BIO 112
Unicellular - an organism with 1 cell (bacteria, yeast)
Multicellular- an organism with many cells (Fugi, plants, animals)
Eukaryotic cells (membrane bound organells)
DNA in eukaryotic cells is found inside the nucleus
Have a nucleus
Extensive internal array of membranes
These membranes define compartments called organelles
Multiple linear chromosomes
Transcription and translation are separated
Transcription in the nucleus
Later translation takes place in the cytoplasm
Genome size 3 Mb to 670,000
Most of the genome consists of sequences that don’t code for proteins.
Cytosol is the region inside the cell and outside of the organelles
Prokaryotic cells (single plasma membrane surrounding the cell)
DNA in prokaryotic cells is located in the cytoplasm
Lack a nucleus
Genetic material is concentrated in the nucleoid
Have a wall surrounding the cell membrane
1-2 micrometers
Genome size 0.5 - 10 mb
High ratio of surface area to volume
Most of the genome consists of protein coding genes.
Absorbed nutrients from environment
One circular chromosome
Translation occurs as soon as the mRNA is transcribed from the DNA template
Some species of prokaryotes have adapted to growth at extreme temperatures >80C.
Mostly unicellular but some multicellular forms do occur.
Globally, biomass of prokaryotes greatly exceeds that of animals
Prokaryotes include bacteria and archaea.
Primary functions of the cell membrane
To separate the internal environment of the cell from the external environment.
To control the movement of material between the interior of the cell and the external environment.
Self replicating cells
Set of instructions (DNA)
Gather materials / energy sources (Proteins)
Make parts
Transform energy
Pass on instructions to new replicates
Mechanisms to read instructions
Have a container to keep everything together
Cell theory
All organisms are made of cells
The cell is the fundamental unit of life
Cells come from pre-existing cells
&
(There is not life without cells
The cell is the smallest unit of life)
Endosymbiont theory
All cells are thought to have evolved from a universal ancestor cell (LUCA- Last universal common ancestor - 3.5 to 3.8 M years ago)
Eukaryotes are thought to have evolved from one cell engulfing another cell (endosymbiont)
Found in all cells
Ribosomes.
Cytosol.
Plasma Membrane.
1oo micrometers in one millimeter
One megabase is 1,000,000 bases
One gigabase is 1,000,000,000 bases
Pre reading quiz
The octet rule - the tendency for an atom, other than hydrogen, to form covalent bonds with other atoms until its valence shell holds eight electrons.
Polar covalent bonds
Polar covalent bonds occur between atoms that differ in electronegativity
Differences in electronegativity result in unequal sharing of electrons between atoms
The polarity of a polar covalent bond increases as the difference in electronegativity increases
The covalent bond between two amino acids in a protein is called a peptide bond
In DNA and RNA the bond between adjacent nucleotides is known as a phosphodiester bond
Molecules like DNA, RNA, proteins and polysaccharides have directionality or polarity because: the molecules contain polar covalent bonds
Proteins, nucleic acids and polysaccharides are polymers composed of smaller units of defined structure. Lipids are chemically diverse molecules that share the property of:
being hydrophobic
What properties of phospholipids determine if they will form micelles or bilayers when mixed with water?- The hydrophilicity of the phosphate-containing headgroup
Micelles - a single layer of lipid monomers
Bilayers - 2 sheets of lipid monomers
Proteins and lipids can freely move laterally within the bilayer.
Hydrophobic transmembrane regions of proteins are embedded in the fatty acid tails of the lipid bilayer.
Hydrophobic - nonpolar
Hydrophilic - polar
Amphipathic - a molecule with both hydrophobic and hydrophilic components
Phospholipid- an amphipathic molecule with a hydrophilic head group and hydrophobic fatty acid tails
Bilayer self assembly- spontaneous arrangement of lipids driven by the hydrophobic effect (tails inwards and heads towards the water) The fluid mosaic model of biological membranes is best described as the lipids and proteins form a dynamic two-dimensional fluid held together by intermolecular non-covalent links.
If bilayer-forming phospholipids are mixed with a hydrophilic dye, they form liposomes suspended in the dye. What will happen to the dye once the liposomes are formed?
The dye will interact with the phospholipid heads, surround the liposome, and fill the centre of the liposome.
The property of phospholipids that drives bilayer formation for cellular membranes are that they are amphipathic, with both hydrophilic heads and hydrophobic tails.
