Module 1 - Cells Flashcards
What is the brain of the cell?
Nucleus
What are the levels of biological organisation?
- The biosphere 2. Ecosystems 3. Communities 4. Populations 5. Organisms 6. Organs and Organ Systems 7. Tissues 8. Cells 9. Organelles 10. Molecules
What is the Biosphere?
Consists of all environments on Earth that are inhabited by life. Includes most regions of land, bodies of water and the atmosphere
What are ecosystems?
An ecosystem consists of all the living things in a particular area, along with all non-living things in which they interact with
What are communities?
The entire array of organisms inhabiting a particular ecosystem (called a biological community)
What are populations?
A population consists of all the individuals of a species living within the bounds of a specified area. The community’s definition is refined by a set of populations
What are organs and organ systems?
The architecture of complex organisms
What are tissues?
A group of similar cells that create a function
What are cells?
Life’s fundamental unit of structure to live
What are organelles?
Various functional components that comprise a cell
What are molecules?
A chemical structure consisting of two or more small chemical units called atoms, which perform various tasks within the cell.
What are emergent properties?
Properties that emerge once you zoom out of the levels of biological organisation, and thus see the bigger picture.
What is the opposite of emerging properties?
Reductionism - the ability to zoom in
What are the five unifying themes within the study of life?
Organisation Information Energy and Matter Interactions Evolution
What are the two main types of cells?
Prokaryotic and Eukaryotic
Define a Prokaryotic Cell
A single celled organism lacking a nucleus or other membrane-bound organelles.
What does DNA stand for?
Deoxyribonucleic acid
The two pairs that make up DNA?
AT CG
What is the fifth building block of nucleotides?
U
What is gene expression?
The entire process, by which the information in a gene directs the manufacture of a cellular product, is called gene expression
What is a genome?
The entire “library” of genetic instructions that an organism inherits
Order of gene expression?
DNA - (Transcription) - mRNA - (Translation) - Chain of Amino Acids - (Protein Folding) - Protein
What is genomics?
The study of whole sets of genes (or other DNA) in one of more specoes
What is proteomics?
The study of sets of proteins and their properties
What is a proteome?
The entire set of proteins expressed by a given cell or group of cells
What are bioinformatics?
The use of computational tools to store, organise and analyse the huge volume of data that results from high-throughput methods.
What are produces?
Plants and other synthetic organisms that pass chemical energy to consumers
What are consumers?
Organisms, such as animals, that feed on producers and other consumers
How many species have biologists discovered?
1.8 million
How many species of fungi have scientists discovered?
100,000
How many species of plants have scientists discovered?
290,000
How many species of vertebrate animals have scientists discovered?
57,000
How many species of insects have scientists discovered?
1 million
Three domains of life in the kingdom of life?
Bacteria, Archaea and Eukarya
What is bacteria?
The most diverse and widespread prokaryotes
What are Archaea?
Some of the prokaryotes known to live in Earth’s extreme environments, such as salty lakes and boiling hot springs
What are the four main domains of Eukarya’s?
Plantae, Fungi, Animalia and Protists
What are protists?
Most unicellular eukaryotes and some relatively simple multicellular relatives. (Scientists debate how to classify these organisms evolutionarily)
What is the mechanism of evolutionary adaption?
Natural selection
Can Bacteria have more than one cell?
No
Two types of Microscopy?
Light microscopy (LM) and Electron Microscopy (EM)
Three parameters in microscopy?
Magnification, resolution and contrast
In microscopy, what is magnification?
The ratio of the object’s size to its image size
In microscopy, what is resolution?
The measure of the clarity of the image
In microscopy, what is contrast?
The difference in brightness between the light and dark areas of the image
What does an Electron Microscopy do?
Focuses a beam of electrons through the specimen or onto its surface, as opposed to light.
What is a SEM?
Scanning electron micrograph
What does an SEM do?
Takes a 3d image of the surface of a specimen
What does TEM stand for?
Transmission Electron Micrograph
What does a TEM do?
Provides a thin section of a specimen
What do SEM and TEM’s use to bend the path of electrons?
An electromagnet
Disadvantage of using an EM?
You have to kill the cells in the process, which may also cause artefacts
What is the study of cell structure?
Cytology
What is cell fractionation?
Where you take a cell apart and separate major organelles and other sub-cellular structures from one another
What do you use for cell fractionation?
A centrifuge
What does a centrifuge do?
Spins test tubes holding mixtures of disrupted cells at a series of increasing speeds
What is fimbriae?
Attachment structures on the surface of some prokaryotes
What are ribosomes?
Complexes that synthesis proteins
What is the plasma membrane?
Membrane enclosing the cytoplasm
What is the cell wall?
Rigid structure outside the plasma membrane
What is the capsule?
Jellylike outer coating of many prokaryotes
What is flagella?
Locomotion organelles of some bacteria
Using a TEM, what must you use to stain the cell?
Heavy metals, which attach to certain cellular structures, thus enhancing the electron density of some parts of the cells more than others
What are the smallest cells known to man?
Mycoplasmas (between 0.1-1.0um)
Typical size of bacteria?
1-5um
Typical size of Eukaryotes?
10-100um
What does the plasma membrane do?
Functions as a selective barrier that allows passage of enough oxygen, nutrients and wastes to service the entire cell
How do phospholipids arrange themselves in a plasma membrane?
