shape of protein
Co transport definition
Coupling of the downhill diffusion of one substance to the uphill transport of another against its concentration gradient
Extracellular matrix
Meshwork surrounding animal cells, consisting of glycoproteins, polysaccharides and proteoglycans synthesised and secreted by cells
Glycoprotein
Protein with one or more covalently attached carbohydrates
Osmoregulation
The process by which solute concentration and water is balanced by a cell across a semi permeable membrane
Phospholipid
Glycerol joined to two fatty acids and a phosphate group
Signal transduction
Linkage of a mechanism, chemical or electromagnetic stimulus to a specific cellular response
Smooth ER functions
Metabolism of carbs, synthesis of lipids for membranes, detoxification (drugs and toxins), storing calcium ions (used as a signal)
Rough ER function
Protein synthesis (secreted and membrane bound enter lumen)
Golgi apparatus function
Glycosylation: addition or modification of carbs to proteins
Make polysaccharides
Sort proteins
Direct vesicle trafficking
Constitutive exocytosis
Continuous secretion, releases ECM proteins
Regulated exocytosis
Occurs due to a signal, releases hormones and neurotransmitters
Pseudopodium
“hands” of cell membrane reaching out to consume food
Phagocytosis
Eating, phagocytic vacuole digested by lysosomes
Pinocytosis
Drinking, uptake vesicle formed with aid of coat protein
Receptor mediated endocytosis
Selective pinocytosis (with receptors). Allows bulk quantities of specific substances to be obtained
Lysosomes
Interiorly acidic, with hydrolytic enzymes to degrade proteins, lipids, carbs, nucleic acids and other substances for other processes. Digest and recycle unwanted substances (called autophagy)
Vacuole
Large vesicle, perform lysosome like functions. Central vacuoles absorb water enabling the cell to grow without large increase in cytoplasm.
The cell needs energy…
For mechanical work, to make new materials, for transport
Glycolysis equation
Glucose -> 2 pyruvate
Oxidative phosphorylation components
Electron transport chain and chemiosmosis
Pyruvate oxidation equation
2 pyruvate -> 3 Acetyl coA
Electron carrier molecules (respiration)
NADH (stage 1 and 2), FADH2 (stage 2)
How is ATP synthesised (chemiosmosis)
ATP synthase protein, acts as reverse ion pump (concentration gradient of ions used to synthesise ATP (ADP + Pi))
How proton gradient exists (respiration)
Proton complexes pump H+ from matrix to intermembrane space using exergonic flow of electrons down electron chain
Where ADP and Pi come from for ATP synthesis
Every time ATP is used it is split up into ADP and Pi with the release of energy
Why does a plasma membrane need to maintain its fluidity
Transport of nutrients in and out of cell, growth and movement, enable proteins to move within membrane
Autophagy
Intracellular digestion of old or unwanted organelles or other cellular structures within autophagic lysosomes
Catabolic
Metabolic pathway involving the break down of molecules into smaller molecules with less energy (smaller units oxidised to release energy)
Anabolic
Metabolic pathway involving synthesis of a large molecule from smaller units
Chemiosmosis
Energy coupling mechanism using stored energy to drive cellular work
Citric acid cycle
Acetyl coA is oxidised to CO2
Collagen
Glycoprotein in ECM of animal cells that forms strong fibres
Cytoplasm vs cytosol
Cytoplasm: contents of cell bounded by plasma membrane, excluding nucleus. Cytosol: actual semi fluid portion of cytoplasm
Cytoskeleton
Network of microtubules, microfilaments, intermediate filaments extending through cytoplasm to serve a variety of functions
Phase 1 cell wall structure
Microfibrils: cellulose fibres
Phase 2 cell wall structure
Matrix: hemicellulose, pectin, extensin
Hemicellulose
Heterogeneous group of polysaccharides (long chain one sugar, others branch off)
