biob10 Flashcards
Discovering cells
Robert Hooke (1665)
Examined cork under microscope
Cork is made up of “cells”
Anton van leeuwenhoek (1674)
Examined pond water under microscope
“Animalcules”
Matthias scheiden (1838), theodor schwann (1839) & rudolf virchow (1855)- proposed the cell theory:
All organisms are composed of one or more cells
The cell is the structural unit of life
Cells can arise only by division from a preexisting cell
Cells possess a genetic program and the means to use it
All cells store their hereditary information (to daughter cells) in the form of double-stranded DNA molecules
The motivation was to find what all cells have in common
Cells are capable of producing more of themselves
Ex. mitosis and meiosis
Templated replication of their hereditary information
Templated polymerization: original template material and split up to 2 cells of identical copy of the original by creating new strands that are complementary to the old strand
. In different types of cells, this process of DNA replication occurs at different rates, with different controls to start it or stop it, and with different auxiliary molecules to help the process along
But the basics are universal: DNA is the information store for heredity, and templated polymerization is the way in which this information is copied throughout the living world.
Cells carry out chemical reactions
Proteins carry out chemical reactions
Enzymes aid in cellular metabolic processes (use ATP)
All rely on energy
Cells take free energy and make a stable functioning compartment in which we can carry out all these activities
Cells can acquire and utilize energy
Photosynthesis and respiration
All cells require ATP as a carrier of free energy
All cells are enclosed by a membrane
Nutrients in, waste out
Membrane transport proteins maintain this semi-permeable barrier
Cells respond to stimuli, carry out mechanical activities, and move!
Use cell surface proteins for this = receptors (detect that there is a different structural protein and will follow it and try to engulf it)
Cells operate at a microscopic scale dominated by random thermal motion
As it grows longer and longer, it will push the plasma membrane in the way it wants
Cells differ in many ways
Obtain free energy in different ways
Phototrophic (sunlight)
Lithotrophic (inorganic chemicals in environment)
Organotropic (other living things and the organic chemicals they produce
Not possible unless we have the 2 above in the environment
Some cells specialize in fixing nitrogen and carbon dioxide and other cells rely on such cells/organisms
Plants fix co2
Nitrogen-fixing bacterial help plants fix n2
Genome diversification and the tree of life
Genomes diversify over evolutionary time, producing new types of organisms
New genes are generated from preexisting genes
Gene duplications give rise to families of related genes within a single genome
The function of a gene can often be deduced from its nucleotide sequence
More than 200 gene families are common to all 3 domains of life
Trying to find whats common between all 3 domains of cells cuz they probably really important
Many are generated by gene duplicaiton
prokaryotes
Prokaryotes
“Pro” meaning “before
“Karyon” meaning “nucleus”
All bacteria
Some unique characteristics
Nucleoid: genetic material not bounded by a membrane
Structurally simpler
Less DNA than eukaryotes-typically, single circular chromosome
No mitosis or meiosis- binary fission instead
Types of prokaryotes
2 major groups
Archaea (archaebacteria)
“Extremophiles” - thermophiles that grow @ 80-105
Bacteria (eubacteria)-all other bacteria
Cyanobacteria-most complex (share photosynthetic membranes with plants and are organized)
Archaea are actually closer to eukaryotes than eubacteria
eukaryotes
Eukaroyoes: “eu” = true, “karyon” = nucleus
Protists, fungi, plants and animals
Some unique characteristics:
Membrane-bound nucleus - nuclear membrane
Structurally more complex - internal organelles; complex cytoskeletal system
More DNA than prokaryotes
Typically, several chromosomes composed of linear DNA molecules
Genomes are rich in regulatory DNA
Division by mitosis or meiosis
Types of eukaryotic cells
Unicellular - protists
Everything that this organism needs to survive is done by the one cell
Mulitcelluar - humans
Different activities are carried out by different types of specialized cells - “cell differentiation”
- many eukaryotes live as single solitary cells
- Eukaryotic genomes can define the program of multicellular development
Similarities between pro- and eukaryotes
Genetic code is identical - information encoded in DNA
Shared metabolic pathways - such as synthesis of ATP
Shared structural elements - cell membrane
The origin of eukaryotic cells
Prokaryotic cells arose before eukaryotic cells - fossil record
Did eukaryotic cells arise from prokaryotes?
