DNA Replication
Enzymes involved
Helicase
unzips the double helix at the replication fork
Primase
is a an enzyme that helps put down a primer (short stretch of RNA) that is needed by DNA pol III to begin
Single Stranded Binding Proteins
bind to unpaired DNA to keep the strands for re-pairing
DNA Ligase
binds the Okazaki fragments on lagging strand and joins 3’ end of DNA that replaces primer to rest of leading strand
DNA Pol I
removes the primer with RNA nucleotides and adds DNA nucleotides
DNA Pol III
adds DNA nucleotides to the 3’ end of the primer
Topoisomerase
is an enzyme that helps relieve strain that was formed during untwisting of double helix which causes tighter twisting and strain ahead of replication fork. Helps relieves this strain by breaking and rejoining DNA strands
Leading Strand
In the leading strand, which go towards the fork….after a primer is placed, DNA Pol III can add DNA nucleotides continuously in the 5’ to 3’ direction.
Lagging Strand
In the lagging strand, which moves away from the the fork and towards the ORI, multiple primers are placed, DNA Pol III creates segments of DNA nucleotides from primer to primer called okazaki fragments.
Types of Replication
Conservative
the two parental strands reassociate with each other after acting as templates, thus restoring the double helix
Semi-conservative
the two strands of the parental model separate and each functions as a template for synthesis of a new complementary strand.
Messelson-Stahl Experiment
Proof of semi conservative. The two cultured bacteria in a heavy 15N and then transferred the bacteria to regular 14N. After each replication, the test tube was centrifuged to observe the location of the bands. After the first replication the band was in the middle because it was a complete mix of 14N and 15nN. After the second replication, there was a middle band and a higher band because now there was DNA with combo fo 15n and 14N in the middle and just 14N DNA at the top of the test tube.
Other Important Experiments
Griffith, Avery, McCleod and McCarty
Took two strain two strains of streptococcus pneumoniae. R strand and S strand. The strand had a capsule (Smooth) and the R did not. The S strain proved to be pathogenic when injected in mice. Living S cells in mice illes the mice, living R cells in mice had no effect on mouse health, heat killed S cells left the mice healthy too, BUT heat killed S cells injected with a mixture of R cells left the mice dead. This proved that the R bacteria had been transformed by some element from the S cells (unknown at the time but later proved to be DNA), was inherited by the R cells and enabled R cells to form capsules too
Hershey and Chase:
Proved that DNA was the source of genetic material. During their experiment they tagged a virus (bacteriophage). They tagged the protein coat of the virus with 35S and tagged the DNA with 32P. Then they observed the bacteriophage attach on to a bacteria observed the 32P tagged DNA had entered the bacteria. The heavy pellet of in a test tube was radioactive
Experiments dealing with proteins
Proteins
Monomer
Amino acids
The building blocks on proteins are called amino acids. They consist of an amino group, a carboxyl group, and an R group. Amino acids bond with other amino acids via the amino and carboxyl groups (main chain and polypeptide backbone) through dehydration reactions. The amino group is positively charged and the carboxyl group is negatively charged. It’s a zwitterion.
Main chain
The main chain of an amino acid consists of the amino group and then carboxyl group
Side chain
R- group
Bonds between R groups
Hydrogen bonds between polar R groups, hydrophobic interactions and Van der Waals between non-groups, and ionic bonds between acidic and basic R groups
Formation of polymer from amino acids
Amino acids are bonded together through dehydration synthesis when an OH from a carboxyl group is bonded to an H from an amino group of another amino acid.
Bonding in Proteins
Covalent peptide bonds between main groups of amino acids in the primary structure. Hydrogen bonding between hydrogen and oxygens of main group in secondary structure. Hydrogen, ionic, and Van der Waal interactions between R groups in tertiary structure. R groups interact in quaternary structure.
effects of physical and chemical agents on protein folding
Proteins and can only fold and function under certain conditions. If the temperature, pH, or salt concentration, etc become too extreme...the bonds holding the proteins together are destroyed causing the protein to unravel. This is called denaturation.
