Biology - Chapter 3: Cell Structure

Magnification formula

Magnification = image size / real size

Why is the tissue put in a cold, buffered solution of same water potential as tissue?

Cold: reduces enzyme activity so they don't break down the tissue
Buffered: so enzymes and proteins don't denature
Same water potential: so water does not move into/out of organelles by osmosis (no net movement of water) and make the organelles shrink/burst.

Order of organelles removed in cell fractionation

Naughty Cheeky Monkeys Like Eating Red Raspberries -
Nuclei, Chloroplasts, Mitochondria, Lysosomes, Endoplasmic Reticulum, Ribosomes

3 Main limitations of SEM

1. Whole system must be in vacuum so can't use living specimens
2. Complex 'staining' process needed though results aren't in colour.
3. Image may contain artefacts - things left from when specimen was prepared, so may not be sure if what's on photomicrograph is actually on specimen.

Eukaryotic cells

Cells that have a distinct nucleus and possess membrane-bound organelles

Mitochondria function

the site of aerobic respiration - responsible for production of ATP

What are ribosomes made of

Two subunits (one large one small), with ribosomal RNA and protein

2 types of ribosomes

80S - in eukaryotic cells
70S - in prokaryotic cells

What are cell walls of fungi made of?

A mixture of:
- chitin: nitrogen-containing polysaccharide
- glycan
- glycoproteins

Organ systems

A group of organs that work together to perform a particular function

6 features of bacterial cells (prokaryotic)

1. Cell wall: made of murein (glycoprotein), excludes certain substances + protects against mechanical damage and osmotic lysis
2. Slime capsule: protects it from other cells + helps them group together for further protection
3. Cell-surface membrane: controls what can enter/exit the cell
4. Circular strand of DNA: contains its genetic information (not associated with proteins)
5. Plasmids: small rings of DNA, helps it in extreme cases
6. Flagella: tail-like structure, helps with movement

How do viruses replicate? (3)

1. Attach to host cell with attachment proteins
2. Inject nucleic acid into host cell - instructions for host cell
3. Host cell's metabolic processes start producing viral components, nucleic acid, enzymes and structural proteins - assembled into new viruses

How to calculate mitotic index?

Number of cells with visible chromosomes / total number of cells (x 100 if want percentage)

Cancer

A group of diseases caused by a growth disorder of cells (as a result of damage to the genes that regulate mitosis and the cell cycle)

3 reasons why cells divide by mitosis

1. Growth (increase in the number of cells and so size of tissues)
2. Repair tissues/organs (replace dead/worn-out cells)
3. Asexual reproduction

What cell structures are present in both prokaryotic and eukaryotic cells? (4)

1. Cell surface membrane
2. Ribosomes
3. Cytoplasm
4. DNA

2 types of microscope

light (uses beams of light) and electron (uses beams of electrons)

Which microscope is better and why?

Electron microscope - higher resolution and magnification as beams of electrons have shorter wavelengths than light, can see internal structure of organelles

Resolution

The minimum distance apart that two objects can be in order for them to be seen separately

Cell fractionation

The process where cells are broken up and the different organelles they contain are separated out.

Cell fractionation steps (4)

1. Tissues put in cold, buffered solution of same water potential
2. Homogenation: cells put in homogeniser, releases organelles from cell in fluid (homogenate).
3. Filtration: homogenate filtered to remove complete cells + large pieces of debris
4. Ultracentrifugation: tube of filtrate placed in centrifuge, spun in slow speed. Then nucleui are forced to bottom of test tube and spun at very high speed - form sediment, supernatant removed and transferred to another tube. Supernatant is transferred and spun in faster speed, process continues so at each higher speed, next heaviest organelle is sedimented and separated.

Two types of electron microscope

Transmission Electron Microscope (TEM) and Scanning Electron Microscope (SEM)

How does a TEM work?

- Electron gun, produces beam of electrons focused onto specimen by electromagnet, passing through thin section
- Dark areas: DENSE, absorbed electrons / Bright areas: electrons passed through
- Photomicrograph: photograph taken of image produced

2 reasons why resolving power of electron microscopes may not be achieved

1. Difficulties when preparing specimen
2. Higher energy electron beams needed may destroy specimen

4 Main limitations of TEM

1. Specimen must be extremely thin so electrons can penetrate - need to take series of sections to build up 3d images, long and time consuming
2. Whole system must be in vacuum so can't use living specimens
3. Complex 'staining' process needed though results aren't in colour.
4. Image may contain artefacts - things left from when specimen was prepared, so may not be sure if what's on photomicrograph is actually on specimen.