Similarities noted between them (genetic code, metabolism)
“Endosymbiont theory”
An endosymbiont is a combination of 2 cells living together in a symbiotic relationship; one cell lives “inside” the other cell
“Endo” means inside or within
Model eukaryotes - 1
Yeast is a model single-celled eukaryote
Easy to grow
Small genome
Mutants available for almost every gene
Many components interchangeable between yeast and humans
Pathways and processes studied in yeast can be extrapolated to humans and other multicellular eukaryotes
Model eukaryotes - 2
Many multicellular models exist:
Arabidopsis thaliana-weed
Produces thousands of offspring per plant in 8 weeks
Caenorhabditis elegans-worm
Has helped us understand controls over cell division and cell death
Drosophila melanogaster-fruit fly
Despite being an insect, has been used as a model for vertebrate development
9 days from egg to adult
Cheaper and easier to breed than vertebrates
Small genome with much lower frequency of gene duplication
Model eukaryotes - 3
Xenopus laevis-frog and Danio rerio-zebrafish
Accessible models to understand cell fate and migration during development
Frog eggs are large and fertilized outside of the animal, so development easy to follow
Zebrafish are transparent for first 2 weeks of life, so can actually watch behavior of cells
Model eukaryotes - 4
Mus musculus-mouse
Most used vertebrate model; rapid, easy breeding, mutants resemble human conditions
Human genome and study of human genetic disorders
Note that 2 people differ in 1-2 out of every 1000 nucleotides = huge variation
provides clues to how different people manifest the same mutations and genetic conditions very differently
Cell differentiation
The process by which an unspecialized cell become a specialized one
Differentiation occurs primarily through signals received by the cell from its environment
The type of signals received depends upon the location of the cell within the embryo
Changes in cell morphology (appearance)
Express “cell-specific” genes -> unique proteins but “housekeeping” proteins will be the same as other cells
Organelles stay the same but their number and location may differ
Cell culture
Cells are grown outside the body “in vitro”
Simplified, controlled environment
Cells are grown in plastic flasks filled with defined media
Primary culture: obtained directly from the organism
Mostly embryonic tissues
Divide ~25-100 times in culture = passages
Cell line: primary cultures that have undergone genetic modification to allow them to grow indefinitely in culture
Can occur spontaneously (mouse cells)
Tumor tissue can be used (HeLa cells) - transformed cell lines
Cell culture in the lab: 2D cell culture
Mimic our cells and tissues as closely as possible in the incubator
Cell culture in the lab: 3-D cell culture
100% geiled ECM: stuff that cell makes and secret out to their environment
Floating in materials they like to grab onto that they secrete in their immediate environment
They have polarity
One side of the plasma membrane is for sticking to the plastic and the other side is for secreting
Advantages of cultured cells
Cells can be obtained in large quantities
Most cultures constitute only one type of cell
Important cell biological phenomena can be studied using cultured cells
Cell movement, cell division
Cells can be induced to differentiate in culture
Cultured cells can be used to test the activity of drugs
Also hormones or growth factors
Size of cells and their components
Not naturally colored cuz they are too small to see
Angstrom (1 hydrogen atom)
Nanometer (microscope)
micrometers/micron (eye)
2-D Cell Culturing:
A sample of cell are placed in a plastic or glass container
Cell sample is usually directly taken from an organism (embryonic tissue)
Instead of a singular cell sample, a population of cells (Cell Lines such as HeLa (tumour tissue) cell line) are used
Layer of agar medium or any other cell culture medium
Placed in a temperature controlled (37 degrees to mimic the human body) oxygen rich environment
Constant contact to cell medium and container
Problems with 2-D Cell Environment:
Unrealistic cell environment as cells in the human body are surrounded by ECM (Extracellular Matrix)
Can often result in insufficient cell division and incorrect image reading
Constant and limitless contact to the Matrix (agar)
Leads to the development of 2 ends of polarity in the cell sample
3-D Cell Culturing
Instead of the cell sample or cell line being placed on directly the plate, it is embedded in ECM (Extracellular Matrix), mimicking its natural environment within the human body
Limited contact with the Matrix
Advantages of 3-D Cell Culturing
Provides accurate imaging of the sample
No real polarity is developed
Light Microscope