The hydrophobic parts of the phospholipids and membrane proteins are found in the interior of the membrane, while the hydrophilic parts are in contact with the aqueous solutions on either side.
Animal Cell: Define Flagellum
Motility structure present in some animal cells, composed of a cluser of microtubules within an extension of the plasma membrane
Animal Cell: Define Centrosome
Region where the cell’s microtubules are initiated; contains a pair of centrioles
Animal Cell: Define Cytoskeleton
Reinforces cell’s shape; functions in cell movement; components are made of protein.
What protein structures can you find inside a cytoskeleton?
Microfilaments Intermediate filaments Microtubules
Animal Cell: Define Microvilli
Projections that increase the cell’s surface area
Animal Cell: Define Peroxisome
Organelle with various specialised metabolic functions; produces hydrogen peroxide as a by-product then converts it to water
What does peroxide produce as a by-product? What does it turn it to?
Hydrogen-peroxide, then turns it to water
Animal Cell: Define Endoplasmic Reticulum (ER)
Network of membranous sacs and tubes; active in membrane synthesis and other synthetic and metabolic processes; has rough (ribosome-studded) and smooth regions
Three sections of the nucleus?
Nuclear envelope, nucleolus and chromatin
Animal Cell: Define Nuclear envelope
Double membrane enclosing the nucleus; perforated by pores; continuous with ER
Animal Cell: Define Nucleolus
Nonmembranous structure involved in production of ribosomes; a nucleus has one or more nucleoli
Animal Cell: Define Chromatin
Material consisting of DNA and proteins; visible in a dividing cell as individual condensed chromosomes
Animal Cell: Define Plasma Membrane
Membrane enclosing the cell
Animal Cell: Define Ribosomes
Complexes that make proteins; free in cytosol or bound to rough ER or nuclear envelope
Animal Cell: Define Golgi Apparatus
Organelle active in synthesis, modification, sorting and secretion of cell products
Plant Cell: Define Call Wall
Outer layer that maintains cell’s shape and protects cell from mechanical damage; made of cellulose, other polysaccharides, and protein
Plant Cell: Define Central Vacuole
Prominent organelle in older plant cells; functions include storage, breakdown of waste products, and hydrolysis of macromolecules; enlargement of the vacuole is a major mechanism of plant growth
What part of the cytoskeleton can be found in an animal cell, but NOT a plant cell?
Intermediate filaments
Plant Cell: Define Chloroplasts
Photosynthetic organelle, converts energy of sunlight to chemical energy stored in sugar molecules
Plant Cell: Define Plasmodesmata
Cytoplasmic channels through cell walls that connect the cytoplasms of adjacent cells
Aside from the nucleus, where else could DNA be found?
In the mitochondria and chloroplasts
Describe the nuclear envelope
Double membrane, each a lipid bilayer with associated proteins roughly 20-40nm apart. Pore structures are 100nm in diameter
What is a pore complex?
Lines each pore and plays an important role in the cell by regulating the entry and exit of proteins and RNA’s (as well as other things)
What lines the nuclear envelope, except at the pores?
Nuclear lamina
What is nuclear lamina?
Lines the nuclear envelope, and consists of a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope.
What assists the nuclear lamina in maintaining the nuclear shape of the nucleus?
The nuclear matrix, a framework of protein fibres on the interior on the nuclear
What are chromosomes?
DNA organised into discrete structures that carry genetic information
What are chromatins?
Chromosomes formed with DNA and proteins, designed to reduce the length of the DNA to fit in the nucleus
What are ribosomes composed of?
Ribosomal RNA and protein
Are ribosomes membrane bounded?
No
Two types of ribosomes?
Bound and free
Describe the metabolic structure of Nucleoli and explain its function
Nucleoli consist of DNA and the ribosomal RNA (rRNA) made according to its instructions, as well as proteins imported from the cytoplasm. Together, the rRNA and proteins are assembled into large and small ribosomal subunits. (These are exported through nuclear pores to the cytoplasm, where they will participate in polypeptide-synthesis)
Main difference between smooth and rough er?
Protein synthesis occurs in the rough er, lipid metabolism in the smooth er
What enzymes do lysosomes release?
Phagyotic enzymes
Where can free ribosomes be found?
Suspended in the cytosol
Where are bound ribosomes found?
Attached to the outside of the endoplasmic reticulum or nuclear envelope
What can be found in the endomembrane system?
The nuclear envelope, the endoplasmic reticulum, the Golgi apparatus, lysosomes, various kinds of vesicles and vacuoles and the plasma membrane.
What are vesicles?
Membrane segments that contribute to the formation of the endomembrane system
What des the word and latin word for endoplasmic mean?
Without the cytoplasm Latin - little net
What are the ER tubules and sacs called?
Cisternae
Why is smooth ER smooth?
It lacks ribosomes
What are the functions of smooth er?
Synthesis of lipids, metabolism of carbohydrates detoxification of drugs and poisons, and storage of calcium ions
How does a muscle contract chemically?
Smooth ER membrane pumps calcium ions from the cytosol into the ER lumen, and when a muscle cell is stimulated by a nerve, calcium ions rush back across the ER membrane into the cytosol and trigger contraction of the muscle cell.
What are most secretory proteins in the rER?
Glycoptroteins
What are glycoproteins?
Proteins with carbohydrates covalently bonded to them
What is the Golgi Apparatus composed of?
Flattened membranous sacs called Cisternae
Two sides of a Cisternae?