How does a SEM work?

- Directs beam of electrons onto specimen surface from above, passed back and forth across a portion of specimen in a regular pattern
- Electrons scattered; pattern of this depends on contours of specimen surface, can be used to build up 3d image with computer analysis

SEM vs TEM

1. How it works
2. TEM: 2D images, SEM: 3D images
3. SEM has lower resolution

5 features of the nucleus

1. Nuclear envelope: double membrane that surrounds the nucleus; controls entry and exit of materials into and out of nucleus + contains reactions occurring within in
2. Nucleolus: small spherical region that manufactures ribosomal RNA and assembles the ribosomes
3. Nucleoplasm: granular, jelly-like material
4. Chromosomes: made up of protein-bound, linear DNA
5. Nuclear pores: small holes on surface that allow the passage of large molecules out of the nucleus

3 features of mitochondria

1. Double membrane: controls entry and exit of materials into and out of mitochondria
2. Cristae: extensions of inner membrane that increase surface area so enzymes and other proteins can attach in order to carry out aerobic respiration - also the site of oxidative phosphorylation
3: Matrix: proteins, lipids, ribosomes and DNA that allow mitochondria to control production of their proteins + are also involved in respiration

3 features of chloroplasts

1. Chloroplast envelope: double-membrane, controls entry and exit of materials
2. Grana: stacks of thylakoids, provides large SA for attachment of chlorophyll (in thylakoids), electron carriers and enzymes in highly ordered fashion so first stage of photosynthesis can take place
3. Stroma: possesses all enzymes needed to make sugars so second stage of photosynthesis can take place - may contain other structures e.g. starch grains
4. Contains both DNA and ribosomes: can quickly and easily manufacture proteins needed for photosynthesis (DNA is shorter, circular and not associated with histones)

3 functions of the nucleus

1. act as control centre of the cell through production of mRNA and tRNA (so protein synthesis)
2. retain genetic material of cell (DNA, chromosomes)
3. make ribosomal RNA and ribosomes

Rough Endoplasmic Reticulum

- System of membranes that has ribosomes present on outer surface of membranes
- Provides large surface area for synthesis of proteins + glycoproteins
- Provides pathway for the transport of materials (esp proteins) throughout the cell

Smooth Endoplasmic Reticulum

- System of membranes that is more tubular, lacks ribosomes on its surface
- Synthesises, stores and transports lipids and carbohydrates

Golgi apparatus (4)

- Cisternae: has vesicles
- Proteins and lipids made by ER pass through it
- Golgi modifies them by adding non-protein groups + labels them to be sorted and sent to correct destinations
- Transported via vesicles

4 functions of Golgi apparatus

1. Stores and modifies lipids and proteins (adds carbohydrates to proteins to form glycoproteins)
2. Produces carbohydrates and secretory enzymes
3. Forms vesicles to transport proteins and triglycerides
4. Forms lysosomes

Lysosomes

Organelle that forms when vesicles from Golgi apparatus contain enzymes (proteases, lipases, lysozymes)

Lysozymes

enzymes that hydrolyse the cell walls of certain bacteria

4 functions of lysosomes

1. Fuse with vesicles, then hydrolyse material ingested by phagocytic cells
2. Release hydrolytic enzymes to outside of cell in order to destroy material around it
3. Digest worn out organelles so useful chemicals they are made of can be re-used
4. Completely break down cells that have died

2 features of cell walls

1. Made up of a number of polysaccharides e.g. cellulose (make up microfibrils)
2. Middle lamella: thin layer, marks boundary between adjacent cell walls + cements them together

3 functions of cell wall

1. Provide mechanical strength to prevent cell bursting due to pressure caused by water entering via osmosis
2. Provide mechanical strength to the plant as a whole
3. Allow water to pass along it - contribute to movement of water through plant - transpiration stream

What are cell walls of algae made of?