Polarity effect on protein folding
If proteins are removed from an aqueous solution to a nonpolar environment, a protein refolds so that the hydrophobic regions now face outward toward the solvent.
Other Macro-molecules
Nucleic Acids
Monomer
Nucleotide
Components of nucleotide
Nucleotide consists of a nitrogenous base, a 5 carbon sugar, and a phosphate group.
Different from nucleoside
A nucleoside has all the components of a nucleotide except a phosphate group
DNA and RNA
DNA VS RNA
DNA is composed of a deoxyribose sugar, is helical in shape, and runs antiparallel. It has the base pair Thymine. RNA is single stranded, has the ribose sugar, and instead of Thymine, as Uracil. The difference between the two sugars is that in the 2 prime location of the sugar, DNA lacks an oxygen so it’s just H at the 2nd carbon. Ribose has an oxygen so at the 2nd carbon there's an OH.
Lipids
Biological molecules that don’t mix well with water and are hydrophobic because they mostly consist of hydrocarbon chains.
Monomers
Do not have any and that's why lipids are not considered polymers
Fat vs Fatty acid
A fat consists of a glycerol molecule attached to fatty acids. Fatty acids are long carbon skeletons that have a carboxyl group at one end that can attach to the OH groups of glycerols
components of triglyceride, including saturated and unsaturated fatty acids
A triglyceride consists of glycerol bonded to three fatty acid chains. Saturated fats are those triglycerides that have fatty acid chains with no carbon double bonds. It’s SATURATED with hydrogens. Unsaturated fats are triglycerides with one or more fatty acid tail that has carbon double bonds. The double bonds in unsaturated fats are mostly cis but when saturated fats become hydrogenated, some trans carbon double bonds can form.
why some triglycerides are liquid at room temperature and some solid
Saturated fats are solid at room temperature because they have no kinks in their fatty acid tails due to the lack of carbon double bonds. This leads to the fatty acid tails being flexible and be able to pack together in solidify. Unsaturated fats are liquid at room temperature because their fatty acid tails have kinks due to the carbon double bonds with leads to reduced flexibility and thus cannot pack together and solidify.
Structure
A triglyceride is composed of a glycerol attached to 3 fatty acid tails. A phospholipid consists of a glycerol, 2 fatty acids, and a phosphate group.-which has a negative electrical charge.
Phospholipids
The hydrophobic fatty acids don’t interact with water but instead interact with other fatty acid tails. The negatively charged phosphate group interact with water The phosphate groups face outside the cell and inside the cell too.
Steroids
A carbon skeleton consisting of 4 fused rings. May occur as components of membranes in the form of cholesterol.
Dispersive
each strand of both daughter molecules contains a pictures of old and newly synthesized DNA
ORI
Site where DNA replication occurs and are short stretches of DNA that have a specific sequence of nucelotides.
Steps for DNA Replication
2. Translation
Translation is the process in which ribosomes in the cytoplasm or ER synthesize proteins after the process of transcription of DNA to RNA in the cell's nucleus.
1. Transcription
Transcription is the first step of gene expression, in which a particular segment of DNA is copied into RNA by the enzyme RNA polymerase.
Post-Transcriptional Modifications
Addition of 5' G-Cap and 3' polyA tail
1. Facilitate the export of mature mRNA from the nucleus
2. They help protect the mRNA from degradation by hydrolytic enzymes
3. they help ribosomes attach to the 5’ end of the mRNA once the mRNA reaches the cytoplasm.
Dehydration Reaction
A dehydration reaction is when two molecules are joined together via a covalent bond at an expense of a water molecule being lost.
Water
Different properties of Water
Adhesion
A water molecule can bond to 4 other water molecules through H-bonds because of the partial charges. This keeps water close together and gives way to the property of adhesion.