Cis (on the same side) face and Trans (on the opposite side) face
How do lysosomes work?
Filled with hydrolytic enzymes, and a high ph, that digests macromolecules. Too many leaking lysosomes can self digest a cell
What is the word for a unicellular eukaryote engulfing a smaller organism?
Phagocytosis
What is a white blood cell called?
A macrophage
What is autophagy?
When a cell uses lysosomes to recycle its own organic material, releasing it into the cell’s cytoplasm
How often does a liver cell renew itself?
It recycles half its macromolecules a week
Where are vacuoles derived from?
The endoplasmic reticulum and Golgi apparatus
What is the Endosymbiont theory?
This theory states that an early ancestor of eukaryotic cells engulfed an oxygen-using nonphotosynthetic prokaryotic cell
What is the name of a cell living within another cell?
Endosymbiont
Infoldings in the inner mitochondria are called?
Cristae
Second layer of the mitochondria’s membrane is called?
The mitochondria matrix
What are stacks of thylakoids called?
Granum
What are the sacs inside a chloroplast called?
Thylakoids
What is the fluid outside the thylakoids in a chloroplast called?
Stroma
What is the chloroplast a specialised member of? (What family of plants?)
Plastids
What is a peroxisome?
A specialised metabolic compartment bounded by a single membrane. They contain enzymes that remove hydrogen atoms from various substrates and transfer them to oxygen, producing hydrogen peroxide (H202)
What are peroxisomes used for?
Some to break down fatty acids to use for ATP in the mitochondria, sometimes they detoxify alcohol.
How does the cell not die from hydrogen peroxide as a by product of a peroxisome?
It converts it to water
How does a cell retain mobility?
Interaction of the cytoskeleton with motor proteins
Structure of a microtubule?
Tubulin polymers Hollow tues
Strcture of microfilaments?
Actin filaments Two intertwined strands of actin
Structure of intermediate filaments?
Fibrous proteins coiled into cables
What type of cytoskeleton anchorages the nucleus?
Intermediate filaments
What are microtubules?
Hollow rods constructed from a globular protein called tubulin. They shape and support the cell and also serve as tracks along which organelles equipped with motor proteins can move. The guide vessels from the ER to the Golgi, and furthermore to the plasma membrane, and also help in separation of chromosomes during cell division.
What are microtubules made from?
A protein called dimer. A dimer is slip into two subunits, a-tubulin and B-tubulin
Where do microtubules for from?
A centrosome
What are centrioles?
Within a pair of centrosomes, nine sets of triplet microtubules arranged in a ring help organise the chromosome.
What are flagella and cilia made from? What is the difference between the two?
Cilia is a plural of flagella, and they are made from microtubules
How is a flagellum/cilia anchored in the cell?
By a basal body, with microtubule triplets in a “9+0” pattern
What motor protein is responsible for bending cilia?
Dyneins
What is the cytolasmic outer layer of a cell called?
The cortex
What is the primary cell wall?
A relatively thin and flexible wall a new plant cell begins with
What glues cell walls to one another?
Middle lamella
What is middle lamella composed of?
A thin layer rich in stick polysaccharides called pectins
What is a secondary cell wall?
The hard, durable matrix that builds between the primary cell wall and the plasma membrane. Wood has many SCW’s
What is the most abundant glycoprotein in the ECM in animals cells?
Collagen (40%) of total protein in human body
What is a proteoglycan?
A molecule consisting of a small core protein with many carbohydrate chains attached
What are integrins?
Membrane proteins with two subunits, bind to the ECM on the outside and to associated proteins attached to microfillaments on the inside. This linkage can transmit signals between the cell’s external environment and its interior and can result in changes in cell behaviour.
What is fibronectin?
Attaches the ECMto integrims embedded in the plasma membrane.
What are the channels of communication between plant cells called
Plasmodesmata
Three types of junctions in an animal cell?
Tight junctions, desmosomes and gap junctions
What are tight junctions?
The plasma membranes of neighbouring cells are very tightly pressed against each other, bound together by specific protein. Forming continuous seals around the cells, tight junctions establish a barrier that prevent leakage of extracellular fluid across a layer of epithelial cells. Fo example tight junctions between skin cells make us watertight.
What are desmosomes
Anchoring functions function like rivets, fastening cells together into strong sheets. Intermediate filaments made of sturdy keratin proteins anchor desmosomes in the cytoplasm. Desmosomes attach muscle cells to each other in a muscle. Some “muscle tears” involve the rupture of desmosomes.
Gap Junctions
Communicating junctions provide cytoplasmic channels from one cell to an adjacent cell and in the way are similar in their function to the plasmodesmata in plants. Gap junctions consist of membrane proteins that surround a pore through which ions, sugar, amino acids, and other small molecules may pass. Ga junctions are necessary for communication between cells in many types of tissues, such as heart muscle, and in animal embryos.
Membrane protein responsible for enabling water to permeate the membrane
Aquaporin
What does a phospholipid that has both hydrophobic and hydrophilic regions called?
Amphipathic
Why does bacon grease turn to lard?
When it’s warm, the membrane of a cell remains fluid. Temperature decreases until the phospholipids settle into a closely packed arrangement and the membrane solidifies.
What happens to cholesterol at hot temperatures in the membrane? How does it work as a fluidity buffer?
