Chapter 1 (Cells): The fundamental units of life

Chapter content: unity and diversity of cells, seeing cell structure, the tree of life, the eukaryotic cell, studying model system

What do all cells share in common that is basic to biochemistry regardless of appearance?

• the ability to reproduce and make copies that allow them to survive

• the ability to make use of resources and produce energy to grow

• Have DNA

What is theorized about all living cells?

That all living cells evolved from the same ancestral cells

What are cells and what do they rely on to survive?

They are the fundamental units of all living organisms and rely on micromolecules; including DNA, RNA, and protein, in order survive

What do living cells contain?

DNA provided instructions, in the form of genes, that contains code determining how the cell looks like and their function

What has to happen in order for DNA to be useful?

The information stored within DNA has to be transcribed into RNA molecules that can then be translated into protein

Why are light microscopes useful?

They allow us to view changes happening in specimens under our eyes up to 1000x and view details as small as 0.2um

How do light microscopes function?

It uses a light source that goes towards the specimen, then the objective lens collect the light, which allows us to see the sample underneath

What is a fluorescence?

A kind of substance that has a unique property to absorb light and is used in fluorescence microscopes

What are fluorescence microscopes?

A type of microscope that uses fluorescence to absorb light

How does a fluorescence microscope utilize fluorescence substance?

It uses it to absorb light to cause a chemical change, pushing energy levels to a higher level. After the substance relaxes, it emits a light that allows the specimen to be viewed

What’s different about Phase-contrast optics and interference contrast optics from bright-field optics?

Unlike bright-field optics, the other two systems exploit differences in the way light travels through regions of the cell with differing refractive indices

What are fixed samples?

Samples that are chemically fixed in order to stabilize their structures, allowing the sample to be seen under a microscope

What is a confocal fluorescence microscope?

A type of microscope that uses a scanning laser beam that focuses on single points at specific depths at a time, forming a 3D image of the samples structure

Why cant a confocal fluorescence microscopes resolution limitation only go up to 200 nanometers?

Due to the microscope not being able to go past the wavelengths of light

What is the resolution a super-resolution fluorescence microscope can go up to?

Up to 20nm

Why can a super-resolution fluorescence microscope break the usual 200nm limit and go up to 20nm?

They can excite fluorophores and cause them to emit a light, while silencing other neighboring molecules, creating a dark background and a clearer view of the sample

What are the 2 kinds of electron microscopes?

Transmission electron microscopy (TEM) and scanning electron microscopy (SEM)

What is a transmission electron microscopy (TEM)?

A type of microscope that uses an electron beam to go target thin slices of fixed samples stained with salts of uranium and lead to view the structures of the sample

Why must samples be cut into thin slices for a TEM/SEM?

The reasoning is that the wavelength of electrons in the beam is very short

What is a scanning electron microscopy (SEM)?

A type of electron microscope that uses an electron beam to target a fixed sample covered with a coating of heavy metal to create a 3D image of the sample

What are the 3 domains that organisms can be assigned to on earth?

• Bacteria

• Archaea

• Eukaryotic

What is the domain with the largest diversity that constitutes a vast majority of life on the planet?

Bacteria

Why does the bacteria domain constitute a vast majority of life on the planet?

Because of their ability to colonize nearly every ecological niche on the planet

What are organisms grouped based on?

Based on their genetic makeup and relating them to one another

How are many new species of bacteria and archaea being discoverd?

Through the use of DNA sequencing of environmental samples

How much does eukaryotes form in the tree of life?

They form a small slice of the earths overall diversity

Why do some scientists suggest merging the eukaryotic and archaea domains into a single domain?

Due to their close kinship with one another in terms of genes and proteins

What are the branches of the tree of life proportional to?

They are proportional to the differences among genomes

What do the tip of the branches on the tree of life represent?

They represent individual species

What ability does an asgard archaeon have?

It has the ability to divide once every 20 days, compared to the common bacteria that can double every 20min

What was the first eukaryotic organism to have its complete genome sequenced in 1996?

Yeast

When does DNA begins to appear in the nucleus?

When cells begin to divide, causing DNA to become visible

What is the mitochondria?

A dense double membrane bound organelle that is responsible for cell respiration and ATP production

What does the mitochondria contain?

Contains proteins in the membrane and mitochondria matrix

What is the hypothesis on how membrane bound organelles emerged?

The theory suggests that an archaea cell formed a symbiotic relationship with an anaerobic bacterium that could utilize oxygen and generate energy. Over time, it is believed that the archaea cell engulfed the bacterium, establishing a permanent partnership, which ultimately led to the formation of the mitochondria.

