Bio - Topic 2 - Cells

Definition of cell

The smallest unit of life

The theory of ‘spontaneous generation’

People used to believe that living organisms could spontaneously appear from non-living matter

Cell theory

All living things are made of individual units, cells, which are the basic units of life, and that all cells arise from other cells.

Features of Prokaryotic Cells

• cell wall

• plasma membrane

• cytoplasm

• naked DNA in a loop

• 70S ribosomes.

• plasmid

• Many also contain flagellum, or pili.

• Gram-positive eubacteria possess a thick peptidoglycan cell wall and lack a capsule-enclosed outer membrane

Features of Eukaryotic Cells

• Nucleus with chromosomes made of dna bound to histones contained in a double membrane with pores

• a plasma membrane enclosing a compartmentalized cytoplasm with 80S ribosomes

• membrane-bound cytoplasmic organelles including mitochondria, endoplasmic reticulum, Golgi apparatus, vesicles, vacuoles, and lysosomes

• cytoskeleton of microtubules and microfilaments.

Features of both Prokaryotic Cells and Eukaryotic Cells

Both have DNA as genetic material.

Both have ribosomes to make proteins.

Both are filled with cytoplasm (jelly fluid).

Both have an outer cell membrane

Animalia cells

Multicellular eukaryotes without a cell wall. Animals are holozoic (eat other organisms with internal digestion of nutrients). The animal kingdom is the largest known kingdom with 1 million known species.

Fungus

Fungi are eukaryotes with a cell wall made with a molecule called chitin. Can be unicellular (eg. yeast) or multicellular (mushrooms)

Light microscopes

microscopes that pass light through a specimen and then use lenses to magnify the image produced

Electron microscope

Electron microscopes pass a beam of electrons through a specimen. Electrons will be absorbed by the denser parts of the sample, and scattered or able to pass through less dense areas, after which they are picked up by an electron detector and used to form an image.

How much can electron microscopes magnify very small objects

electron microscopes can magnify very small objects by about 500 000 times

Freeze fracture microscopy

Freezing a sample and then using a specialised tool to break the sample into small pieces which are then observed using an electron microscope to see the internal structure. This is a particularly useful technique for being able to visualise structures that are not normally visible, such as the internal plasma membrane.

Cryogenic electron microscopy

involves freezing a sample to cryogenic temperatures to fix the molecules, making them more firm or stable. The specimen is then viewed using electron microscopy. Freezing the sample improves the resolution of the image formed and reduces damage that may occur from the electron beam.

Immunofluorescence

Immunofluorescence is a laboratory technique that uses antibodies tagged with fluorescent dyes to detect and visualize specific proteins or other target molecules within cells or tissues under a fluorescence microscope.

Fluorescent dyes

Fluorescent dyes can be used in light microscopy. When the dye is added to the sample it will preferentially attach to certain structures. As in immunofluorescence, the labelled areas will appear as brightly coloured spots, allowing visualisation of the target molecule throughout the specimen.

Resolution of a microscope

Resolution is the shortest distance between two separate points in a microscope’s field of view that can still be distinguished as separate objects. The higher the resolution, the smaller this distance is and the clearer the image produced. Remember that a resolution of 0.1 nm is higher than a resolution of 200 nm. The lower the value, the higher the resolution.

True or False: Viruses can be viewed using a light microscope.

False

Prokaryotic - cell wall

Found outside the cell membrane. It has an important role in protecting the prokaryotic cell against toxins that may be in the external environment, resisting high osmotic pressures and maintaining the shape of the cell.

Prokaryotic - Plasma membrane

The plasma membrane separates the cell’s interior from its external environment and controls what can enter and exit the cell.

Cytoplasm

The cytoplasm is a water-based jelly-like fluid that fills the cell, suspends ions, organic molecules, DNA and ribosomes, and is the site of metabolic reactions.

Prokaryotic - Naked DNA in a loop:

DNA stores the information necessary for synthesising proteins. In prokaryotes, the DNA is naked, which means that it is not associated with histone proteins (as it is in eukaryotic cells) and is mostly found in a region called the nucleoid. However, recent studies have identified hundreds of candidate histone-like proteins in various bacterial species.

Prokaryotic - 70S ribosomes

Where translation (protein synthesis) occurs. Prokaryotic ribosomes are smaller and lower mass than eukaryotic ribosomes.

Prokaryotic - Plasmid

Small, circular pieces of DNA that can be transferred from one prokaryotic cell to another. This is known as horizontal gene transfer (in contrast to the vertical gene transfer that occurs from reproduction).

Prokaryotic - capsule

An outer layer of polysaccharides that protect the organism and allow it to adhere to surfaces.