It makes the membrane less fluid by restraining phospholipid movement. However, because cholesterol also hinders the close packing of phospholipids, it lowers the temperature required for the membrane to solidify. Thus, cholesterol can be thought of as a fluidity butter, for it resists changes in membrane fluidity caused by temperature.
Two major populations of membrane proteins?
Integral and peripheral proteins
What are Integral proteins?
Integral proteins penetrate the hydrophobic interior of the lipid bilayer
What are the majority of integral protein?
Transmembrane proteins, which span the membrane; other integral proteins extend only partway into the hydrophobic interior
What does the hydrophobic region of an integral protein consist of?
One or more stretches of nonpolar amino acids, usually coiled into a-helixes
What happens when a membrane protein has a hydrophillic channel?
It allows hydrophillic substances to pass through, such as water
What are peripheral proteins?
The are no embedded in the lipid bilayer at all; they are appendages loosely bound to the surface of the membrane, often to exposed pats of integral proteins
Six major functions of membrane proteins?
Transport Enzymatic activity Signal transduction Cell-cell recognition Intercellular joining Attachment to the cytoskeleton and ECM
Membrane protein: define transport
A protein that spans the membrane may provide a hydrophilic channel across the membrane that is selective for a particular solute. Other transport proteins shuttle a substance from one side to the other by changing shape. Some of these proteins hydrolyse ATP as an energy source to actively pump substances across the membrane.
Membrane protein: define enzymatic activity
A protein built into the membrane may be an enzyme with its active site exposed to substances in the adjacent solution. In some cases, several enzymes in a membrane are organised as a team that carries out sequential steps of a metabolic pathway.
Membrane protein: define signal transduction
A membrane protein (receptor) may have a binding site with a specific shape that fits the shape of a chemical messenger, such as a hormone. The external messenger (signalling molecule) may cause the protein to change shape, allowing it to relay the message to the inside of the cell, usually by binding to a cytoplasmic rotein.
Membrane protein: define cell-cell recognition
Some glyco-proteins serve as identification tags that are specifically recognised by membrane proteins of other cells. This type of cell-cell binding is usually short-lived compared to intercellular joining membranes
Membrane protein: define intercellular joining membranes
Membrane proteins of adjacent cells may hook together in various kinds of junctions, such as gap junctions or tight junctions. This type of binding is more long-lasting than cell-cell recognition
Membrane protein: define attachment to the cytoskeleton and ECM
Microfilaments or other elements of the cytoskeleton may be non-covalently bound to membrane proteins, a function that helps maintain cell shape and stabilises the location o certain membrane proteins. Proteins that can bring to ECM molecules can coordinate extracellular and intracellular changes.
What does glyco refer to
The presense of carbohydrates
How are carbohydrates and proteins bound together?
Via covalent bonds
How do blood types (A, B, AB and O) identify one another?
Though glycoproteins (the carbohydrates are where the differences lie)
Where are carbohydrates added to proteins to make glycoproteins?
In the ER, where the protein is made as well. Inside the Golgi apparatus, the undergo further carbohydrate modification.
Where are carbohydrates added to lipids to make glycolipids?
Unlike the glycoprotein which is formed entirely in the ER, only the lipid is formed in the (smooth) ER. Inside the Golgi apparatus, the lipid undergoes carbohydrate modification. This
Inorganic ions that must be transported across the cell membrane via a protein?
Na+, K+, CA^2+ and CL-
Four characteristics of a non-polar molecule?
- Made up of one element 2. Noble gases 3. A molecule that contains only carbon and hydrogen 4. If the molecule has symmetry (like to be carbon)
What are channel proteins?
A type of transport protein that functions by having a hydrophilic channel that certain molecules or atomic ions use as a tunnel
At what rate does the aquaporin allow water to pass through the membrane versus simple permeation of the wall?
It is ten times faster
How much faster is a red blood cell’s channel for glucose?
50,000 times faster than having it permeate through the wall
Why can O2 and CO2 cross a lipid bilayer easily?
They are non-polar; 02 is made of one element, and CO2 is symmetrical
Why would an aquaporin be more likely to allow the passage of a glycerol (three headed alcohol group) through the membrane as oppossed to a hydronium ion? (H30+), even though the glycerol is much larger?
A hydronium is charged, which is an even bigger factor to not letting it through than the size of the molecule
What is diffusion
The movement of particles of any substance so that they spread out into the available space
What is the concentration gradient?
The region along which the density of a chemical substance increases or decreases
Simple rule of diffusion
In the absence of other forces, a substance will diffuse from where it is more concentrated to where it is less concentrated. In other words, any substance will diffuse down its concentration gradient.
What is diffusion of a substance across a biological membrane called?
Passive transport
What is osmosis?
The diffusion of free water across a selectively permeable membrane, whether artificial or cellular
What is the ability of a surrounding solution to cause a cell to gain or lose water called?
Tonicity
What does the tonicity of a solution depend on?
On its concentration of solutes that cannot cross the membrane relative to that inside the cell.
What does an isotonic solution mean?
If a cell without a cell wall, such as an animal cell, is immersed in an environment that is isotonic, there will be no net movement of water across the membrane. Water diffuses across the membrane at the same rate in both directions.
What is a hypertonic solution?
If a cell without a cell wall, such as an animal cell, is immersed in an environment that is hypertonic, water diffuses across the membrane from the cell to its outside environment.
What is a solution that is hypotonic?
If a cell without a cell wall, such as an animal cell, is immersed in an environment that is hypotonic, water diffuses across the membrane from the outside environment into the cell.