Problem with using light microscopes is that it cannot go past the wavelength its using
Its limitations are around 2 μm (micrometer), big enough to see cells and bacteria but not the organelle in depth
The higher the wavelength or lambda, the worse the resolution or quality becomes
Bright-field light microscopy
Microscopes produce enlarged images of an object
Cells are placed on a stage between the light source and our eyes
View light that is diffracted by the cells
Resolution: the extent to which details of a specimen are retained in the image (if there’s 2 points on your specimen, how close can they be and you can still tell them apart when you look down the microscope)
The resolution of a microscope depends both on the wavelength of light as well as numerical aperture of the lens system (wavelength of light is directly proportional to resolution) (big wave length, big resolution = low resolution)
The numerical aperture impacts the light-gathering capacity of a lens:
Related to the angle of the cone of light entering the lens
Related to the refractive index of the medium that the lens is operating in
Bright Field Microscope (incident light (white))
Microscopes produce enlarged images of an object
Cells are placed on a stage between the light source and our eyes
View light that is diffracted by the cells
Resolution: the extent to which details of a specimen are retained in the image (if there’s 2 points on your specimen, how close can they be and you can still tell them apart when you look down the microscope)
The resolution of a microscope depends both on the wavelength of light as well as numerical aperture of the lens system (wavelength of light is directly proportional to resolution) (big wave length, big resolution = low resolution)
The numerical aperture impacts the light-gathering capacity of a lens:
Related to the angle of the cone of light entering the lens
Related to the refractive index of the medium that the lens is operating in
Stained molecules, dye combined to something like DNA, plasma membrane, er
What you see is not absorbed by the stained
Stained sample
Incident light is used
Usually not great for high-resolution
Dark Field Microscope
The background is darkened, the sample is white
Oblique light is used so that the scattered rays that hit the sample and are bent toward the viewer are the only thing that shows
Depends on the bending of light
Phase contrast & differential interference contrast
Waves in phase are used
Waves out of phase show contrast
Dic = fancy filter= looking at the refraction index of the cell and converting to an intensity
If nucleus is dense, it’ll give the intensity of the nucleus something different from the rest of the cell
Why some part of the cell looks darker than other parts
Looks at rate of change
Stains used in light microscopy
Tissues: embed and section first
A tissue was dissected out of an organism and placed in this wax so its fixed in place and stained
Can cut little slices of the wax and take a paintbrush and place it onto a slide and then put that slide to dry and then can immerse it in all kinds of different dyes
Can see the layers
Haemotoxylin & eosin staining (H&E):
Haemotoxylin stains nucleic acids (blueish) and eosin stains proteins (pinkish)
This type of staining is good to see what might be happening
Electron microscopy (EM)
Uses electrons as “light” source
Short wavelength
Image formed when electrons pass through a specimen
Provides much greater resolution
The resolution of a microscope is conversely proportional to the wavelength of its light source:
The longer the wavelength; the poorer the resolution
Light-constant wavelength
Electrons-wavelength varies with speed
Speed controlled by accelerating voltage applied in scope
Very short wavelength possible = very high resolution
Transmission electron microscope (TEM)
Specimens have to be fixed, embedded & sectioned
Stained with heavy metal solutions
These bind to cellular macromolecules
Metals scatter electron path
Image of scattered electrons is caught on photographic emulsion or recorded using a high-resolution digital camera
Parts of the image that appears dark are regions where electrons have been scattered away by metal atoms (high density)
TEM images
Best used for viewing detailed structures within cells and tissues
Cryoelectron microscopy
Not fixed in chemicals but using rapid freeing = cryofixation
Water in the sample is supercooled into a noncrystalline state called boisterous ice
Cryoelectron tomography
It gets it from all different angles
Tilts the stage in order to do that
Algorithm organizes the images and produces a model
Freeze fracture and freeze etching techniques
Cells are rapidly frozen in low-temperature liquids
Knife edge used to strike frozen cells