Cellulose, glycoprotein or mixture of both

Vacuoles

Fluid-filled sac bounded by a single membrane - the tonoplast. Contains solution of: mineral salts, sugars, amino acids, wastes and pigments

3 functions of vacuoles

1. Make cells turgid to support herbaceous plants and parts of woody plants
2. Act as a temporary food store due to sugars and amino acids
3. Attract pollinating insects due to pigments that colour petals

After completing homogenisation and filtration during cell fractionation, how do you separate the chloroplasts / mitochondria (for animal cells) from the nuclei?

Spin at lower speed to separate nuclei
Spin again at a higher speed to separate chloroplasts / mitochondria - they are less dense so lighter than nuclei

Specialisation

the process where a cell develops its own individual characteristics that suit its function, which it will perform when it is mature

Order of organisation

Cells -> Tissues -> Organs -> Organ systems

Tissue

A collection of similar cells that perform a specific function

Organs

A group of tissues that work together to perform a variety of functions, although the often have one predominant major function

Prokaryotic cells

Cells that have no nucleus or membrane-bound organelles

Prokaryotes vs Eukaryotes (9)

P vs E:
- no nucleus vs nucleus
- no membrane-bound organelles
- smaller
- divide by binary fission vs mitosis/meiosis
- DNA is circular + not associated with proteins vs linear + associated with histones
- smaller ribosomes (70S vs 80S)
- Murein cell wall vs Cellulose cell wall (plant cells)
- No chloroplasts (only chlorophyll) vs chloroplasts
- Slime capsule, flagella, plasmids vs none

Viruses

Acellular, non-living particles - smaller than bacteria

6 features of viruses

1. Attachment proteins: allow virus to identify and attach to a host cell
2. Genetic material (DNA/RNA): used to multiply but can only occur in host cells
3. Capsid: a protein coat that protects the genetic material from the environment
4. Lipid envelope
5. Matrix
6. Reverse transcriptase

Mitosis

The part of the cell cycle in which a eukaryotic cell divides to produce two daughter cells, each with the identical copies of DNA produced by the parent cell during DNA replication.

5 stages of mitosis

1. Interphase: Cell grows, prepares for division by replicating DNA, chromosomes invisible
2. Prophase: Chromosomes visible, then condense (shorten and thicken) and become 2 chromatids (pairs) joined at centromere, nuclear envelope and nucleolus disappear, spindle apparatus (centrioles in animal cells) form at poles
3. Metaphase: Spindle fibres form and attach to chromatids at centromere, chromatids line up on centre (equator) of cell
4. Anaphase: Spindle fibres contract, centromeres divide in 2, identical chromatids pulled to opposite poles of cell
5. Telophase: chromosome reach poles and become indistinct (longer and thinner) to leave chromatin, nuclear envelope and nucleolus reform, spindle disintegrates. Cytoplasm divides in cytokinesis to produce two daughter cells.

4 stages of binary fission

1. Circular DNA molecule replicates, both copies attach to cell membrane.
2. Plasmids replicate.
3. Cell membrane grows between the two DNA molecules and pinches inward to divide cytoplasm into 2
4. New cell wall forms between two DNA molecules, dividing cell into two daughter cells

Mitotic index

The percentage of cells undergoing mitosis

3 phases of cell cycle:

1. Interphase (most of cell cycle, no division, DNA replicates)
2. Nuclear division (mitosis/meiosis)
3. Cytokinesis (division of the cytoplasm - produces 2/4 new cells)

2 factors that affect the rate of mitosis

1. The cell's environment
2. Its growth factors

How does chemotherapy work? (3)

The drugs prevent DNA from replicating
The drugs inhibit the metaphase stage of mitosis by interfering with spindle formation
This stops the growth of the cancer cells

What is a problem with chemotherapy?

The drugs work best with rapidly-dividing cells - they also affect normal cells that divide rapidly e.g. hair-producing cells

Why are chromosomes visible and randomly arranged during prophase?