What happens if you put an animal in a lake with too much salt water?
The environment is hypertonic, and water gushes out of the cells eventually into its environment, causing the animal to shrivel and die.
What is osmoregulation?
The control of solute concentrations and water balance.
Define turgid
Very firm (relation to cell wall)
Opposite of turgid?
Flaccid
Define plasmolysis
As a plant cell shrivels, its plasma membrane pulls away from the cell wall at multiple places (in a hypertonic environment)
What is facilitated diffusion?
Polar molecules and ions impeded by the lipid bilayer of the membrane diffuse passively with the help of transport proteins that span the membrane.
Two type of transport proteins?
Channel and carrier proteins
What are channel proteins that transport ions called? How do they function?
Ion channels; that function as gated channels
If a Paramecium caudatum swims from a hydrotonic environment into an isotonic environment, will its contractile vacuole become more or less active? Why?
It will decreasein activity, since it pumps out water typically. This would only happen in a hydrotonic environment; with less water gushing in, it needs to physically pump out less.
What is the membrane potential?
A voltage across the membrane in active transport
What are the two forces that drive the diffusion of ions across a membrane? What is the combination of these two forces called when acting on an ion?
The chemical force and the electrical force. Combined, when acting on an ion, is called the elctrochemical gradient.
What is the transport protein that generates voltage across a membrane called? What does it transfer?
The electrogenic pump; there is a net transfer of one positive charge from the cytoplasm to the extracellular fluid, a process that stores energy as voltage
What is the main electogenetic pump of plants, fungi and bacteria called? What does it do?
The proton pump, which actively transports protons (hydrogen ions, H+) out of the cell
What is cotransport?
A transport protein (a cotransport) can couple the “downhill” diffusion of the solute to the “uphill” transport of a second substance against its own concentration gradient.
Given the internal environment of a lysosome, what protein would you expect to see in its membrane?
A proton pump, for a lysosome is very acidic and would need to pump out H+ as much as it can via the pump
What is exocytosis?
When a cell secretes certain molecules by the fusion of vesicles with the plasma membrane
What is endocytosis?
When the cell takes in molecules and particulate matter by forming new vesicles from the plasma membrane.
What are ligands?
A term for any molecule that binds specifically to a receptor site on another molecule
What is phagocytosis?
A cell engulfs a particle by extending pseudopodia around it an packaging it within a membranous sac called a food vacuole. the particle will be digested after the food vacuole fuses with a lysosome.
What is pinocytosis?
A cell continually “gulps” droplets of extracellular fluid into tiny vesicles, formed by infoldings of the plasma membrane.
What is receptor-mediated endocytosis?
A specialised type of pinocytosis that enables the cell to acquire bulk quantities of specific substances, even though substances may not be very concentrated in the extracellular fluid.
Difference between channel protein and transport protein?
Channel proteins are the ones that work the with ions (and water), and transporter for larger molecules
When Na+ and Glucose are entering a cell in a cotransporter, what can be said of the concentration gradient?
Glucose goes against the concentration gradient (salt is the concentration gradient, thus salt doesn’t go against its own gradient)
What is a Prokaryotic cell’s DNA called?
Naked DNA
Five functions of the cell membrane?
• Encloses and protects the cell contents • Provides and supports mechanical structure • Transport in and out of the cell • Markers and signalling • Metabolic Activities
What are the three hypothesised models of DNA replication? What is the correct one?
Conservative, semiconservative and dispersive. Semiconservative is right
Where does the replication of chromosomes begin?
Sites called origins of replication
What does Helicase do?
Unwinds and separates the parental DNA strands
What does topoisomerase do?
Breaks, swivels, and rejoins the parental DNA ahead of the replication fork, relieving the strain caused by unwinding
What does Primase do?
Synthesis RNA primers, using the parental DNA as a template
What do single-strand proteins do?
Stabilising the unwound parental strands
What is the initial nucleotide chain (made of RNA) produced during DNA sythesis?
The primer
What enzyme synthesises theprimer?
The enzyme primase
What does DNA polymerase do?
Catalyse the synthesis of new DNA by adding nucleotides to a preexisting chain
How many polymerase in eurkaryotes?
11
What does DNA polymerase 3 do?
Adds a DNA nucleotide to the RNA primer and then continues adding DNA nucleotides, complementary to the parental DNA template strand, to the growing end of the new DNA strand.
Difference between ATP and DNA bases?
The sugar component; deoxyribose in DNA and ribose in ATP
Why is the lagging strand named as such?
Because the synthesis is delayed slightly relative to synthesis of the leading strand; each new fragment of the lagging strand cannot be stated until enough template has been exposed at the replication fork
Segments of the lagging strand are called:
Okazaki fragments
What molecule forms an okazaki fragment?
DNA pol III
What does DNA polymerase I do?
One RNA nucleotides are placed down on the lagging strand in DNA replication, DNA pol I replaced those RNA nucleotides with DNA
What molecule forms a bond between the new DNA strand and the original strand?
DNA Ligase
What does a primase do?
Synthesises an RNA primer at the 5’ end of a leading strand and at the 5’ end of each okazaki fragment of lagging strands
How long did life evolve in the water before spreading onto land?
Three billion years
Which is more electronegative? Oxygen or hydrogran? What is the result? How does this happen?
Oxygen is; thus the electrons of the covalent bond spend more time closer to oxygen via polar covalent bonds
What makes water a polar molecule?