What formed after the archaea cell engulfed the anaerobic bacteria?

A nuclear envelope, ER, and a precursor of aerobic eukaryotes

What is still seen in mitochondria?

Similar DNA sequences that is found in bacteria, even though a majority of the DNA has escaped

What strategy was developed to help people with a defective mitochondria?

The 3 parent strategy

What is the 3 parent strategy?

A strategy where a 3rd female parent helps introduce healthy mitochondria DNA to the child of the original mother

What is the chloroplast?

a plant organella that has a unique membrane compartment where photosynthesis occurs

What is theorized about the tree of life?

That theres a common ancestor due to a shared gene and codon

What diverges from the common ancestor?

Bacteria and archaea, which eventually formed a symbiotic relationship that formed the mitochondria, while some single-celled eukaryotes acquired chloroplasts

What is the ER?

A single membrane organelle has the largest surface area out of any other with a sheet like structure

• Within the structure, there are ribosomes that are the mechanisms for translation

What is the function of the ER?

To produce proteins through the ribosomes and lipids through the smooth ER

What is different about the golgi apparatus in different species?

They take on different forms in different species but share similar functions

What is the function of the golgi apparatus?

To receive proteins and lipids then sort, modify, and transport them to their final destination

What occurs in plant and animal cells when proteins and/or lipids are damaged?

They are cleaned out to avoid permanent damage to the cell

What is the cytosol?

a concentrated aqueous gel that contains many large and small molecules that are crowded with one another

What occurs if the cytosol is not organized?

It begins to get stressed and will eventually kill the cell

What is the endomembrane trafficking system?

A pathway that involves 2-way communication that uses endocytosis to bring material into the cell and exocytosis to expel material out from the cell

• with the pathway being mediated by vesicles

What are the 3 kinds of cytoskeletons?

• Actin filaments

• Microtubules,

• Intermediate filaments

how are the cytoskeletons each organized differently?

Through the use of polymeric structures that have small protein sub units that come together to perform different jobs

What are microtubules?

They are a highly dynamic cytoskeleton that is essential in cell replication for the accurate distribution of genomes to daughter cells

What are protozoans?

They are unique single-celled structures capable of drastically changing their shape, enabling them to engulf other cells. Their forms, functions, and environments vary.

Why is bacteria widely used?

Due to their ability to double their DNA every 20 mins, allowing for it to be easily broken down and isolated

What is yeast?

A simple eukaryote that can be easily transformed and introduced to foreign DNA, along with the ability to precisely insert DNA into its genome, and can double every 90 minutes per generation.

How is yeast treated as by scientists?

They are treated as a super model to study cell structure and function

What does a portion of the eukaryotic family tree show?

it shows that fungi are closely related to animals

What is Arabidopsis thaliana?

A small genome that is the most adopted genetic model for plant related problems

What has Arabidopsis thaliana allowed us to do?

Generate mutations and introduce genes that can be expressed by the genome.

What is an Adult C.elegant?

A clear worm that consists of only 959 somatic cells with a life cycle of around 30days from birth to death

What has been traced completely in an Adult C.elegant?

The embryonic origin and lineage of all the cells

What has Adult C.elegant helped in?

Identifying mutations causing developmental abnormalities has led to isolating and characterizing genes that control development and differentiation.

Why are fruit flies crucial in developmental biology?

they help identify the function of different genes and aid in answering questions about development in multicellular organisms

What are zebrafish?

They are organism with a 6 month lifespan that allows for different ways to manipulate and generate mutants

What do zebrafish produce?

They are able to produce different phenotypes that allow genes and other things related humans to be view

What do cultured cells in chemically defined media allow for?

For studies on signaling mechanisms that normally control cell growth and differentiation within the intact organism

What is functional complementation?

A process where healthy genes are cloned based on their function and are introduced into a cell with a mutant gene in order to recover that gene

What can be performed on isolated animal cells that are cultured in fiberglass?

biochemistry and genetic studies can be done on the cell to view what can be changed within the cells

What kind of proteins do viruses have?

They have spike proteins that allow them to communicate with a host cell and enter them

What do viral proteins rely on?

Many rely on communication with the host proteins in order to mimic them in order to blend in, allowing them to use host cells to replicate themselves

Why is the mouse considered to be the most common mammalian model system?

They can have genetic mutations performed on them, allowing for potential phenotypes that are genetic to be performed

How is genome size measured?

They are measured in nucleotide pairs of DNA per haploid genome