chapter 3 Bio

Vocabulary practice flashcards covering cell structure, light and electron microscopy, cell fractionation, eukaryotic organelles, prokaryotic adaptations, tissues and organs, the cell cycle, and viruses.

Magnification

How many times bigger an image appears compared to the real size of the object, calculated using the formula: $\text{magnification} = \frac{\text{size of image}}{\text{size of real object}}$.

Resolution

The minimum distance apart that two objects can be in order for them to appear as separate items; it governs the clarity and precision of the produced image.

What happens when magnification increases

Magnification increases the size of the image but does not always increase the resolution. Every microscope has a limit of resolution. Up to this point magnification will increase showing more detail but beyond this point increasing the magnification will not do this

Cell fractionation

The laboratory process where cells are broken up and their various organelles are separated out for individual study

Why is the tissue place in cold buffered solution before cell fraction?

Cold-reduce enzyme activity that break down organelle

Same water potential as tissue-prevent organelles from bursting or shrinking as result osmotic gain or loss of water

Buffered-pH does not fluctuate, change in pH can alter structure of organelle or affect enzyme function.

Homogenisation

The initial stage of cell fractionation where cells are broken apart in a homogeniser to release organelles into a resultant fluid known as homogenate. Is then filtered to remove large debris or any complete cells.

Ultracentrifugation

The process of separating organelle fragments in a filtered homogenate by spinning them in a centrifuge at successively higher rotational speeds.

For animals what is the process of ultracentrifugation.

• Tube of filtrate is placed in the centrifuge and sun at slow speed.

• Heaviest organelles, the nuclei are forced at the bottom of the tube where they form pellet

• Supernatant is removed, leaving just sediment of the nuclei

• Supernatant is transferred to another tube and spun in the centrifuge at faster speed than before

• The next heaviest organelles, mitochondria are forced to the bottom of the tube

• The process is continued so that they form pellet next heaviest organelle is sedimented and separated out

Supernatant

The fluid remaining at the top of a centrifuge tube after denser organelles have formed a sediment at the bottom.

Pellet

The sediment of heavier organelles deposited at the bottom of a centrifuge tube after spinning at a specific speed.

Advantages of an electron microscope

• The electron beam has short wavelength and the microscope therefore has a high resolving power

• Electrons are negatively charged the beam can be focused using electromagnets

What is a TEM?

Consists of an electron gun that produces a beam of electrons that is focused onto the specimen by a condenser of electromagnets.

• How does a TEM work?

• A beam passes through a thin section of a specimen

• Parts of this specimen absorb electrons and therefore appear dark

• Other parts of the specimen allow electrons to pass through and so appear bright

• An image is produced on a screen and this can be photographed to give photomicrogaph

Resolving power of a TEM is 0.1nm why can this always not be achieved in practice?

• Difficulties preparing the specimen limit the resolution can be achieved

• Higher energy electron beam is required and this might destroy the specimen

What are the main limitations of a TEM?

• The whole system must be in a vacuum and therefore living specimens cannot be observed

• Complex staining processes is required and even then image is not in colour

• The specimen must be extremely thin

• Image may contain artefacts

What is SEM?

Directs beams of electrons on to the surface of the specimen from above rather than penetrating below

How does SEM work?

• Beam is passed back and forth across a portion of the specimen in a regular pattern

• Electrons are scattered by the specimen and therefore appear dark pattern of this scattering depends on the contour of the specimen surface

• You can build up a 3D image by a computer analysis of the pattern of scattered electrons and secondary electrons produced

Difference between a SEM and a TEM?

• In a SEM specimens do not need to extremely thin as electrons do not penetrate compared to TEM

• The basic SEM has a lower resolving power than a TEM around 20nm

• TEM is 2D where as SEM is 3D

Eyepiece graticule

A transparent glass disc with an etched measuring scale (typically 100 sub-divisions) placed in the eyepiece of a microscope to measure specimens.

Why should you leave the eyepiece graticule calibrated?

The eyepiece graticule cannot be directly used to measure the size of objects under a microscope’s objective lens because the objective lens will magnify to a different degree. The graticule must be first calibrated for a particular objective lens. Once calibrated can be remained for future use and saves time recalibrating each time.

Stage micrometer

A calibrated microscope slide with a precise scale (commonly $2\,\text{mm}$ long with divisions of $0.01\,\text{mm}$ or $10\,\mu\text{m}$) used to calibrate an eyepiece graticule.

Eukaryotic cell

A larger, complex cell containing a distinct nucleus surrounded by a nuclear envelope and possessing membrane-bound organelles.