Cohesion
Water being a polar molecule, can H-Bond to other polar molecules as well and these feature is known as cohesion.
Surface Tension
Related to cohesion is water surface tension because at the surface water i molecules are arranged that they are bonded to molecules next to each other and to the water below. This asymmetry gives water an unusually high surface tension.
Specific Heat
It takes a large amount of energy to cause a change in temperature and this due to its hydrogen bonds. A water molecule can potentially bond to 4 other water molecules. A calorie of heat causes a relatively small change in temperature because much of the ehat is used just to break the bonds before the water molecules can begin to move faster, increasing kinetic energy and thus temperature.
Heat of Vaporization
Water also has a high heat of vaporization-the quantity of heat a liquid must absorb for 1g of it to be converted to the gas phase. The high heat of vaporization is due to water’s hydrogen bonding abilities with other water molecules. A lot of energy is needed before the H-Bonds are broken before the molecules can exit the liquid state. This property leads to the phenomenon of evaporative cooling, fastest/”hottest” molecules escape reducing average kinetic energy.
Heat
When water absorbs heat, hydrogen bonds break
When bonds form, heat is released
Types of Bonds
Polar Covalent
between two atoms with different electronegativities
Non-polar Covalent
between two atoms with similar electronegativities.
Ionic
between cation and anion and doesn’t share electrons.
Hydrogen Bonds
attraction between hydrogen and an electronegative atom.
Hydrophobic
between non-polar molecules; they aggregate in polar environments
Van Der Waal
individually weal and occur only when atoms and molecules are very close together.
Functional Groups
Hydroxyl
-OH, polar, hydrophilic
Methyl
CH3, non-polar, hydrophobic
Phosphate
OPO3 2-, acidic, hydrophilic
Carbonyl
-C—O, polar, hydrophilic
Carboxyl
-COOH, acidic, hydrophilic
Amino
-NH2, basic, hydrophilic
Sulfhydryl
-SH, polar, hydrophilic
pH
pH is the negative logarithm of hydrogen ion concentration in the water. It is measured by the amount of Hydrogen ions are in the water.
A buffer is a substance that minimizes changes in the concentration of H+ and OH- in a solution. Carbonic acid is used in human blood. When the H+ ion concentration in the blood begins to fall, the reaction of creating HCO- and H+ increases. And vice versa for when the H+ concentration increases.
Isomers
are compounds that have the same number of atoms of the same elements, but different structures and hence different properties.
Types of Isomers
structural
Cis/trans
enantiomers
Asymmetric carbon is a carbon with 4 different types of atoms or groups of molecules. Asymmetric carbon forms enantiomers which are isomers that are mirror images of each other and differ in shape.
Carbon can form chains of carbon, can be able to branch out, can create double bonds in any position, and even create rings.
Reasons why Carbon has versatile bonding
The electron configuration of carbon gives it covalent compatibility with many different elements
Its small atom size and 4 valence electrons which can be shared by other atoms that can share electrons creating covalent bonds
its ability to bond to 4 other chemical bonds gives carbon the ability to form versatile bonds
Carbohydrates
Monomer
Monosaccharide
Glucose
Fructose
Galactose
Disaccharide
Sucrose
Fructose+Glucose
Lactose
Glucose+Galactose
maltose
Glucose+glucose
Polysaccharide
Glycogen
Animals
amylose
amylopectin
Cellulose
Starch
Plants
Use alpha Glucose in structure
Has -OH on bottom plane of Glucose structure
Use Beta glucose in strucutre
Has -OH on top of Glucose structure
Beta Glucose alternates up and down facing in cellulose.
Miller Urey Experiment
It was a chemical experiment that simulated the conditions of early earth. He added various types of gases and sparked it to create the primitive building block that are necessary for life to thrive.
