Chapter 1 - GCD 3033

What are some universal features of cells?

- Vary widely in size and shape, but all living things are constructed from cells

- All cells are believed to have evolved from an ancestral cell that existed >3 billion years ago

- New cells are formed from pre-existing cells (1st proposed in 1830s)

- All cells are bounded by a plasma membrane

What are features of a plasma membrane?

Lipid bilayer, permeable, hydrophobic interior, hydrophilic exterior

Why can’t most cells be seen by the naked eye?

The eye’s limit of resolution is ~200 µm or 0.2 mm

How much are light microscopes able to magnify cells?

up to 1000x (resolution is ~0.2 µm or 200 nm)

What are you able to observe with light microscopy?

some sub-cellular structures or organelles (e.g. nucleus). With thin samples, one can study unstained, living cells.

How is the bright field technique used to enhance contrast?

low contrast images in living cells, often fix and stain cells to add contrast

How are the phase contrast & differential interference contrast techniques used to enhance contrast?

look at structures that refract light

How is fluorescence microscopy used to enhance contrast?

stain specific structures with fluorescent dyes

How is confocal fluorescence microscopy used to enhance contrast?

optical sectioning of thicker samples with laser beam

Why is electron microscopy useful?

allows higher magnification of fixed cells (resolution is ~0.2 nm)

Why is transmission electron microscopy (TEM) useful?

Used to look at very thin sections of cells. This allows detection of more sub-cellular organelles

Why is scanning electron microscopy (SEM) useful?

Used to look at surface details of cells

What classes of cells are prokaryotic cells?

two distinct, distantly related classes of cells; bacteria and archaea

What are key features of prokaryotic cells?

No membrane around DNA (no nucleus)

- Most are single-celled organisms, but sometimes cluster together 

- Cell walls are common, greater diversity/habitat 

- Smaller genomes

What are key features of eukaryotic cells?

Membrane-bound nucleus

- Both single cell (protists) and multi-cellular organisms 

- Larger genomes, more regulatory DNA sequences 

- Bigger, more elaborate cells with multiple organelles 

- Includes plants, animals, and fungi

What is the nucleus?

- usually the largest organelle

- contains DNA packaged with protein into chromosomes

What is the nucleus surrounded by?

Double membrane called the nuclear envelope

How is traffic in and out of the nucleus regulated?

Small holes in the nuclear envelope called the nuclear pores

What occurs in the nucleus?

DNA replication and transcription, RNA processing, ribosome assembly

What happens to the nuclear envelope during cell division?

breaks down and lets chromosomes condense

What kind of membrane structure do mitochondria have?

double membrane structures

Do mitochondria have their own DNA and how do they reproduce?

contain their own DNA and reproduce by division

What are mitochondria DNA sequences related to?

DNA sequence related to bacterial DNA sequences

How did mitochondria evolve?

evolved from bacteria engulfed by ancestral cell

What do mitochondria do?

perform cellular respiration to generate chemical energy (ATP) from food and O₂, then release CO₂ and H₂O

What types of cells are mitochondria present in?

nearly all eukaryotic cells, variable in size, shape, and number

What types of cells are chloroplasts in?

only plants and alga

How did chloroplasts evolve?

photosynthetic bacteria engulfed by ancestral cell

Do chloroplasts contain their own DNA, and how do they reproduce?

contain their own DNA and reproduce by division

What is the membrane structure of chloroplasts?

triple membrane structures, the third membrane contains the pigment chlorophyll, traps energy from sunlight

What do chloroplasts do?

perform photosynthesis, use CO₂, H₂O, sunlight to make sugars, ATP, and release O₂

What is the endoplasmic reticulum?

network from nuclear envelope throughout cytoplasm

What happens in the endoplasmic reticulum?

