Small Concepts Lectures 1 - 3 Flashcards
Explain why the cell is considered the smallest unit of life.
- if any of the components of the cell were removed, the cell would die (if any individual organelles were removed the cell would die)
- the cell exhibits all functions required for life
What are all the functions required for life?
- energy consumption/aquisition (Photosynthesis, Glucose-ATP)
- reproduction (transcription/translation)
- internally regulated (homeostasis)
- high organized
- engages in mechanical activities (microtubules transport molecules, scaffolding changes cell shape, proteins can anchor cells to other cells)
- responds to stimuli in their environment
- cells evolve
- carry out a variety of chemical reactions
Who observed the first cells?
Robert Hooke. observed dead cork cells (probably from a wine bottle)
What are the tenants of cell theory?
- all organisms are composed of one cell or more
- the cell is a structural unit of life for all organisms
- new cells can only be formed by pre-existing cells
What is the smallest measurement a light microscope can make visible? What can you see and not see with a light microscope?
200nm minimum resolution.
Can see: some bacteria, mitochondria, human egg.
cannot see: small bacteria, viruses, macromolecules, ribosomes, proteins.
How is a sample prepared for use in an electron microscope?
Cells are dead. Sections/samples are coated with metal for contrast. Electrons beamed through the section, and are scattered by the metals.
If using a scanning EM, the electrons scatter across the sample.
What is visible under an electron microscope? What is not visible?
1nm minimum resolution
visible: ribosomes, cell wall, nucleus, vacuoles, mitochondria, endoplasmic reticulum, golgi apparatus are easily visible in a transmission electron micrograph.
not visible: moving cells/molecules
What is the difference between confocal microscopy and fluroescence microscopy?
Fluorescence: helps pinpoint specific structures/organelles/gene expression/especially proteins
Confocal: similar to fluorescence mircroscopy but a little better at displaying small details
-a laser scans across the sample and is focused at a specific depth (only displays one plane of focus at a time)
What is Super Resolution Microscopy?
fancy laser can depict images up to 20nm
example: can view a nuclear membrane and small molecules as distinct pieces from one another
Why are cells small?
because most cells rely on simple diffusion (doesn’t require energy) to move molecules around the cell.
If a cell were not small, their volume would increase, but their surface area decreases making them less efficient.
Name and explain some exceptions to large cells.
some neurons are very long, however their axons remain thin.
Epithillium in the intestine use microvili to increae surface area.
Eggs are large in size, but they have a small amount of protoplasm and surrounded by a lot of yolk.
Describe the differences between Prokaryotic and Eukaryotic cells.
Prokaryotic, developed 3.7 billion years ago. Eu - 2 billion years ago
Pro-bacteria and archae. Eu-protists, animals, plants, fungi.
Pro-single celled. Eu-mutlicellular.
Pro-single plasma membrane/no membrane bound organells. Eu-double plasma membrane/organelles are membrane bound.
Pro-small. Eu-usually larger
Pro- DNA floats in a specific location in the cell but no nucleus. Eu- DNA contained in nucleus
Pro-binary fission to reproduce. Eu- mitosis/meiosis
Pro-simple cytoskeleton. Eu-complex cytoskeleton
Describe the similarities between Prokaryotic and Eukaryotic cells
- plasma membrane similar in structure
- genetic code uses ACTG
- transcription and translation are similar
- shared metabolic pathways (glycolysis/citric acid cycle)
- use ATP
- similar photosynthesis
- similar methods for synthesizing and inserting membrane proteins
Are viruses alive?
Not really. they don’t generate their own energy, instead they use the hosts energy.
- viruses do not have homeostasis mechanisms
- they do not respond to the environment
What is E.coli used to study?
great for studying DNA replication, transcription and translation because it is small and easy to keep alive.
What is Saccharomyces cerevisiae good to study for?
simplest eukaryotic model.
what is arabidopsis thaliana good to study for?
great model because it grows fast, but doesn’t get super tall. has a small genome so it is easy to manipulate genes.
What are C. elegans commonly used to study?
great for developmental biology because their cell count is very specific (only about ~1000). also has short life cycle which makes them easy to work with (more experiments, less waiting time)
what are Drosophila melanogaster commonly studied for?
used in developmental biology and basic human biology as well.
What are zebra fish used to study?
a simple vertebrate, good for early developmental biology.
Mus musculus
the mouse is the easiest mammal to use for genetic studies.
Is genome size correlated with the complexity of the organism?
No its not. humans and mice both have ~30,000 genes. Drosophila has about 15,000 genes.
Explain what hydrophobic means.
molecules that are insoluble in water. However, they are still soluble in non-polar liquids such as chloroform.
describe what polarity is with examples.
when different parts of a molecule has different charges. Example H20, DNA,
Describe what amphiphatic is.
a molecule that is both hydrophilic and hydrophobic (polar and non-polar). proteins are commonly both polar and non-polar. So are Phospholipids!