Fracture plane spreads from point of initial contact, splitting cells into 2
Cellular structures deviate the place of fracture either upward or downward - irregular surface - etching removes thin layers of ice
Deposit heavy metals on top of this fractured surface to get a “replica” of the plane
Carbon is then deposited over the metals to cement them in place
This metal-carbon replica is viewed by EM
Freeze fracture: describes the technique of breaking a frozen specimen to reveal internal structure
Freeze etching: sublimation of surface ice under vacuum to reveal details of the fractured face that were originally hidden
Scanning electron microscope (SEM)
Specimens prepared by careful drying procedures
After drying, coated with carbon and metals
Image is formed by electrons reflected back by the specimen
Referred to as “backscattered” electrons
Gives surface view of cells, tissues, and whole animals
A 3-D quality to the image
SEM images
Best used for viewing extensions or processes that cells use to interact with the environment
Something else to think about: cell replacement therapy
Self-renewing
Present in large quantities/ can give rise to every blood cell
Stem cells for cell replacement
Stem cells:
Undifferentiated cells
Can self-renew
Can differentiate into 2 or more cell types
Most organs in humans contain stem cells
Adult cells
Transplantation of such cells to specific areas could be future therapy
Human embryonic stem (ES) cells:
Are derived from human embryos (IVF clinics)
Are pluripotent = capable of differentiating into every cell type in the body
Can be cultured for extended periods
Phenomenal resource for cell replacement therapy
ES-derived oligodendrocytes - spinal cord injury patients
Problems:
Immunological rejection (not a problem with adult stem cells)
ethical/political debates
Customizing ES cells
Changing the genetic makeup of the cells to match that of the patient who needs the cell transplant
Problems:
Creating an embryo just as a source of ES cells
Major ethical questions
Induced pluripotent stem cells (iPS cells)
reprogramed somatic cells by introducing of specific genes into them
Do away with the need for human oocytes/embryos
A core set of transcription regulators defines and maintains the ES cell state
Cell chemistry
Reactions take place in an aqueous environment (cells are 700% water)
Based overwhelmingly on carbon compounds
Most are enormous polymeric molecules (macromolecules)
Composed of complex reactions that allow cells to obtain and use energy
Built with macromolecules in mind
Water
Two atoms connected by a covalent bond may exert different attractions for the electrons of the bond. In such cases, the bond is polar, with one end slightly negatively charged and the other slightly positively charged
Overall neutral charge (having the same number of electrons and protons), the electrons are asymmetrically distributed making the molecule polar
The oxygen nucleus draws electrons away from the hydrogen nuclei, leaving the hydrogen nuclei with a small net positive charge
The excess of electron density on the oxygen atom creates weakly negative regions at the other 2 corners of an imaginary tetrahedron
Hydrogen bonds
Because they are polarized, 2 adjacent H20 molecules can form a noncovalent linkage known as a hydrogen bond. Hydrogen bonds have only about 1/20 the strength of a covalent bond
Hydrogen bonds are strongest when the three atoms lie in a straight line
Water structure
Molecules of water join together transiently in a hydrogen-bonded lattice. Even at 37 degrees, 15% of the water molecules are joined to four others in a short-lived assembly known as a flickering cluster
The cohesive nature of water is responsible for many of its unusual properties, such as high surface tension, high specific heat capacity, and high heat vaporization
Hydrophilic molecules
Substances that dissolve readily in water are termed hydrophilic. They include ions and polar molecules that attract water molecules through electrical charge effects. Water molecules surround each ion or polar molecule and carry it into solution
Ionic substances such as sodium chloride dissolve because water molecules are attracted to the positive (Na+) or negative (Cl-) charge of each ion
Polar substances such as urea dissolve because their molecules form hydrogen bonds with the surrounding water molecule
Hydrophobic molecules
Molecules that contain a preponderance of nonpolar bonds are usually insoluble in water and are termed hydrophobic. This is true, especially for hydrocarbons which contain many C-H bonds. Water molecules are not attracted to such molecules and so have little tendency to surround them and carry them into solution
Cells are formed of carbon compounds
certain combination of atoms, functional groups (carbon + friends), occur repeatedly in cells