Nucleus

Contains the organism hereditary material and controls cell’s activities usually spherical and between 10 and 20um in diameter

• Acts as control centre through the production of mRNA and tRNA and hence protein synthesis

• Retains the genetic material of the cell in form of DNA and chromosomes

• Manufacture ribosomal RNA and ribosomes

Nuclear envelope

A double membrane surrounding the nucleus whose outer membrane is continuous with the endoplasmic reticulum, controlling entry and exit of substances and contains reactions happening inside the nucleus

Nuclear pores

Openings in the nuclear envelope, typically $40\text{--}100\,\text{nm}$ in diameter (around 3,000 per nucleus), that allow the exit of large molecules such as messenger RNA.

Nucleoplasm

Jelly like material that makes up the bulk of the nucleus

Chromosomes

Consist of protein bound linear DNA

Nucleolus

A dense spherical region within the nucleoplasm responsible for manufacturing ribosomal RNA ($\text{rRNA}$) and assembling ribosomes.(there can be more than one)

Mitochondrion

• Double membrane that controls the entry and exit of material

• Cristae extensions of the inner membrane where species extend across the whole width of the mitochondrion

• Matrix remainder of the mitochondrion containing proteins lipids ribosomes and DNA that allows the mitochondria to control the production of some of their own proteins

Cristae

Infoldings of the inner mitochondrial membrane that provide a large surface area for proteins and enzymes involved in aerobic respiration.

Why is the mitochondria responsible for-the production of ATP

Mitochondria is the site of aerobic respiration therefore responsible for the production of the energy carrier molecule ATP from respiratory substrate such as glucose. Because of this the size of mitochondria and the number of their cristae are high in cells that have a high metabolic activity and therefore require plentiful supply of ATP.

Chloroplast

The organelle that carries out photosynthesis 1um in diameter

Chloroplast envelope

Double plasma membrane that surrounds the organelle, highly selective in what it allows to enter and leave the chloroplast

Grana

Stacks of 100 disc like structures called thylakoids. Within the thylakoids there is photosynthetic pigment called chlorophyll, the grana are where the first stage of photosynthesis takes place

Stroma

Fluid filled matrix where the second stage of photosynthesis takes place with in the stroma their are a number of other structures

How do chloroplasts adapt to their function of harvesting sunlight and carrying out photosynthesis?

• The granal membranes provide a large surface area for the attachment of chlorophyll electron carriers and enzymes that carry out the first stage of photosynthesis. The chemicals are attached to the membrane in highly ordered fashion.

• Fluid from the stroma possesses all the enzymes needed to make sugars in the second stage of photosynthesis

• Chloroplasts contain both DNA and ribosomes they can quickly and easily manufacture some proteins needed for photosynthesis

Tonoplast

The single membrane bounding the fluid-filled central vacuole of a plant cell.

Chitin

A nitrogen-containing polysaccharide that forms the structural cell wall of fungi, alongside glycan and glycoproteins.

Tissue

An aggregation of similar specialised cells coordinated together to perform a specific, focused physiological function.

Organ

A combination of distinct tissues aggregated and coordinated to carry out a major physiological function within an organism.

digestive system

digests and process food made up of organs including salivary glands oesophagus, stomach duodenum, ileum, pancreas and liver

Organ system

A collection of organs working cooperatively as a single unit to execute complex, large-scale body functions efficiently.

Prokaryotic cell

A cell type spanning $0.1\text{--}10\,\mu\text{m}$ that lacks a membrane-bound nucleus and true membrane-bound organelles.

Murein

A rigid polymer of polysaccharides and peptides (peptidoglycan) that forms the bacterial cell wall.

Plasmids

Small, autonomous, circular loops of DNA found in bacteria that replicate independently and may carry genes for antibiotic resistance.

Capsule

A mucilaginous protective layer secreted outside the cell wall of some bacteria that prevents desiccation and provides protection against host defenses.

Interphase

The non-dividing stage occupying the majority of the cell cycle during which cell growth and DNA replication occur.

Cytokinesis

The concluding physical division of the cytoplasm into two daughter cells following nuclear division.

Tumour

An expanding group of abnormal cells caused by uncontrolled cell division and mitosis due to damage in regulatory genes.

Viruses

Acellular, non-living infectious particles ranging from $20\text{--}300\,\text{nm}$ that contain nucleic acid cores and only reproduce inside host cells.

Capsid

The outer protective protein coat enclosing the genetic material (DNA or RNA) of a virus.

Attachment proteins

Surface molecules situated on a virus's capsid or lipid envelope that permit specific binding to host cell surface receptors.