The unequal sharing of electroncs and water’s V-like shape, meaning the overall charge is unevenly distributed.
What are the charges of oxygen and hydrogen in water?
Oxygen has a partial negative charge, while hydrogen has a partial positive one
When water is in its liquid form, how strong are the hydrogen bonds?
Very weak, about 1/20th the strength as a covalent bond
How is water so versatile?
Hydrogen bonds are extremely weak, and jump between oxygen molecules.
What process keeps water together?
Cohesion, hydrogen bonds holding the substance together
What is the clinging of one substance to another?
Adhesion
What is surface tension?
How difficult it is to stretch or break the surface of a liquid
What is kinetic energy?
The energy of motion
What is thermal energy?
The kinetic energy associated with the random movement of atoms or molecules
What is temperature a measure of? What about total thermal energy?
Energy that represents the average kinetic energy of the molecules in the body of matter, regardless of volume, whereas the total thermal energy depends in part on the matter’s volume.
What has more thermal energy; a swimming pool or pot of hot coffee?
The pool, for it contains a much greater volume
What is thermal energy in the transfer from one body to another called?
Heat
What is a calorie a measure of?
The amount of heat required to raise the temperature of 1g of water by 1 Celsius, also the amount it cools by 1 Celsius
What is a kilo-calorie?
The quantity of heat required to raise the temperature of 1kg of water by 1 Celcius
What is specific heat?
The amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1 Celcius.
What is heat of vapourisation?
The quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state.
How does a steam burn work?
These burns are caused by the heat energy released when steam condenses into liquid on the skin
Why is it as liquid evaporates, the surface of the liquid that remains cools down?
Evporative cooling; the fastest, hottest molecules leave first, while the remainder are slower and cool down
What structure is ice?
A crystalline lattice
Why does ice float on water?
It is less dense
When does ice begin to form?
From 4 celcius
Why does ice form?
Water begins to freeze because more and more of its molecules are moving too slowly to break hydrogen bonds. Hydrogen bonds keep the molecules at ‘arms length’, making ice 10% less dense.
What is a solution?
A liquid that is a completely homogenous mixture of two or more substances
What is a solvent?
The dissolving agent of a solution
What is a solute?
A substance dissolved in a solution
What is an aqueous solution?
Is one in which the solute is dissolved in water; water being the solvent.
What is a sphere of water molecules around each dissolved ion called?
A hydration shell
Example of a hydrophilic substance that does not dissolve?
Cotton
Measurement of atom weight?
Dalton
How many daltons in 1g?
6.02 x 10^23
What is Molarity?
The number of moles of solute per litre of solution
Why does humidity suck?
High humidity dampers the evaporation of sweat
What happens when a hydrogren atom leaves a water molecule for another?
It leaves an electron behind (hydrogen ion H+) leaving the once water molecule to be a hydroxide ion.
What is a hydrogen ion H+?
A single proton with a charge of 1+
What is the charge of a hydroxide ion?
1-
What happens when a hydrogen attaches to a water molecule?
It becomes a hydronium ion (h3o+)
What is an acid?
A substance that increases the hydrogen ion concentration of a solution
What is a base?
A substance that reduces the hydrogen ion concentration of a solution
What does [H+] < [OH-] imply?
It’s a base
What does [H+] > [OH-] imply?
It’s an acid
What does [H+] = [OH-] imply?
Neutrality
How many times more acidic is ph 2 to 3?
A thousnad times
Ph of human blood? what is the danger range?
7.4 - under 7 or above 7.8
What is a buffer?
A substance that minimises changes in the concentrations of H+ and OH- in a solution. It does so by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions to the solution when they have been depleted. Most buffer solutions contain a weak acid and its corresponding base, which combine reversibly with hydrogen ions.
Buffers in the blood?
Carbonic acid (H2CO3)
How is carbonic acid formed?
When CO2 reacts with water in blood plasma
What is ocean acidification?
When CO2 dissolves in water and lowers the ph
Equation for number of moles?
N (number of moles) = mass (grams) / molecular weight (Da)
How is concentration expressed?
Sometimes (g/litre), but mostly: mol/L or (M)(molar/molarity)
Equation for concentration?
C (Concentration) = N (number of moles of substance) volume (Litres)
What is log base log10?
The common logarithm of x is the power to which the number 10 must be raised to obtain the value x. For example, the common logarithm of 100 is 2 (i.e., log10 of 100 = 2)
Where does ATP synthase spin? When?
In the membrane during ATP synthesis
When does chemiosmosis occur?
During oxidative phosphorylation, chemiosmosis couples electron transport to ATP synthesis
What is chemiosmosis?
Chemiosmosis is the diffusion of ions across a selectively permeable membrane. More specifically, it relates to the generation of ATP by the movement of hydrogen ions across a membrane during cellular respiration.
What are the four components of ATP synthase?
The rotor, the stator, the rod and the stationary knob
What does the rotor do in ATP synthase?
A rotor within the membrane spins clockwise when H+ flows past it down the H+ gradient
What does the stator do in ATP synthase?
A stator anchored in the membrane holds the knob stationary
What does the rod do in ATP synthase?
A rod (or “Stalk”) extending into the knob also spins, activating catalytic sites in the knob
What does the knob do in ATP synthase?
Three catalytic sites in the stationary knob join inorganic phosphate to ADP to make ATP
What is the DNA cutting enzyme for correcting base paired structures?