Cellulose
Long ribbons (bonds through and across), very strong, resist tension, form microfibrils
Pectin
Branched, negatively charged polysaccharides which hold cell wall together (gel like properties)
Extensin
Protein which controls extensibility of cells by cross linking with pectin and cellulose to dehydrate cell wall and increase strength
Rosettes
Cellulose synthase, big transmembrane proteins which put glucose monomers together and push out as cellulose microfibrils running parallel to cortical microtubules
Cytoskeleton
Network of microtubules, microfilaments and intermediate filaments throughout the cytoplasm
Middle lamella
Mostly pectin, serves as glue holding cells together
Cell wall functions
Morphology (regulating shape) (e.g ordered=expansion in specific directions), structural support (protoplast pushes against cell wall), prevents excessive water uptake
Vacuoles function
High concentration of solutes, so water osmoses in, allowing plant cell to stay turgid, protoplast push against cell wall
Secondary cell wall
UNDERNEATH primary, thicker, stronger, provides more structural support. More cellulose, lignin, less pectin
Lignin function
Acts to exclude water and increase strength and rigidity
Plasmodesmata function
Communication and transport of resources between cells, free exchange of small molecules. Cell walls quite dynamic so require this communication
Proteoglycans structure and function
Proteins with extensive sugar attachments (can be 95% carb) (sticky), trap water in ECM to resist compression
Microtubules structure and function
(biggest diameter cytoskeleton component)
Spiral of tubulin monomers forming tube, may radiate out from centrosome.
Motility: motor proteins walk along them to transport vesicles or organelles, arranged to make cilia or flagella
Microfilaments structure and function (smallest diameter cytoskeleton component)
Twisted ropes made of double chain of actin subunits. Resist tension, interactions with motor proteins allow movement (e.g actin-myosin muscle contraction, cytoplasmic streaming, amoeboid movement)
Intermediate filaments
Different proteins throughout body (eg keratins in hair, lamins in nucleus, neurofilaments in neurons) Supercoiled into cables, stronger, less dynamic. Maintain cell shape, anchor organelles
Desmosomes
Anchor cells together
Tight junctions
Prevent fluid movement between cells, continuous seal, variability in tightness
Gap junctions
Cytoplasmic contact between cells, quick cell to cell communication
Integrins (membrane proteins)
Membrane proteins which attach to fibronectins which attach to ECM
Fibronectins (glycoproteins)
Attach to collagen fibres and integrins to connect cells
Ribosomes structure and function
Made of ribosomal RNA and proteins, two subunits (one large one small). Translation
Nuclear envelope
Double membrane, perinuclear space continuous with lamen of ER
Nuclear Lamina
Intermediate filaments on the inside of the nuclear envelope made of lamins, provide structure and help with packing DNA
Nuclear pores
Channels made of proteins (nucleoporins) form complex, span two membranes, control nucleo-cytoplasmic exchange
What’s allowed in to nucleus
Signals, building blocks for mRNA, energy for chemical synthesis
What’s allowed out of nucleus
tRNA, mRNA
Nucleolus
Non membrane bound prominent part of nucleus in non-dividing cells responsible for making rRNA and subunits
DNA packaging process
2nm interacts with histones to 10nm strand (beads called nucleosomes), interacts with different histone to 30nm strand, folds in flower shape to form 300nm strand, folds into chromosome
Euchromatin
Less densely packed DNA in nucleolus, active genes as transcription machinery can access it
Heterochromatin
More densely packed DNA in nucleolus, inactive genes as transcription machinery cannot access it. Dynamic relationship between euchromatin and heterochromatin.