Protein and hormone synthesis

What is bound in the rough endoplasmic reticulum?

ribosomes

What happens in the rough endoplasmic reticulum?

synthesis of transmembrane proteins

What happens in the smooth endoplasmic reticulum?

steroid hormone synthesis and Ca²⁺ uptake

What is the Golgi apparatus?

a stack of flattened membranes near the nucleus

What happens in the Golgi apparatus?

receives and modifies molecules made in the ER, then packages them for delivery to other locations or to the plasma membrane for secretion

What are lysosomes?

small, irregularly shaped organelles

What happens in lysosomes?

intracellular digestion, they are particularly abundant in long-lived cells (filled with undigested junk)

What are peroxisomes?

small membrane-enclosed organelles

What happens in peroxisomes?

generation and degradation of toxic molecules

What are transport vesicles?

vesicles involved in transport between different membrane compartments

What is transport from the plasma membrane inward called?

endocytosis

What is transport to the plasma membrane for secretion called?

exocytosis

What is the cytosol?

a concentrated mixture of molecules filling the inside of the cell

What is the cytoskeleton?

filamentous proteins that provide structural framework for cell

What are actin filaments used for?

contraction and transport

What are intermediate filaments used for?

mechanical stabilization

What are microtubules used for?

support and transport

What are advantages of using E. coli as a model organism?

- normally lives in the gut, but can be grown cheaply in simple media

- reproduces rapidly (several times an hour) 

- small genome (4.6 million bp of DNA, 4300 proteins)

What is E. coli used to study?

used to study DNA replication and genetic code

What is the main disadvantage of studying E. coli as a model organism?

not a eukaryote

What are advantages of using Saccharomyces cerevisae (a.k.a. Brewer’s or Baker’s yeast) as a model organism?

- relatively simple eukaryote, genome only 2.5x E. coli 

- easy to grow in defined media, rapid generation time (several times a day) 

- carries out basic cellular functions 

- good genetics, large number of mutants available

What is Saccharomyces cerevisae (a.k.a. Brewer’s or Baker’s yeast) used to study?

study organization of chromosomes and cell division cycle

What is the main disadvantage of studying Saccharomyces cerevisae (a.k.a. Brewer’s or Baker’s yeast) as a model organism?

not multicellular

What are the advantages of studying C. elegans as a model organism?

- slightly smaller and simpler than Drosophila, 97 million bp, 19,000 genes 

- detailed knowledge of cell fate from fertilized egg to 959 cells of adult worm 

- worm counterparts exist for ~70% of human genes

What is C. elegans used to study?

animal development, programmed cell death

What are the advantages of studying Drosophila melanogaster (fruit fly) as a model organism?

- good model for insect, animal development 

- easily grown in laboratory under controlled conditions

- numerous genetic mutants available  

- genome size is 185 million bp, 13,000 genes, including counterparts for many genes known to be critical in human disease

What is Drosophila melanogaster (fruit fly) used to study?

Development, neurodegenerative diseases, innate immunity, behavioral genetics

What are the advantages of studying cultured cells?

- can grow, divide, and display differentiated properties 

- maintained in a controlled environment

\- can be studied in ways that are not possible for whole organisms

What are the advantages of studying zebrafish as a model organism?

• lifespan 2-3 years, generation time 3-4 months

  • transparent embryos

• easily maintained in freshwater aquaria

• large mutant collection, sequenced genome, convenient tools exist to knockdown gene expression

• Casper mutant with transparent adult

What are the advantages of using mice as model organisms?

- good model for mammalian development and disease 

- mouse strains can be generated with classical and genetically engineered mutations 

- genes are closely related to human genes 

- rapid generation time

What are the advantages of studying humans?

-human genome project and large number of genetic defects described 

-good organism for self-reporting 

-sequenced genome, ~24,000 protein coding genes

What is the main disadvantage of studying humans?

large genome size & long generation time

What is NOT a reason scientists study yeast?

It lacks a nucleus so it is easy to genetically manipulate.

In comparing the complete genomes of five bacteria, one archaean, and one eucaryote (yeast), it was found that 239 families of protein-coding genes have representatives in all three domains. Which of the following families of genes would you not expect to be included here?

Those involved in the trafficking of molecules in and out of the nucleus.

Mitochondria are thought to have evolved from anaerobic bacteria.

False

Lysosomes are small organelles where fatty acid synthesis occurs.

False

__________ are fairly small organelles that provide a safe place within the cell to carry out certain biochemical reactions that generate harmful, highly reactive oxygen species. These chemicals are both generated and broken down in the same location.

peroxisomes

Which model organism is the simplest and best used to study immunology?

mouse