Endosymbiosis
Certain organelles within eukaryotic cells closely resemble engulfed prokaryotic cells
Chloroplasts and mitochondria are thought to have involved from an endosymbiont because they are
1. Surrounded by 2 membranes
2. Have inner membranes with structures that closely resemble certain prokaryotic cells
3. Contain circular genomes that code for genes that are very similar to bacterial genes
Polars bonds - atoms with
O-H
N-H
S-H (weaker)
C-O
O-P
Nonpolar bonds- atoms with
C-H
C-C
A major macromolecule in cells is DNA
Monomers that make up a macromolecule include amino acids, fatty acid chain and glucose
4 major macromolecules are
Proteins (in the cell membrane, transporter. Enzymes in the cytoplasm or Ribosomes as Organelles)
Lipids
Carbohydrates ( cell walls - energy)
Nucleic acids ( DNA- inside the nucleus and RNA in the ribosomes or travelling to the ribosomes)
An organic molecule contains at least one C-H bonds (carbon to hydrogen bond)
There is directionality in all 3 of the below bonding
In polypeptide (protein) chains the amino group always bonds to the carboxyl group
For Nucleic acids the Phosphate group bonds to the deoxyribose sugar group on the 3’ carbon
For carbohydrates the macromolecule is called carbohydrates but the monomers are called monosaccharides (simple sugars). The 4’ end of the incoming monomer is added to the 1’ end of the original monosaccharide
Lipids polymerize (bond) differently than others
Lipids do not have the same directionality as the above because they have heads and tails
Lipids (triacylglycerol) are the macromolecule but the monomer is a fatty acid, the bond that turns 2 fatty acids into a lipid is called an ester bond
Polymers of nucleic acids, proteins and carbohydrates exhibit polarity. That means they have a directionality to them and are asymmetric. Polymer has two chemically distinct ends.
Amino group is referred to as the N terminus (N). The Carboxyl group is referred to as the C group.
N -aa-aa C is normally how it's written (best answer) but if it's written C-aa-aa-N that is acceptable since in life the chain flips around and moves.
The reason it has such directionality and polarity is so they can bond and elongate in the correct way. The amino and carboxyl groups will not flip around in the middle of the chain at random, they will not bond.
Nucleic acid
DNA monomers = deoxyribonucleotides
RNA monomers= ribonucleotides
Phosphate group (5’ carbon) bonds to the 3’ carbon of the first monomer (phosphodiester bond)
Do not confuse directionality and polarity with bond polarity. Polar bonds are electronegativity differences between bonded atoms.
Carbohydrates
Monomers = glucose
4 ‘ carbons of a new glucose molecule is added to the 1 ‘ carbon (primary) of the first monomer
Lipids / triacylglycerol (different than other macromolecules! They don't bond with directionality)
One of more fatty acids tail is added to the head group with an ester bond
Membrane lipids - phospholipids - Glycerophospholipids or Sphingolipids
Glycerophospholipids
Backbone - glycerol
Nonpolar tails - fatty acids
Polar head group - PO4 and alcohol
Hydrophilic vs hydrophobic
Hydrophilic- Interact with water
-Pollar, charged, ionic interactions, make H bonds, Hydrophilic properties
Hydrophobic -
weak or little interactions with water
Typically nonpolar bonds
Phospholipids are amphipathic
Amphipathic - Phospholipids have Hydrophilic and hydrophobic properties
Phospholipids
Head (Polar head group + Glycerol backbone) is hydrophilic
Tails (fatty acids) are hydrophobic
Kink in the chain is due to double bonds
Macromolecular assembly (mostly non covalent bonds)
Macromolecules (polymers) assemble into functional structures such as
Proteins (folded) (most proteins fold but not all)
DNA double helix
Lipid bilayers
Lipids can spontaneously form a membrane so
They can repair
During replication they need to form a bilayer
Monomers to polymers (polymerization) uses covalent bonds. Polymers to functional structures (macromolecular assembly) use mostly non covalent bonds
Water is the “matrix of life”
Makes up 70% of cell mass
Universal solvent for the cell
PD-PD (Permanent dipole) bond would be the noncovalent bonds between two water molecules
bond would be happening between water and a lipid head group
In addition to Carbon and Hydrogen, the major bioelements found in Nucleic Acids are
oxygen
nitrogen
phosphorus
In addition to Carbon and Hydrogen, the major bioelements found in Proteins are:
Nitrogen
oxygen
sulfur
In addition to Carbon and Hydrogen, the major bioelements found in Lipids are:
Nitrogen
sulfur
phosphorus
In addition to Carbon and Hydrogen, the major bioelements found in Carbohydrates are:
Oxygen
Osmosis- When water moves into an area of high solute concentration until it is counteracted by a force such as a cell wall
The characteristics that would increase the ability of a molecule to diffuse across a lipid bilayer include:
No ionic charge
Small size
Few polar functional groups
the primary driver for active transport across biological membranes is:
The molecule transported is moving from an area of lower concentration to higher concentration, which is energetically unfavourable.