Confer distinct physical and chemical properties
Formation of biological macromolecules
Macromolecules are polymers of building blocks known as monomers
Polymers form by joining monomers-condensation reaction = water is removed
Polymers are broken into monomers-hydrolysis reaction = water is added
Carbohydrates: monosaccharides
Have 2 or more hydroxyl groups
Contains either an aldehyde group and is called aldoses or a ketone group and are called ketosis
Carbohydrates: rings and isomers
Ring formation: in aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of the same molecule, thereby closing the molecule into a ring
Isomers: many monosaccharides differ only in the spatial arrangement of atoms-that is, they are isomers
These small differences make only minor changes in the chemical properties of the sugar. But they are recognized by enzymes and other proteins and therefore can have major biological effects
α and β links
The hydroxyl group on the carbon that carries the aldehyde or ketone can rapidly change from one portion to the other. These 2 positions are called α and β
As soon as one sugar is linked to another, the α or β form is frozen
Carbohydrates: linking monosaccharides
Linked by covalent bonds: between C1 of one sugar and hydroxyl (OH) of another sugar
Generates C-O-C linkage between sugars
carbohydrates: polymers
Disaccharides: 2 monosaccharides covalently bonded together
Energy storage
Ex. sucrose, maltose, lactose
Oligosaccharides: a small chain of sugars (oligo = a few)
Attached to lipids or proteins converting them to glycolipids and glycoproteins
Polysaccharides: a long chain of sugars bonded together
Very large molecules with a structural or storage function
Ex. chitin, cellulose, scratch, glycogen
Carbohydrates: polysaccharides
Glycogen: stores of chemical energy in most animals (linkage in 1 configuration)
Scratch: stores of chemical energy in most plants
Cellulose: durable structural polymer (ex: plant cell walls)
Chitin: polymer of N-acetylglucosamine
Durable structable polymer (ex: exoskeletons of invertebrates)
Sugar derivatives
The hydroxyl groups of a simple monosaccharide such as glucose can be replaced by other groups
Lipids
A large group of non-polar biological molecules
Composed mainly of C, H, and O
Dissolve in organic solvents but not in water
Lipids with important cell functions:
Fats, steroids, phospholipids, glycolipids
Dont like water; organize itself away from water
Lipids: fats
Fats = triacylglycerol = glycerol + 3 fatty acids
Fatty acids linked by ester bonds
Fatty acids: long hydrocarbon chains with a single carboxy at one end
Fatty acids vary in length
No double bonds = saturated
Double bonds = unsaturated
Lipids: steroids
Complex ring structures - 4 hydrocarbon rings
Ex. cholesterol - important animal plasma membrane component
Building blocks of many steroid hormones
Lipids: phospholipids
Composed of glycerol = 2 fatty acids + phosphate + head group
Major components of plasma and organelle membranes
Hydrophobic on one end and hydrophobic on the other = amphipathic
Lipids: glycolipids
Glycolipids: like phospholipids, these compounds are composed of a hydrophobic region, containing two hydrocarbon tails, and a polar region, which contains one or more sugars. Unlike phospholipids, there is no phosphate
Lipids form biological membranes
Arrange into a bilayer
Hydrophobic regions point inwards (interior); hydrophilic regions on the outside
Lipid aggregates
Fatty acids have a hydrophilic head and a hydrophobic tail
In water, they can form either a surface film or small, spherical micelles
Their deviates can form larger aggregates held together by hydrophobic forces
Triacylglycerols form large, spherical fat droplets in the cell cytoplasm
Phospholipids and glycolipids form self-sealing lipid bilayers, which are the basis for all cell membranes
Nucleic acids
DNA (deoxyribonucleic acid) and RNA (ribonucleic acid)
DNA: genetic material; governs all cellular activities; codes for proteins required for the cell’s functions
RNA: many roles; central to the synthesis of proteins; regulates expression of genes; genetic material of some virus
Types: transfer RNA (tRNA); messenger RNA (mRNA); ribosomal RNA (rRNA)
Polymers of nucleotides
Nucleic acids: nucleotides
A nucleotide consists of a nitrogen-containing base, a five-carbon sugar, and one or more phosphate groups
Nucleotides are the subunits of the nucleic acids
What is the difference between a nucleotide and a nucleoside?
Nucleoside: Consists of a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil) attached to a sugar molecule (ribose in RNA, deoxyribose in DNA).
Nucleotide: Contains a nucleoside (nitrogenous base + sugar) and one or more phosphate groups attached to the sugar.