Visible - still condensing (becoming shorter and thicker)
Randomly arranged - no spindle / spindle fibres to attach to

Outline the role of organelles in the production, transport and release of proteins (eukaryotic cells) (6)

1. DNA in nucleus codes for protein
2. Ribosomes and RER produce protein in protein synthesis
3. Mitochondria carries out aerobic respiration, produces ATP to release energy for protein synthesis
4. Golgi apparatus modify proteins + add carbohydrates to form glycoproteins
5. Vessicles / RER transport the protein
6. Vessicles fuse with cell-surface membrane

Malignant vs Benign tumours

Malignant: grow rapidly, less compact (spread across body), more likely to be life-threatening
Benign: grow slower, more compact (in one location), less likely to be life-threatening

When carrying out the microscopy practical, why do you only use the first 5mm from the tip of an onion root?

- Where dividing cells are found
- To get soft tissue that will squash
- Length that will fit under cover slip

When carrying out the microscopy practical, why do you need to press down firmly on the cover slip?

Squash tissue, form single/thin layer of cells/tissue so light passes through them, making the cells visible

Microscopy practical (9)

1. Heat 1 moldm-3 HCl at 60 degrees in a water bath
2. Cut 5mm of root tip with a scalpel
3. Transfer to HCl and incubate for 5 mins
4. Remove from HCl, wash sample with cold, distilled water and remove the very tip with a scalpel
5. Place tip on a microscope slide and add a few drops of toluidine blue stain
6. Use a mounted needle to break up the tissue, and spread the cells of the root tip out onto the slide
7. Lower coverslip down carefully onto slide - make sure there are no air bubbles
8. Use lowest objective lens, focus with coarse and fine focussing knob until image is clear
9. Calculate mitotic index

When carrying out the microscopy practical, why do you need to add a few drops of stain?

To make the chromosomes visible so you can see which cells are undergoing mitosis

When carrying out the microscopy practical, why do you need to lower the cover slip carefully (while pushing down hard) and make sure there are no air bubbles?

- Air bubbles: may distort the image
- Push down carefully: so coverslip doesn't slide sideways, may break the chromosomes

When carrying out the microscopy practical, how do you make sure that the mitotic index obtained is accurate / how to improve accuracy of mitotic index? (4)

- Examine a large number of cells to ensure representative sample
- Repeat count many times (at least 5 times) to ensure figures are correct
- Only count whole cells to standardise counting
- Select random fields of view

From a diagram of some cells undergoing mitosis, how can you tell that they are currently undergoing anaphase?

- Chromatids pulled to opposite poles of spindle
- V-shape, have been pulled apart by spindle fibres at their centromeres

The events that take place during interphase and mitosis lead to the production of two genetically identical cells. Explain how. (4)

- DNA replicates
- Replication involves use of complementary base pairings (semi-conservative replication)
- During mitosis, identical/sister chromatids form
- Spindle fibres pull on centromeres of chromatids, split into two, each half is pulled to opposite poles of cell

How did scientists distinguish between artefacts and cell organelles?

- Had to repeatedly prepare a specimen in different ways, with different techniques
- If saw a particular object in a specimen prepared using one preparation technique, but not another, the object was more likely to be an artefact rather than an organelle

Describe the role of the centromere in mitosis (3)

1. Holds chromatids together
2. Attaches chromatids to spindle
3. Allows chromatids to be separated and move to opposite poles during anaphase when the centromere divides

Why are two chromatids connected at the centromere during mitosis?

DNA replication

Why might an organelle not be visible when looking at a cell with a microscope? (2)

The image is only a section of the entire cell OR the organelle was not stained

Describe how to use a microscope to measure the diameter of a droplet (2)

Measure the length with the eyepiece graticule and calibrate with a stage micrometer

What organelles are too small to be seen on an optical microscope? (5)

Mitochchondria, ribosome, endoplasmic reticulum, lysosome, cell-surface membrane

In the microscopy practical, why do you need to put the plant tip in a bottle of hydrochloric acid?

To break down cell walls and to stop mitosis

What are some precautions when working with HCl? (4)

1. Wear eye protection

2. Wear gloves

3. Add water to spills immediately

4. Do not pour down sink

3 structural features found in all virus particles

Genetic material, capsid and attachment proteins

Why are viruses described as acellular?

Not made of cells + no cell-surface membrane

Why are viruses described as non-living?

Have no metabolism / cannot respire

Why do SEMs produce 3D images, while TEMs produce 2D ones?

When using SEM, electrons are deflected, while when using TEM, electrons are transmitted

How are temporary mounts made? (3)

1. Thin section

2. Stain is put on it

3. Lower cover slip carefully