Nuclease
What is the DNA repair system called?
Nucleotide excision repair
Protective ends at the end of DNA?
Telomere
Tolemere enzyme?
Tolomerase
What are histones?
Proteins responsible for the first level of DNA packing in chromatin
What histones are used for DNA packing?
Histones 2A, 3 4 and 5
What is euchromatin and heterochromatin?
Euchromatin is not highly condensed, whereas heterochromatin is. Euchromatin is generally accessible for transcription
Where can DNA polymerase join new nucleotides to?
The 3 end of the pre-exsisting strand
What are the stop codons?
UAA, UGA and UAG
Main difference between how DNA and RNA polymerase work?
RNA polymerase can start a chain from scratch - it doesn’t need a primer
What is the DNA sequence that RNA polymerase attaches to?
The promoter
What is the sequence at the end of transcription in bacteria called?
The terminator
What is the transcription unit?
The stretch of DNA downstream from the promoter that is transcribed into an RNA molecule
What is RNA polymerase 2 used for?
Pre-RNA synthesis
Three stages of transcription?
Initiation, elongation and termination
Three stages of transcription
Initiation, elongation and termination
What is upstream and downstream?
downstream refers to the direction of transcription, upstream is the opposite direction
What is the transcription unit?
The stretch of DNA downstream from the promoter
How many RNA polymerase in Bacteria?
1
What are transcription factors?
A collection of protein that mediate the binding of RNA polymerase ad the initiation of transcription
List of transcription for rna in eukaryotes
- Promoter 2. Transcription Factors 3. Polymerase 2 + additional TF
What is the complex called with RNA polymerase and transcription factors?
The transcription initiation complex
What are Adenine and Guanine?
Purines
What are Cytosine and Thymine?
Pyrimidines
What enzyme adds nucleotide bases on to the leading and lagging strands
DNA Polymerase 3
What direction does the leading strand follow?
5’ - 3’
Central Dogma of molecular biology?
DNA -> Transcription mRNA -> Translation -> Polypeptide
Central Dogma of molecular biology in Eukaryote?
DNA -> Transcription mRNA -> Pre-mRNA -> RNA Processing -> mRNA -> Translation -> Polypeptide
What is the non-template strand called?
5” - 3” The Coding Strand
What is the poly-adenylation signal?
AAUAA
What is the 5” cap of mRNA?
A modified form of Guanine (G)
What is a poly-a molecule?
A string of 50-250 nucleotide bases of Adenine
What are the non-coding segments of nucleic acid the lie between coding regions called?
Intervening sequences, or introns
What are the coding segments of nucleic acid the lie between coding regions called?
Extrons
What molecule splices mRNA?
Splicesome
How does a spliceosome work?
Attaches to either end of an intron, the rapidly regrades it
What are ribozymes?
RNA molecules that function as enzymes
What is exon shuffling a process of?
Alternative RNA splicing
What is tRNA?
Transfer tRNA - In the process of translation, a cell ‘reads’ a genetic message ad builds a polypeptide accordingly. The message is a series of codons along an mRNA molecule, and the translator is called tRNA
What are the characteristics of tRNA?
Has a specific nucleotide triplet called an anticodon at one end and a corresponding amino acid at the other
What shape does a tRNA have?
Cloverfield
What enzyme binds tRNA and the amino acid?
Aminoacyl-tRNA synthetases
How many phosphates does Aminoacyl-tRNA use?
2, ATP - AMP
What is the third nucleotide called in the tRNA?
The wobble
What percentage of ribosomes are _ and _?
Proteins (1/3rd) and rRNAs (2/3rds)
What are the three binding sites of RNA?
P, A and E
What is the P site in RNA?
Holds the tRNA carrying the growing polypeptide chain
What is the A site in RNA?
Holds the tRNA carrying the next amino acid to be added to the chain
What is the E site in RNA?
Where discharged tRNA’s leave
What provides energy for translation
GTP (Guanosine triphosphate)
What are initiation factors?
Proteins required to bring all the translation components together
What protein holds protein structure shapes together?
A chaperone protein (chaperonin)
What are polypeptides that are bound for the ER marked with?
Signal peptide
What particle functions a an escort that brings the ribosomes to a receptor protein built into the ER?
Signal-recognition particle (SRP)
What are ribosomes trailing along the mRNA called?
Polyribosomes
What is the mutation of one nucleotide called?
Point mutation
What is a silent mutation?
A change in a nucleotide pair that results in the same amino acid
What is a missense mutation? What effect does it have?
Substitutions that change one amino acid to another. The new amino acid may have properties similar to those of the amino acid it replaces or it may be in a region of the protein where the exact sequence of amino acids is not essential to the protein’s function
What are nonsense mutation?
A point mutation chanfges a codon for an amino acid into a stop codon.
What are frameshift mutations?
Nucleotides downstream from the mutation (removed nucleotide) re improperly grouped. Usually ends in early termination.
True or false: Exons are cut out before mRNA leaves the nucleus
False, introns are cut
What does the anticodon of tRNA bind to? [book question]
The corresponding mRNA codon (not triplet, must be specific)
Can nucleotides be added at both ends of RNA?
Yes
How do amino acids link together to form polymers?
Via peptide bonds
What is a peptide bond?
A covalent bond formed by a dehydration process; the removal of water (in protein)
Difference between a polypeptide and a protein?