Catabolic
Metabolic activity which breaks down
Anabolic
Metabolic activity which builds up
Nuclease generic function
Enzyme that can remove nucleotides
Polymerase generic function
Enzyme that can add nucleotides
Characteristics of life
Cellular organisation, reproduction, metabolism, homeostasis, heredity, response to stimuli, growth and development, adaptation through evolution
Natural selection requirements
Variance, inheritance, selection, time
4 macromolecules nearly all life is composed of
Proteins, nucleic acids, complex carbohydrates, lipids
Nucleic acid functions
DNA: carries genetic instructions for all cellular processes, RNA: protein synthesis, gene regulation, genome for some viruses
Protein definition
Molecules by which cells perform their functions in the whole organism
Complex carbohydrates functions
Recognition, energy, structure
Cell functions
Make cellular materials, obtain raw materials, remove waste, generate energy, control all of this
Organelle functions
Provide compartments with special conditions, keep incompatible substances apart, form concentration gradients, package things for transport/export
What affects membrane fluidity
Composition of fatty acids (saturation), temperature, cholesterol
Membrane protein functions
Signal transduction, cell recognition, intercellular joining, linking cytoskeleton and ECM, membrane transport
Difference between passive and active membrane proteins
Passive: don’t require energy to change shape (but may require a signal), Active: require ATP to change shape
Types of membrane proteins
Channel and carrier
Endomembrane system definition
Membrane system interconnected by direct physical contact or transport by vesicles
Organelles in the endomembrane system
Nuclear envelope, endoplasmic reticulum, Golgi apparatus, vesicles, lysosomes, vacuoles, plasma membrane
How is the golgi oriented
Cis facing ER, trans facing cell membrane
Vesicles definition
Membrane bound organelle, move along pathways bound to proteins moving along microtubules
Vesicles function
Transport, secretory, vacuoles, artificial (liposomes: drug and vaccine delivery)
Evidence for endosymbiont theory
Mitochondria and chloroplasts have their own DNA, ribosomes (so can produce some of their own proteins)
Resulting gamete chromosome numbers from nondisjunction in meiosis I
n+1, n+1, n-1, n-1
Resulting gamete chromosome numbers from nondisjunction in meiosis II
n, n, n+1, n-1
Down Syndrome cause
Trisomy 21
Familial Down Syndrome cause
Centric fusion: Robertsonian translocation (1/2 21, 1/2 14)
Klinefelter Syndrome cause
XXY
Turner Syndrome cause
X0
Lejeune Syndrome cause
Deletion of tip of short arm of chromosome 5
Deletion chromosomal abnormality
Chromosomal segment removed (chromosome may be visibly shorter)
Inversion chromosomal abnormality
Segment reversed
Most don’t involve centromere
Chromosomes loop around to try and match up
Duplication chromosomal abnormality
Segment repeated
Translocation chromosomal abnormality
Segment from one chromosome moved to non homologous chromosome
Broken in middle of gene: misregulated gene resulting in overexpression
Reciprocal: swap
Why does X inactivation occur in mammalian females
Dosage compensation to balance X linked gene expression levels
Why do most X chromosome genetic diseases not show a mosaic effect
Because the gene product can move throughout the body
Components needed for PCR
DNA template, primers, DNA polymerase, dNTPs (free nucleotides)
PCR denaturing
Temperature increased to separate DNA strands
PCR annealing
DNA primers made to bind by decrease in temperature
PCR extension
Starting at 3’ end of primer, DNA polymerase adds nucleotides to extend molecule in 5’ -> 3’ direction
Possible number of combinations due to independent assortment
2^n
Actin
Globular protein that links into chains, two of which wist helically about each other to form chains
Chromatin
Complex of DNA and proteins (histones) making up eukaryotic chromosomes
Cilia (flagella)
Membrane bound appendage on surface of eukaryotic cell composed of a specific arrangement of microtubules and responsible for motility of cell
Electron acceptor
Oxidising agent that accepts electrons transferred from another compound
FADH2
Redox cofactor created during citric acid cycle and utilised during the last part of respiration in the electron transport chain
Histone
Small protein with high proportion of positively charged amino acids that binds to negatively charged DNA and plays a key role in chromatin structure
Hydrolytic enzyme
Digestive enzyme which can break contents within food vacuoles down
Ligand
Molecule that binds specifically to another molecule, usually a larger one