Nucleic acids: nucleotides
- pentose: a five carbon sugar
- each numbered carbon on the sugar of a nucleotide is followed by a prime mark
- two kids of pentoses are used
Nucleic acids: nitrogenous base
- the bases are nitrogen containing ring compounds, either pyrimidines or purines
- pyrimidine (one ring): u,c,t
purine (two ring): a, g
Nucleic acids: polynucleotide strands
- nucleotides are joined by sugar-phosphate linkages
- 3’ hydroxyl attaches to 5’ phosphate of the adjoining nucleotide (phosphodiester bond)
Nucleic acids
To form nucleic acid polymers, nucleotides are joined together by phosphodiester bonds between the 5’ and 3’ carbon atoms of adjacent sugar rings. The linear sequence if nucleotides in a nucleic acid chain is abbreviated using a one-letter code such as AGCTT, starting with the 5’ end of the chain
Nucleotides and their derivatives have many other functions
As nucleotide di- and triphosphates, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds (example ATP)
They combine with other groups to form coenzymes (example: coenzyme A; CoA)
They are used as small intracellular signaling molecules in the cell (example: cyclic AMP; cAMP)
How do cells obtain and use energy
The second law of thermodynamics states the degree of disorder, or entropy, increases in any isolated system in the universe
How then do cells appear to defy this law by generating order?
Cells take in energy from the environment and use it to generate order within it. The many chemical reactions that create this order in cells, convert some of this energy to heat. The heat released then creates disorder in the cell’s environment, increasing entropy and hence abiding by the second law of thermodynamics
Hate generating reactions within the cell are coupled to those that generate molecular order
Each cell is a tiny factor and carries out millions of chemical reactions every second
Catalyze the oxidation of organic molecules in small steps -> allows useful energy to be harvested
The vast majority of these chemical reactions only occur in cells under normal temperatures because of proteins known as enzymes. These catalalysts increase the rate of reactions by lowering the activation energy required
Enzymes can speed up reactions, but they cannot force energetically unfavorable ones to occur
ΔG is a measure of the change in the amount of energy available to do work
Favorable reactions decrease the ΔG (negative ΔG) and increase the disorder of the universe
The cell uses reaction coupling to drive energetically unfavorable reactions
We use the standard free energy change, ΔG° (standard conditions, same concentrations, same concentrations of reactants), of reactions to predict the course of biological reactions
energetically favourable vs not
energetically favourable: the free energy of Y is greater than the free energy of X. there G < 0, and the disorder of the universe increases during the reaction
energetically unfavourable: G > 0 and the universe would become more ordered
carrier molecules
Cells catalyze the oxidation of organic molecules in small steps -> allows useful energy to be harvested
This energy is stored in a small set of the activated “carrier molecules” which diffuse through the cell through sites in which they are generated to sites in which biosynthesis will occur
Cells use these carrier molecules like money to pay for reactions that would not otherwise occur
The activated carrier molecules are formed by coupling to favorable reactions
The carrier molecule (bucket) picks up sufficient energy to power an unfavorable reaction elsewhere
The activated carrier molecules are formed by coupling to favorable reactions
The carrier molecule (bucket) picks up sufficient energy to power an unfavorable reaction elsewhere
glucose and other food we eat are broken down by stepwise oxidation reactions to produce chemical energy in the form of ATP and NADH
These reactions also help produce many of the small molecules that are the substrates for biosynthesis of macromolecues
Macromolecules like glycogen and fats can be stored in cexlls as a major source of energy
Proteins
About 1x10^4 proteins made in every mammalian cell
Carry out almost all cellular functions. Examples:
Enzymes: accelerate chemical reactions in the cell
Signaling: kinases, phosphatases are involved
Hormones: long range messenger molecules
Growth factors
Membrane receptors: communication between cells
Cell movement: cytoskeleton
Proteins: amino acids
Polymers of amino acids; 20 different types
Amino acids:
Amino (NH2) and carboxyl (COOH) groups
These groups are separated by a single carbon (α-carbon)
R groups (side chains) give amino acids their variability
4 categories of R groups:
- Polar charged - can form ionic interactions
- Polar unchanged - can form H bonds
- Nonpolar - mostly hydrocarbons
(Hydrophobic
Usually in the core of protein structure (away from water) - Other (glycine, cysteine, and proline)
peptide bonds