Lipids
Phospholipids are amphipathic
-polar heads
-Nonpolar tails
Lipids tails tun into lipid polymers (phospholipids turns into membranes
This process is spontaneous in water
Phospholipids interact via non covalent interactions in a bilayer
Membrane formation is spontaneous due to thermodynamics principles and the hydrophobic effect
Macromolecular assembly
The process of molecules, or complexes of molecules forming a particular three dimensional conformation or structure as a result of
Intramolecular interaction (covalent, ionic, hydrophobic)
Intermolecular interaction (non-covalent)
Interaction with surrounding water molecules
Thermodynamics
A study of system stability
A field of chemistry that deals with the likelihood of reactions occurring in a system
System stability depends on delta G = delta H (enthalpy) + (-Tdelta S(Entropy))
System stability depends on enthalpy ( measures how strongly bonded a system is)
System stability depends on Entropy ( measures the freedom to move of components of a system)
Energy favorable process = spontaneous
(likely to happen in this direction - reaction moved from less stable to more stable)
Energetically unfavorable process = not spontaneous
(requires energy input to happen in this direction, ration moved from more stable to less stable)
Note: favorability /spontaneity does not tell you about reaction speed or rate.
Thermochemistry
Study of heat energy associated with chemical reactions
Phosolipid assembly in water is
Spontaneous
Energetically favorable
Delta G is less than zero (ΔG <0)
System moves from less stable to more stable
Lipid bilayer formation
Both enthalpy and entropy contribute to bilayer stability
The largest contributor to system stability in bilayer formation is entropy of the water (increase in motional freedom of the water molecules)
The hydrophobic effect
Burying nonpolar groups away from water increases the systems stability
Water will permeate the bilayer first, then glycerol, toluene and then phosphate
In a aqueous environment when a lipid bilayer forms, most water molecules acquire greater motional freedom
Hydrophobic effect
Allows for building and stabilizing lipid bilayers as well as the 3D structure of proteins and DNA
Membrane transport
Passive transport
Simple diffusion - (diffuses through the lipid bilayer)
Facilitated diffusion -(uses protein transporter)
Channel mediated- , can be open or gated, selective for specific molecules. Chanel provides a hydrophilic passageway and aqueous pore. This type of diffusion is usually quicker then carrier proteins. Molecules have to interact with the protein channel
Carrier mediated - carrier proteins are gated; they have an open and closed formation. Carriers transport specific types of molecules (more specific than channels) . The protein undergoes a shape change.
Active transport - Will go against the concentration gradient and requires energy
Primary active transport - using energy directly
Move molecules against concentration gradient
ATP is used as an energy source to pump
Sodium is moving outside of the cell, potassium is moving inside the cell
Called primary because energy is used directly for the pumps
Na+ K+ pump
Na+ (sodium) transport protein (pump) is in ‘open conformation’ in the cytoplasm (inside the cell)
Na binds to this open conformation
ATP is de-phosphorylated to ADP. This directly provides energy to change the conformation
The transport protein changes shape and Na+ is released to the outside (extracellular space).
Primary = ATP is the primary energy source
The protein is now in open conformation outside the cell (closed inside the cell)
K+(potassium) binds to this open conformation (as Na + is released)
Binding of K+ causes a conformational change in the protein.
K+ is transported into the cell and the open conformation of the protein is now on the cytoplasmic side of the membrane.
Molecules can move in either direction but there can be a net direction of movement (into the cell)
Water can be transported by both simple diffusion and facilitated diffusion (osmosis)
In facilitated diffusion glucose moves along the concentration gradient, molecules can move in both directions but have a net direction. Energy is not required to transport glucose
Secondary active transport - indirectly uses energy
Uses energy indirectly to move molecules against a concentration gradient.
Protons (H+) are transported across the membrane by a transporter protein
This is active transport. Now for step 2 there is an established electrochemical gradient. The protons cannot move back across their membrane due to their charge. Step 3, transporter protein 2 allows the movement of H+ down/ along the concentration gradient and back into the cell. This provided the energy to move other molecules outside the cells.