Early Life on Earth
chemical evolution hypothesis
It was an explanation in which living things were produced from nonliving molecules. the primitive atmosphere would eventually create some primitive amino acids and nucleic acids. Then they would form proteins and nucleic acids which would’ve formed a protocell and eventually from an actual cell.
What is needed in a molecule to start biological evolution?
A biological molecule should have the ability to replicate itself and the ability to hold information
Prokaryotes
Bacteria
Obligate Aerobes
Obligate aerobes can only survive when oxygen is present
Obligate Anaerobes
Obligate anaerobes can only survive when there is no oxygen present.
Facultative anaerobes
Facultative anaerobes can either survive in oxygen or in a lack of oxygen.
Archaea
Halophiles
Halophiles live very well in salty conditions
Thermophiles
Halophiles live very well in salty conditions
Methanogens
methanogens survive in anaerobic conditions, usually converting CO2 to CH4
Eutkaryotes
Endosymbiotic theory
It was a theory in which a prokaryotic cell engulfed a small cell but didn’t get digested. Instead it helped out the large cell through a symbiotic relationship. The small cell soon became an organelle found in all eukaryotes: the chloroplast in plants and mitochondria in both plants and animals.
Animal Cell
Organelles
Nucleus
contains the DNA of the cell.
Plasma membrane
is the membrane that encloses the cell and allows certain molecules to enter or exit the cell.
Ribosomes
complexes that produce proteins. Can be bound to ER or free floating.
Golgi
: is active in synthesis, modification, sorting, and secretion of cell products.
Lysosomes
digestive organelle where macromolecules are hydrolyzed.
Peroxisomes
produces hydrogen peroxide as a by-product and then converts it to water.
Endoplasmic Reticulum
network of membranous tubules within the cytoplasm of a eukaryotic cell, continuous with the nuclear membrane. It usually has ribosomes attached and is involved in protein and lipid synthesis.
Rough ER
The Rough makes and packages proteins.
Smooth ER
The Smooth helps in protein and lipid storage.
Vacuoles
a space or vesicle within the cytoplasm of a cell, enclosed by a membrane and typically containing fluid.
Food vacuoles
contains digestive enzymes that digest nutrients
Contractile vacuole
vacuole pump excess water out of the cell, thereby maintaining a suitable concentration of ions and molecules inside the cell.
Central vacuole
develops by a coalescence of smaller vacuoles. The solution inside the central vacuole, called cell sap, is the plant cell’s main repository of inorganic ions, including potassium and chloride. Also absorb water.
Organelles
Mitochondria
Mitochondria is the site of cellular respiration, which uses O2 to create ATP by extracting energy from sugars and fats
Extracellular Matrix
Components of ECM include Proteoglycan molecule, Proteoglycan complex, and collagen fiber.
Cytoskeletal elements
Microtubules
made of tubulin, maintains the shape of the cell, cell motility, chromosome movement in cell division, and organelle movements
Microfilaments
: made of actin. Maintain cell shape, changes cell shape, muscle contraction, cytoplasmic streaming, cell motility, cell division.
Intermediate filaments
made of one of several different proteins of the keratin family. Maintenance of cell shape, anchorage of nucleus and certain other organelles and formation of nuclear lamina.
Types of Junctions
desmosomes
tight junctions
gap junctions
Plant Cell
Organelles
Chloroplast
Chloroplasts are the site of photosynthesis which converts solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic molecules such as sugars from CO2 and water.
Cell Wall
Primary cell wall > secondary cell wall > plasma membrane
Type of Junction
Plasmodesmata
Similar in the sense that they both have cytoplasmic channels that connect one cell to another.
Immune cells
Macrophages
large phagocytic cell found in stationary form in the tissues or as a mobile white blood cell. Has the ability to locate and eat infectious particles.Macrophages have more lysosomes in order to deal with the digestion of food particles.
B cells
responsible for producing antibodies. B cells have a lot of ribosomes, ER, and golgi in order to deal with the release of antibodies.