What are fats made of?
Fats/lipids are made of a glycerol head, which is linked to ester bonds and three fatty acid chains.
Describe fatty acids and their properties.
unbranched hydrocarbons with a carboxyl group (COOH)
- they are amphiphatic (phospholipids are polar, fatty acid chains are non-polar).
- when shaken in water, it will form a micell (monophospholipid bilayer)
example: soap
Describe saturated fatty acids.
made of singular bonds between the carbons (more van der Walls forces at play here).
- electrons are shared equally
- solid at room temperature
Describe unsaturated Fatty Acids.
have one or more double bonds, causes a kink in the chain. doesn’t allow for other carbons to bind.
They are liquid at room temperature.
These type of fats come from plants
Explain why lipids are a required food source?
they are a source of energy in our diet
- they store energy
- some hormones are made from lipids (steroids, prostaglandins),
- vitamins are derived from lipids
- they are the basic structural elements of biological membranes
Describe Carbohydrates.
ring structures made of C6H1206. can be found in the form of monomers, disaccharides or polysaccharides
What is the difference between alpha-glycosidic bonds and beta-glycosidic bonds?
All molecules are dynamic. Therefore monosaccharides spontaneously shift between alpha and beta rings.
- “alpha-ring” when a monosaccharide binds to another monosaccharide via H on top and OH on bottom
- beta-ring when a monosaccharide binds to another monosaccharide via OH on top and H on the bottom.
- Human amylase can only break down Alpha-bonds.
- Beta rings form cellulose (fiber)
Describe a dehydration reaction
loss of a hydroxyl (OH) group from one monomer and the loss of Hydrogen from another monomer forms a glycosidic bond.
what are oligosaccharides? what is their function?
small chains of monosaccharides.
often there are different types of monosaccharides found linked in the chain.
can be added onto proteins and lipids to make glycoproteins and glycolipids.
Usually found in the ECM.
How are oligosaccharides involved in determining blood type?
ABO glycosyltransferase adds sugars (monomers) to the antigens attached to the outside of the blood cell. Whichever sugar is added, determines what blood type someone is.
If you are A Blood Type…which antibodies are present? which antigen is present?
Anti-B. A-antigens
If you are blood type B, which antibodies are present and which antigen is present?
Anti-A. B-antigens
if you are blood type AB which antibodies are present? which antigens are on the red blood cell?
no antibodies. A and B antigens on the red blood cell.
if you are blood type O which antibodies are present? which antigens are on the red blood cell?
Anti-A and Anti-B are present in the plasma. no antigens are on the red blood cell
Describe polysaccharides. What is their function?
They are long polymers of sugars.
some serve as an energy source (glycogen, starch).
some serve structural roles (cellulose, chitin)
What is a gene?
a piece of DNA that encodes a protein or RNA. It is also the smallest unit of heredity
What is transcription?
a gene/exon is transcribed by RNA Polymerase to make RNA (mRNA, tRNA, rRNA).
What is translation?
the making of a protein.
Briefly explain the process of translation.
RNA moved out of the nucleus, into the cytoplasm. Attaches to ribosomes, tRNA brings appropriate amino acids.
What are nucleic acids? What is their function?
polymers of nucleotides. they store and transmit genetic information.
How are nucleotides connected to each other?
connected via 5’ - 3’ phosphodiester bonds between 3’ OH of a nucleotide and a phosphate attached to the 5’ Carbon of the next nucleotide
(5’ Phosphate, 3’ Hydroxyl)
Describe some features of RNA.
- they are single stranded (usually)
- they can fold back on themselves to form 3D structures (via basepairing). example: ribosomes
- some RNA have catalytic activity (ribozymes)
- RNA encodes the genetic message of DNA, it is the genetic material of some viruses
- RNA does not have a OH at its 3’ end
What is a Phosphoanhydride bond
phosphate and oxygen bound together
what is a nucleoside?
phosphate, oxygen, and five carbon sugar
what is a nucleotide?
phosphate, oxygen, five carbon sugar, and nitrogenous base (purine/pyrmidines)
which nucleotide does Adenine bind to and how?
binds to Thymine via two hydrogen bonds.
which nucleotide does cytosine bind to and how?
binds to guanine via three hydrogen bonds
What are the functions of nucleotides?