Prokaryotic - Flagella

Some prokaryotic cells have a flagellum. The flagellum is responsible for the locomotion of the organism, spinning to propel the cell through its medium.

Prokaryotic - Pili

Some prokaryotic cells contain pili on their surface (singular: pilus). Pili are protein filaments on the cell wall that help in cell adhesion and in transferring of DNA between two cells.

Compartmentalisation

• The formation of membrane-bound regions (organelles) within a eukaryotic cell that isolate specific chemical reactions and allows for the interior of the organelles to have separate conditions to the cytoplasm of the cell.

Advantages of compartmentalization

The ability to create higher concentrations of certain substances within organelles

The ability to separate toxins and potentially damaging substances from the rest of the cell. For example, hydrolytic enzymes can be stored in structures called lysosomes, away from the cell cytoplasm

Control over conditions inside organelles (such as pH) to maintain the optimal conditions for the enzymes that function in those parts of the cell (see section C1.1.8).

Eukaryotic - Mitochondria

Double-membrane-bound organelles that convert glucose (ADP) into ATP (the cell’s energy currency) in the process of respiration.

Eukaryotic - 80S ribosomes

Where translation (protein synthesis) occurs. Both attached and free-floating eukaryotic ribosomes are larger and have a higher mass than prokaryotic ribosomes.

Eukaryotic - Nucleus

• stores the DNA which is associated with histone proteins and is organised into chromosomes.

• The nucleus contains the nucleolus, which is involved in the production of ribosomes.

• via gene expression the nucleus coordinates the cells activites, including growth, metabolism, protein synthesis, and division

eukaryotic - Smooth endoplasmic reticulum

Produces and stores lipids, including steroids.

eukaryotic - Rough endoplasmic reticulum

• part of endomembrane system which is a system of interconnected membranes which form a series of flattened sacs and tubes that work together to modify, process, and ship molecules within and out of the cell

• Has ribosomes attached to its surface which synthesise proteins that are sent to the golgi apparatus.

• Inside of the tubes - lumen

eukaryotic - Golgi apparatus

• part of endomembrane system which is a system of interconnected membranes which form a series of flattened sacs and tubes that work together to modify, process, and ship molecules within and out of the cell

• composed of flattened membrane sacs called cisternae

• Processes and packages proteins synthesized by ribosomes which enter in the cis face, which are then released in Golgi vesicles from the trans face

• proteins are transported to:

  • lysosomes or vacuoles for digestive enzymes

  • plasma membrane

  • cell exterior

Prokaryotic - Vesicle

Small sac that transports and releases substances produced within the cell by fusing with the cell membrane.

Eukaryotic - Vacuole

Helps to maintain the osmotic balance of the cell. It may also be used to store substances and sometimes has hydrolytic functions similar to lysosomes.

Prokaryotic - Cytoskeleton

A system of protein fibres called microtubules and microfilaments. The cytoskeleton helps to hold organelles in place and maintain the structure and shape of the cell.

Steps in using an eyepiece graticule

Insert the eyepiece graticule into the eyepiece and view a stage micrometer under the microscope.

Align the graticule scale with the stage micrometer scale.

Calibrate by counting how many graticule units line up with a known stage micrometer distance, for the objective lens being used (since magnification changes the scale value).

Remove the stage micrometer and replace it with the actual specimen slide.

Measure the specimen by counting how many graticule units it spans.

Convert graticule units to actual size using the calibration value calculated for that objective lens.

How to draw a diagram with a scale bar

Measure the actual size of the specimen (or the field of view) using a calibrated eyepiece graticule.

Decide on a convenient round-number length for the scale bar (e.g., represents 100 µm or 1 mm).

Calculate the length of the scale bar as it should appear on your sketch, based on the magnification of your drawing relative to the actual specimen size.

Draw a straight line of that calculated length next to your sketch.

Label the scale bar clearly with the actual length it represents (e.g., "100 µm").

State the magnification of the drawing if required, alongside the scale bar.

Lable: eg. Figure 1. Tetrahymena thermophilia viewed with a light microscope at 400x magnification.

All cells contain:

Semipermeable membrane made of lipids. Cytoplasm primarily made of water. Genetic material for building polypeptides and ribosomes to assemble them (polypeptides fold into complex 3-dimensional structures to form functional proteins)

ATP stands for

Adenosine Triphosphate

Compartmentalization in cells definition

Organization of different functions and processes within specific areas/structures within the cell that are separated by plasma membranes to enable specialized functions and efficient metabolic reactions.

Which cell components are not included as organelles

Cell wall, cytoskeleton and cytoplasm are not considered organelles because they are either not membrane bound or perform a specific function

Eukaryotic DNA

Super coiled DNA because the strands are wrapped around histone protein molecules. Linear DNA (chromosomes) inside the nucleus.