Microfibrils
Made of cellulose molecules and synthesised by cellulose synthase secreted into the intermembrane space where they become embedded in a matrix of other polysaccharide proteins
NADH
Electron donor to electron transport chain
Nucleotide parts
Five carbon sugar, nitrogenous base, one to three phosphate groups
Plastid
One of a family of closely related organelles, including chloroplasts and chromoplasts (found in the cells of photosynthetic eukaryotes)
Why must pyrimidines bond with purines
2 rings + 3 rings, DNA has a constant diameter
A,T hydrogen bond number
2
C, G hydrogen bond number
3
Pyrimidines
C, T, U
Purines
A, G
Nucleic acid strands synthesised in which direction
5’ -> 3’
3’ position
3rd carbon, chemically reactive, interact with negatively charged phosphate group
Bonds joining nucleotides
Phosphodiester
Where are DNA origins of replication
in A, T rich areas
Describe DNA structure
Double stranded, helical, anti parallel
How is the leading strand synthesised
DNA polymerase III continuously adds DNA nucleotides
How is the lagging strand synthesised
Nucleotides added in okazaki fragments in 5’ -> 3’ direction, but overall growth toward replication fork (semi discontinuous)
What direction is the template strand read in
3’ -> 5’
Helicase function
Recognise origins of replication, pull strands apart
Primase function
Internal 3’ hydroxyl group to start adding nucleotides from. Can only add RNA nucleotides, makes a short stretch of RNA primer
DNA polymerase III function
Adds DNA nucelotides, knocks ssbp off as it moves, proof reads
Single strand binding proteins function
Prevents strands snapping back together or being degraded
DNA polymerase I function
Removes RNA nucleotides and fills gaps with DNA nucleotides
Ligase function
Forms phosphodiester bonds to link fragments together
Topoisomerase function
Moves ahead of replication fork, cuts strands and glues back together to release tension
Exonuclease function
During replication process, removes nucleotide from end of strand using 3’ -> 5’ DNA polymerase III exonuclease activity
Endonuclease function
After replication process, removes nucleotides from within a sequence (big chunk removed around mistake, re extends from exposed 3’, ligase rejoins strand)
How are sister chromatids held together
Centromere
Interphase G1
Metabolic activity and growth, replication of organelles
Interphase S
Synthesis (replication of DNA), metabolic activity and growth
Interphase G2
Metabolic activity, growth and preparation for cell division (enzymes produced)
Prophase
Chromosomes duplicated, start to condense, nuclear envelope starts to disintegrate, spindle starting to form
What are spindle fibres
Microtubules
Prometaphase
Nuclear envelope finishes disintegrating, kinetochore microtubules connect to centromeres, non kinetochore microtubules form, cytoskeleton disassembles as spindle fibre forms, centrioles migrate to opposite poles
Metaphase
Chromosomes line up on metaphase plate
Anaphase
Sister chromatids pulled apart by spindle fibre, degradation of proteins holding chromatids together, non kinetochore microtubules lengthen to push cell poles apart
Telophase
Cleavage furrow starting to form by constricting belt of actin filaments forming contractile ring. Spindle has disintegrated (broken down into tubulin to be recycled)
Cytokinesis
Final division into separate cells, chromosomes come together in new nuclear envelope and decondense
How do plant walls separate (cytokinesis)
Vesicles form expanding membrane partition called cell plate
Prophase I
Homologous chromosomes align and synapse (join), crossing over occurs at chiasmata
What lines up on metaphase plate in metaphase I
Chiasmata (but kinetochores still attach to centromeres)
When does independent assortment/segregation occur
Metaphase I
Random fertilisation
Source of diversity in sexual reproduction: random which sperm fertilises which egg
Aneuploidy
Failure of chromosomes to separate properly during meiosis (result of nondisjunction)
Polyploidy
Possession of multiple sets of chromosomes
Autopolyploid
Self fertilisation can be viable as can pair up properly
Allopolyploid
Different species breed, only viable if chromosome doubling occurs
How does a phosphodiester linkage form
Condensation reaction between OH of phosphate group and H of OH group on ribose sugar C3
What is at the 5’ end of a DNA strand
Phosphate group
What is at the 3’ end of a DNA strand
Hydroxyl group on 3rd carbon of pentose sugar. (why primers have internal 3’ hydroxyl groups)
Does ligase make phospodiester bonds or DNA Pol I remove RNA primer first?
DNA Pol I removes RNA primer