The difference between a ball of yarn and a sweater; a protein has many polypeptides precisely twisted, folded and coiled into a molecule of a unique shape.
What are globular proteins?
Circular proteins
Chemical equation for respiration?
C6H12O6 + 6O2 -> 6CO2 + 6H20 + ATP
How much energy produced from each mole of glucose?
686 kcal
What is an enzyme?
A macromolecule that acts as a catalyst, speeding up the reaction without be consumed
What is the difference between a phospholipid and a fat molecule?
The phospholipid has only two fatty acids attached to glycerol rather than three, with the third hydroxyl being attached to a phosphate group
What is a steroid?
A lipid characterized by carbon skeleton consisting of four fused rings
Eight main functions of proteins?
Enzymatic proteins Hormonal proteins Transport proteins Receptor proteins Storage proteins Defensive proteins Contractile and motor proteins Structural proteins
Four types of protein structures?
Primary, secondary and tertiary. Fourth being Quaternary structure, but only in a special condition
When does a Quaternary structure arise?
When a protein consist of two or more polypeptide chains
What is a primary structure of protein?
A simple long chain of amino acids
What is a secondary structure of protein?
Regions stabilized by hydrogen bonds between atoms of the polypeptide backbone of every 4 hydrogen atoms on an a-helix
What is a tertiary structure of protein?
Three-dimensional shape stabilized by interactions between side chains
Label an Animal Cell
1 - Endoplasmic Reticulum
1a - Rough ER
1b - Smooth ER
2 - Flagelium
3 - Centrisome
4 - Cytoskeleton
4a - Microfilaments
4b -
4c - Microtubules
5 - Microvilli
6 - Peroxsome
7 - Mitochondrion
8 - Lysosome
9 - Golgi Apparatus
10 - Ribosomes
11 - Plasma Membrane
12 -Nucleus
12a - Nuclear Envelope
12b - Nuceleolus
12c -Chromatin
What are no found in plant cells?
Lysosomes
Centrioles
Flagella
Difference between Cholesterol and Testosterone?
a) - Transport
b) - Enzymatic activity
c) - Signal transduction
d) - Cell-cell recognition
e) - Intercellular joining
f) - Attachment to ytoskeleton and ECM
1 - Proteoglycan molecule
2 - proteoglycan complex
3 - collagen fiber
4 - fibronectin
5 - integrin
6 - microfilaments of cytoskeleton
7 - plasma membrane
1 - outer membrane
2 - periplasm
3 - cytoplasmic membrane
4 - peptidogylcan
5 - lipoprotein
6 - phospholipid
7 - lipopoly-saccharide
8 - porin
9 - protein
10 - lipid A
11 - core polysaccharide
12 - O-polysaccharide
1 - Bacterial chromosome
2 - pili
3 - nucleotide
4 - ribosomes
5 - plasma membrane
6 - cell wall
7 - capsule
8 - flagella
1 - H+ ions folowing down their gradient enter a channel in a stator, which is anchored in the membrane
2 - H+ ions enter binding sites within a rotor, changing the shape of each subunit so that the rotor spins within the membrane
3 - Each H+ ions makes one complete turn before leaving the rotor and passing through a second channel in the stator into the mitochondrial matrix
4 - Spinning of the rotor causes an internal rod to spin as well. This rod extends like a stalk into the knob below it, which is held stationaty by part of the stator
5 - Turning of the rod activates catalytic sites in the knob that produce ATP from ADP and Pi
Label a plant cell
1a - Chromatin
1b - Nuceleolus
1c - Nuclear envelope
2 - Centrosome
3 - Golgi apparatus
4 - Mitochondrion
5 - Peroxisome
6 - Plasma membrane
7 - Cell wall
8 - Wall of adjacent cell
9 - Plasmodesmata
10 - Chloroplast
11 - Cytoskeleton
11a - Microfilaments
11b - Intermediate filaments
11c - Microtubules
12 - Tonoplast
13 - Central vacuole
14 - Ribosomes
15 - Smooth ER
16 - Rough ER
What shape are A and G in DNA?
Purines
What shape are C, T and U in DNA/RNA?
Pyrimidine
How wide is a double helix?
2nm
Summary of respiration pathways?
Glycolysis (one glucose, two pyruvate and 2 NADH)
Pyruvate oxidation (two acetyl coa and 2 NADH)
Citric Acid Cycle (6NADH + 2FADH2 + 2ATP)
Oxidative Phosphorylation (26-28 ATP)
Synthesis of leading strand steps?
Topoisomerase breaks DNA
Primase syntehsis RNA primers
Helicase unwinds and seperates DNA
Single strang proteins stabilise DNA
After RNA primer is made, DNA pol III starts to synthesis leading strand
Steps involved in synthesis of lagging strand? (7 steps)
- Topoisomerase breaks DNA, Helicase unwinds and seperates DNA, Single strang proteins stabilise DNA
- primase joins RNA nucleotides into a primer
- DNA pol III adds DNA nuceltodies to the primer, forming Okazaki fragment 1
- After reaching the next RNA primer to the right, the DNA pol III detaches
- Fragment 2 is primed. Then DNA pol III adds DNA nucleotides, detaching when it reaches the fragment primer
- DNA pol I repalces the RNA with DNA, adding nucleotides to the 3’ end of fragment 2 (and earlier, fragment 1)
- DNA ligase forms a bond between the newest DNA and the DNA of fragment 1
- The lagging strand in this region is now complete