-make up DNA/RNA
-used as regulatory molecules (cAMP, GTP)
-used to transfer energy for metabolism
example Phosphates (ATP) and co-enzymes (NAD-NADH)
What are proteins? Define the different classes of proteins.
polymers of amino acids
Globular proteins; found inside the cell. usually are folded into tertiary and quaternary structures
Example (insulin, histones, immunoglobulines, hemoglobin, myoglobin)
Fibrous proteins; usually found in the ECM. mostly form primary and secondary structures
example: keratin and collagen
Name the role of proteins inside the cell
- enzymes
- structural elements (microtubules)
- contractile elements (myosin/actin in muscle fibers)
- transcription factors (histones)
- transport (across membranes g-proteins,channels. along tubules, dynein, kinesins)
- carriers (hemoglobin, ATPases, carriers of hormones)
- antibodies (immune cells-cytokines)
Describe the structure of an amino acid
made of an alpha-carbon, amine group, carboxyl group, and a functional R group.
They have an N-terminus (beginning) and a C-terminus (the end)
How are amino acids linked together to form polypeptide chains?
a dehydration reaction occurs. one peptide loses a OH and another loses a H
Name and describe the qualities of polar charged amino acids.
Side chains are hydrophilic -acts as an acid or a base -forms ionic bonds -often involved in chemical reactions (GALAH) Glutamic acid, asparitic acid, lysine, arginine, histidine
Name and describe the qualities of polar uncharged amino acids.
STAGT Serine, Threonine, Asparagine, Glutamine, Tyrosine -side chains are hydrophilic -tend to be partially charged -form hydrogen bonds -often associate with water
Name and describe the qualities of nonpolar amino acids.
TAVLIMP
Tryptophan, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalaline
-side chains are hydrophobic
-mostly C and H atoms
-tend to form the inner core of soluble proteins
-common in phospholipid bilayers too
what is a primary structure?
the sequence of amino acids
What is the secondary structure? give an example
amino acids forming alpha-helix or beta-sheets
- can also create “hinges”, turns, loops, and disordered sections
- Hydrogen and Nitrogen bonds are the backbone of these structures (backbone holds the structure together)
example: DNA
What is a tertiary structure? give an example
a protein folded into a 3D shape. Formed by the R-groups interacting with different amino acids
-Hydrophobic R-groups found on the inside
-Hydrophilic R-groups found on the oustide
-non-covalent bonds stabilize the protein’s shape (van der Walls and disulfide bridges)
Example: Acetylcholinesterase, myoglobin
Define a quaternary structure and provide an example.
protein complexes made of more than one protein. (not all proteins will form a quaternary structure)
-a quaternary structure also includes protein that briefly come together to perform a function and then separate shortly after
Example: Hemoglobin
What is a homodimer?
two proteins encoded by the same gene
what is a heterodimer?
two or more different proteins encoded by different genes
what is a heterotrimer?
three or more different proteins encoded by different genes
example: some g-proteins
what is a heterotetramer?
four or more different proteins encoded by different genes
Define a Y2H assay.
a yeast two-hybrid assay is used to confirm protein - protein interactions through downstream activation of a reporter gene.
What would be the purpose of using a Y2H assay?
To map the activities of a protein/gene; seeing which proteins it interacts with.
This type of information can tell you where the protein travels in the body, and what general functions/processes it may be involved in.
-It is also useful to check if a protein has mutated. If the protein is not interacting with its usual proteins, then it may have changed.
-Be aware, there are a lot of uncertainties using Y2H assays because it interacts with many different proteins.
Describe X-ray Crystallography
- “grow” a protein into a crystal shape
- place protein crystal into a strong x-ray beam
- x-rays interact with the atoms within the protein as they pass through the crystal
- x-rays bouncing off the atoms produce a defraction pattern
- rotate the crystal and create another defraction patter
- use a computer to analyze the patters of defraction (an electron density map)
- then an atomic 3D model can be made
Describe the process of using a synchotron.
- “grow” a protein into a crystal shape
- using high powered magnets, electrons are spun around a giant machine (99.99995 speed of light)
- shine an x-ray beam into the tunnel, the x-ray photon is carried by the electron
- electrons pass through the crystal and produce defraction images
- used for: designing new drugs, making computer chips, safer medical implants
Cons to using crystallography.
- some proteins (membrane proteins) cannot be turned into crystals/very difficult to work with because the solution is aqueous
- since the protein is grown into a crystal shape, it may not be the natural form of the protein
- does not work with large protein complexes
Describe the process of Cry-electron microscopy.
- new technology (10-15 years)
- purify the protein
- spot them on a grid
- flash freeze the protein with liquid ethane/liquid nitrogen (-190C)
- look at frozen protein with a Transmission Electron Microscope
Describe Nuclear Magnetic Resonance Spectroscopy.
- place a protein in solution
- put the sample in a very strong magnet
- nuclei of some atoms will behave like magnets
- add light or radio frequency and nuclei will resonate at specific frequencies
- frequencies are measured and converted into an NMR spectrum