Peptide bonds: carboxyl group of one amino acid becomes attached to the amino group of another
Forms polypeptide chains = proteins
Protein structure
Protein structures are defined by 4 different levels of organization
Primary structure (1°): specific sequence of amino acids
Determined by the sequence of the gene encoding the protein (DNA)
20^n variations of proteins (20 amino acids)
N = the number of amino acids in the chain
Typical protein is over 100 amino acids long - infinite number of sequences possible
Sequence contains most of the information needed to specify 3-D shape and function of protein
Changes in the primary structure can have dire consequences for protein function - ex. Sickle cell anemia
Affects red blood cell shape- sickle-shaped
Clogs arteries
chaperones
While some proteins do fold by a process of simple self-assembly, most proteins need some help
Help = chaperons = proteins that aid in the folding of newly made proteins by preventing inappropriate interactions
Prevent inappropriate interactions with other cellular components
Bind hydrophobic segments of proteins
Are single proteins or a large protein complex with intricate structure
Secondary structure: (2°)
Conformation of portions of the polypeptide chain
Arranged to maximize the number of H-bonds made between neighboring amino acids of peptide backbone only
2 common folding patterns: α-helix and β-pleated sheets
Protein structure
α-helix:
Hydrogen bonding that links the C=O of one to the N-H of another (between every fourth amino acid)
Cylindrical twistin spiral
R groups project outwards
β-pleated sheets:
Hydrogen bonds extend from one part of the chain to another
Polypeptide segments lie side by side
Tertiary structure (3°)
Conformation of the entire protein
Interactions between R-groups in the protein
Hydrophobic interactions
Van der Waals interactions
Disulfide bridges
3 types: fibrous, globular, and intrinsically disordered proteins
Non-covalent bonds that hold protein tertiary structure together
Fibrous proteins:
Elongated shape
Usually structural materials outside of cells
Keratin, collagen (hair, skin, fingernails)
Form long strands or flattened sheets that resist shearing forces
Globular proteins:
Compact shape
Polypeptide chain folds into complex shapes
Usually have functions within the cell
Enzymes, hormones
Most proteins
Intrinsically disordered proteins:
Loops or tails (or entire proteins) that remain disordered in structure
Contain repeated sequences of amino acids
Have important functions
E.g. elastin (stretchy)
Parts of a protein folded into the tertiary structure can have distinct functions from other regions
Modules or domains of proteins
Substructure produced by any continuous part of a polypeptide
Can function in a semi-independent manner
Can be swapped between proteins
Allow for unique protein activities
Ex. move independently; bind different molecules
Domains can be constructed from alpha-helices, beta-sheets, or various combinations of fundamental folding elements
Quaternary structure:
Linking of multiple proteins to from large complexes with multiple “subunits”-multiprotein complexes
Intermolecular interactions of R groups
Disulfide bonds
Noncovalent interactions-mostly
Proteins can be modified & regulated
Cleaved into smaller polypeptides (“pro-form” cut into smaller fragments)
Sugar chains can be added (“glycoproteins”)
Lipids added (anchored to cell membranes)
metal/ions added (important for function)
Phosphate groups added (signaling functions; alters structure or interactions)
GTP or calcium binding (alters protein activity)
Degradation (controls protein lifespan)
Regulating proteins
Regulation by degradation
The life span of proteins differs a great deal
Few minutes = mitotic cyclins
Your whole life = crystallin in lens for the eye
Controlled by regulated degradation pathways
Many degradation pathways exist in the cell:
Lysosomes
Autophagy
Proteasomes = 90% of protein degradation in mammalian cells
Proteasomal degradation:
In a “cellular chamber of doom,” proteins suffer “a death by a thousand cuts”
The proteasome degrades proteins for turnover (regulates life span) but also degrades misfolded proteins
How can it tell which ones needs to degrade?
Mark = ubiquitination
Ubiquitin (Ub) = 76 reside protein
Typically multiple copies of Ub are attached to a protein tagged for proteasomal degradation = polyubiquitination (4 or more Ub)
Required the activity of E1, E2, anf E3 enzymes that work in sequence to bring about polyubiquitination
Regulating proteins: GTP binding
Non-covalent binding to GTP can act as a “switch” to regulate protein activity
GTP binding proteins = GTPases
GTP bound = active = regulate the activity of target proteins (effectors) in this state
GDP bound = inactive
The rate of GTPases activity diffeers between proteins
GEFs and GAPs aid in regulating the “switch” that regulates these protein
Noonan syndrome:
mutations in gene encoding
Ras = a GTPase
mutant Ras has defective (decreased) intrsitic GTPase activity and is resistant to GAPs