Prokaryotic DNA

Naked: not associated with histone proteins. Circular DNA + plasmids. DNA is not contained in a nucleus but found in the nucleoid.

Membranes:

Surround cells + organelles, controlling the exchange of material between the internal+ external enviornment.

Membranes are composed of:

Lipids, proteins, and carbohydrates. Lipids: eg. phospholipids, glycolipids, and sterols (eg. cholesterol). Small amount of carbohydrates in the form of glycolipids + glycoproteins. The lipids and some proteins are amphipathic molecules (both hydrophobic (non-polar) and hydrophilic (polar) regions).

Lipid bilayer on cell membrane

Includes: phospholipids (backbone and mostly glycerol (3 carbon alcohol). attatched to backbone are negatively charged phosphate molecule linked to molecules like choline or serine forming a polar (hydrophilic) ‘head’ group which forms hydrogen bonds with water. 2 non-polar fatty acid chains forming hydrophobic tails (could be saturate or unsaturated, unsaturated leads to kinks in the tail). Also includes glycolipids + sterols. Phospholipids arrange themselves so hydrophobic tails are shielded from water (tails point inwards while heads point outwards)

Organelles

Subunits of cells that perform specific functions.

Compartmentalization - plasma membrane

A thin, selectively permeable layer of phospholipid and protein molecules that surround the cell. It works as a boundary and regulates the passage of molecules and ions throughout the cell.

Membrane bound organelles are only found in:

eukaryotic cells

Benefits of compartmentalization in cells

Cell can separate chemical reactions and other cellular processes, which allows cells to increase the rate of chemical reactions.

How does compartmentalization benefit lysosomes

Lysosomes are a vesicle containing hydrolytic (digestive) enzymes used for intracellular digestion. They break down and recycle waste materials within the cell. The enzymes are more efficient as the structures are small, therefor there is a higher enzyme concentration. Without compartmentalization, the hydrolytic enzymes would digest and destroy the cell's own proteins, membranes, and organelles if they were released freely into the cytoplasm.

what parts of eukaryotic cells are not organelles

Cytoskeleton, cell wall, and cytoplasm.

Transcription and translation in the nucleus

• Nucleus regulates genes through the transcription of DNA into mRNA

• Cytoplasm is responsible for translation of mRNA into proteins on the ribosomes.

• Both transcription and translation occur in cytoplasm.

Post-transcriptional modification

mRNA needs to be changed by removing pieces of mRNA, it occurs before translation in the nucleus and it is not possible in prokaryotes because they lack a nucleus. A working protein can only be made after this is done.

How does compartmentalization allow cytoplasm to send signals to the nucleus

Cytoplasm receives an extracellular signal (eg. hormone) and passes it to the nucleus to change gene expression through increased/ decreased transcription. Altering gene expression allows the cell to adjust to produce different amounts or types of proteins to adjust to different conditions.

8 process that all living things cary out

Metabolism, response to stimuli, homeostasis, movement, growth, reproduction, excretion, nutrition. HM MR GREN

Metabolism

Chemical reactions that take place within the cell(s) of an organism

Homeostasis

Maintaining constant internal conditions

Growth

Increase in cell size or # of cells over a period of time

Reproduction

Production of offspring - sexual or asexual

Excretion

Removal of metabolic waste products

Nutrition

Intake or production of nutrients. Heterotrophic organisms obtain their nutrients from their external environment. Autotrophic produce nutrients from inorganic material

Animal cells - centrioles

2 cylindrical organelles that help establish and organize the microtubules and play an important role in cell division

Animal cells - Lysosomes

Membrane-bound bags of hydrolytic enzymes that break down and destroy biological molecules and old cellular components

Fungal cell - cell wall

Made of polysaccharide: chitin

Fungal cell - vacuole

Large vacuole that degrades molecules in the cell and also acts as a storage site for small molecules such as ions

Fungal cells - centrioles

Responsible for producing and organizing the cytoskeleton and also important in cell division. however not present in most fungi and the main function is to produce cilia during interphase and the aster and the spindle during cell divison.

parts of a fungal cell

Cell membrane, centrioles, SER, RER, nucleus, ribosomes, bud, cytoskeleton cytoplasm, mitochondrion, vesicle, cell wall

Discrepancies in cells

Red blood cell (no nucleus, has hemoglobin), aseptate fungal hyphae (many nuclei), skeletal muscle fiber (many nuclei), phloem sieve tube element (no nucleus)

cells with no nucleus

red blood cell, phloem sieve tube element

cells with many nuclei

aseptate fungal hyphae, skeletal muscle fiber

Mitochondria contains how many membranes?

2 - inner and outer

Mitochondria - outer membrane

• permeable to many small molecules and ions

Mitochondria - inner membrane

• highly folded → forming structures called cristae

• increases the surface area → more enzymes needed for ATP can be present

• increases the efficiency and speed of cell respiration by increasing the # of enzymes available for various reactions

mitochondria - matrix

• cristae creates an enclosed space between the inner membrane - the matrix

• contains many enzymes and other molecules in high concentration needed for the krebs cycle

Mitochondria - intermembrane space

• space between inner and outer membrane

• relative small → high concentration of molecules can accumulate

• creates a concentration gradient across the inner membrane required for ATP synthesis

chloroplast contains how many membranes?

3 → outer membrane, inner membrane, and thylakoid membranes

chloroplast contains how many spaces?

3 spaces → intermembrane space, the stroma, and thylakoid lumen

chloroplast - thylakoid membrane

• forms thylakoids → look like stacked pancakes

• where the light dependent reactions of photosynthesis take place

• thylakoid membrane has chlorophyll to absorb light energy and generate ATP to power photosynthesis

• disk like structure maximizes surface area and increases the amount of chlorophyll + other enzymes → faster rate of photosynthesis

chloroplast - granum (plural grana)

• stack like structure formed of thylakoids

• connected by thylakoid membranes called lamellae which creates a continuous thylakoid space

chloroplast - thylakoid space

• separated from the stroma by thylakoid membranes

• small space which allows chloroplasts to generate a high concentration gradient

• seperates potentially damaging chemicals from the rest of the chloroplast

chloroplast - stroma

• space between inner and thylakoid membranes

• contains all enzymes and substrates required for the remaining steps of photosynthesis → calvin cycle, which creates glucose molecules

How many nuclear membranes

2 - inner + outer

nuclear membrane

• Double membrane → barrier between genetic material inside nucleus + rest of cell

• breaks down into vesicles during mitosis and miosis and then reforms

• nuclear pores of the create a selective passageway through which molecules are able to travel between the nucleus and the cytoplasm

nuclear membrane - outer

• has ribosomes attached and is continuous/joined with RER

nuclear membrane - inner

• assists in regulating gene expression → controls entry + exit of signaling molecules + transcription factors

nuclear membrane - nuclear pores

• nuclear pores are integral proteins that serve as channel proteins that also regulate mRNA leaving the nucleus for the rough endoplasmic reticulum or free ribosomes.

nuclear membranes - nuclear envelope in cell division

• The nuclear envelope breaks down to allow for the separation of chromosomes

• After mitosis and meiosis is complete, the nuclear membranes must reassemble to enclose the newly formed nuclei

• This process is initiated by the formation of small membrane-bound vesicles from the ER → contain proteins and lipids that are specific to the nuclear membrane and initially bind to the chromosome

• The vesicles join together surrounding the chromosomes and fuse together to form the double membrane of the nucleus with the chromosomes inside

formation of embryo

zygote (totipotent)→ morula → blastocyst (pluripotent) → embryo

zygote

• the first single cell formed when a female egg and a male sperm join together during fertilization

• totipotent -

morula

• a solid ball of 16 to 32 cells that forms from a fertilized egg about 4 days after fertilization

• appears like a mulberry fruit

blastocyst

• a ball of 100 to 200 cells that forms about five to six days after a sperm fertilizes an egg

• contains the outer layer of cells called the trophoblast, and the inner cell mass (ICM)

• ICM has pluripotent stem cells

• trophoblast will eventually develop into the placenta, whereas the ICM will become the embryo

embryo

• the early developmental stage of a multicellular organism, lasting from fertilization until it becomes a fetus or hatches

Morphogen gradients

• Mechanism: A signaling center secretes morphogens that diffuse outwards, creating a high-to-low concentration gradient.

• Impact: Embryonic stem cells detect their local morphogen concentration. Different concentration thresholds act as switches—activating or silencing specific genes to dictate the cell's developmental fate

cell differentiation

• The process by which unspecialized cells (like stem cells) become specialized in structure and function to perform specific tasks within a multicellular organism.

Stem cell potency - totipotent

• Can differentiate into any type of cell including placental cells.

• Can give rise to a complete organism.

• totipotent stem cells

• cells in early-stage animal embryos are totipotent but soon become pluripotent,

• morula is totipotent but then organizes to become blastocyst and becomes pluripotent

Stem cell potency - pluripotent

• Can differentiate into all body cells, but cannot give rise to a whole organism.

• e.g. embryonic stem cells of the blastocyst

Stem cell potency - multipotent

• Can differentiate into a few closely related types of body cell.

• e.g. hematopoietic stem cells found in bone marrow are multipotent: red blood cell, white blood cell, or platelets