CONNECTION: (Abby):
Hydrogen bonds are the bonds that must be broken in order for replication to occur.When hydrogen bonds are broken by Helicase proteins they are ready for replication
CONNECTION (Abby):
Histones(a protein) gives support for Chromosomes which hold DNA
This unique arrangement acts as a formidable barrier to the free passage if polar molecules and ions.
Polar vs. Non Polar
Nonpolar Molecules (O + CO2): they can easily diffuse the lipid bilayer because they are soluble in the hydrophobic interior.
Polar Molecules (Glucose + Ions): Struggle to pass through the lipid bilayer because of their interaction with the hydrophobic region.
In organelles
Further Modification Occurs
Protein folds into 3D shape
Amino Acids "tell" proteins where they must go
Concept Map 1
Prokaryotic Cells
Cell Wall
Structure: The cell wall is one of the outermost layers of the cell. It's composed of cellulose microfibrils and cross linking glycans which are embedded in a highly cross-linked matric of pectin polysaccharides.
Function: While the cell wall surrounds the plasma membrane of plant cells, it also provides a tensile like strength and protection against mechanical and osmotic stress and other enemies that reveal as a threat to the cell. It also allows the cell to develop turgor pressure which is the pressure of the cell contents against the wall. It's basically a wall meant to protect all the components of the prokaryotic cell.
Plasmid
Structure: A small, circular, double stranded DNA molecule that's distinct from a cell's chromosomal DNA. They naturally exist in bacterial cells. These genes often carry the plasmids provide bacteria with genetic advantages, like antibiotic resistance. Most commonly found in the cytoplasm.
Function: They're used in this genetic engineering to amplify as many copies of genes as possible. They are typically tools of cloning, transferring, and manipulating genes.
Flagella
Function: Gives motility organelle that enables movement and chemotaxis. They spin around and propel the cells very quickly. They act as little fins or tails to help the cell move.
Structure: A coiled, string-like structure that's sharp bent and consists of a rotary motor at its base and are composed of the protein flagellin. The basal body, a rod and a system of rings embedded in the cell envelope; the hook, which functions as a universal joint; and the filament, composed of thousands of copies of protein flagellin arranged helically and ending with a filament cap composed of an oligomer (a molecule that consists of few repeating units which could be derived, actually or conceptually from molecules)
Pili
Structure: Resembles hair attached to the outside of the prokaryote (attached to cell wall). It's typically associated with bacterial adhesion related to bacterial colonization and infection. They are primarily composed of oligomeric pili proteins, which arrange helically to form a cylinder. When new pili protein molecules are made, they insert into the base of the pilius.
Function: They initiate contacts between mating pairs. They also facilitate the transfer of genetic material and they draw mating cells into close contact which increased the fertility of the union. They also have a role in the movement process but are most commonly involved with the adherence to surfaces which facilitates infection and is the key to virulence characteristic.
Capsule
Structure: It's the sticky, outermost layer of the cell which is usually made of polysaccharides.
Function: This helps prokaryotes attach to each other and to various other surfaces in their environment, it also helps prevent the cell from drying out. It's also a sort of boundary which protects bacteria from toxic compounds and desiccation (drying out) and allows them to again adhere to surfaces and escape the immune system of the host.
Nucleoid
Structure: Largely composed of about 60% DNA, plus a part of it is made up of RNA and protein. It is proven to had a defined, and self-adherent shape and an underlying longitudinal shape. It lacks membrane and is located within the cytoplasm. It contains proteins, including enzymes and RNA as well as DNA.
Function: for controlling the activity and reproduction of the cell. In the nucleoid, it's the place where transcription and replication of DNA takes place. It binds proteins leading them to have a lower molecular mass. This alters the shape of the nucleoid itself.
Eukaryotic Cells
Rough ER
Structure: Flattened membrane sheets (Cisternae), they surround a part of the nucleus and extend across the cytoplasm. Sections of this Cisternae has ribosomes attached and held together by microtubules of the cytoskeleton.
Function: Produces/Transfers proteins throughout the rest of the cell to function. Its ribosomes are small and round whose function is to make those proteins
Structure: Lives in the double membraned organelle, withholds the nucleolus, holds 25% of volume. Chromatins are found within the nucleus containing proteins and DNA
Function: The respiratory of genetic information and is the cell's control center. DNA replication and transcription, as well as RNA processing all take place within the nucleus.
Smooth ER
Structure: Tube like structure located near the cell periphery. These tubes sometimes branch and form a network that is reticular on first glance. The network of smooth ER allows an increased surface area to only have the purpose of storage to key enzymes
Function: Responsible for the synthesis of the essential lipids like phospholipids and cholesterol. Its also responsible for the production and secretion of steroid hormones and the metabolism of carb. Lastly, it stores and releases calcium ions.
Centriole
Structure: 9 circularly arranged triplet microtubules. There paired barrel shaped organelles located in the cytoplasm of animal cells near the nuclear envelope.
Function: Play the role of organizing microtubules so that they can serve their functions as the cell's skeletal system. They help to determine the locations of the nucleus and other organelles in the cell.
Golgi apparatus
Structure: Stack of flattened cisternae and associated vesicles. This transfers proteins and lipids coming from the ER from the cis face and exiting through the trans face.
Function: Works as a factory where proteins coming from the ER are processed and sorted for transport to their designated destinations. As well as synthesizing glycolipids and sphingomyelin within the golgi
Structure: Has its own double membrane with inner and outer mitochondrial membranes, and is separated by an intermembrane.
Function: The powerhouse of the cell. Generates most of the chemical energy needed to power the biochemical cell reactions.
Chemical Bonds
Covalent Bonds
Polar Covalent Bond
A bond where electrons are unequally shared by the atoms and spend more time close to one atom than the other.
Because of the unequal distribution of electrons between the atoms of different elements, slightly positive and slightly negative charges develop in different parts of the molecule
Non Polar Covalent Bond
A bond between two atoms of the same element, or between atoms of different elements that share electrons more or less equally.
Ionics Bonds
Ionic bonds are formed between two or more atoms by the transfer of one or more electrons between atoms. Electron transfer produces negative ions called anions and positive ions called cations.
Hydrogen Bonds
Interaction involving a hydrogen atom located between a pair of other atoms having a high affinity for electron; such a bond is weaker than an ionic bond or covalent bond but stronger than van der Waals forces.
organelles in common
cytoplasm
Structure: Gel like fluid inside the cell. It provides a sort of like a stabilization to keep all the other organelles in place, which gives the cell itself its shape.
Function: This holds all the works for cell expansion, cell growth, and cell replication throughout it. While doing this, it also protects the cells from damage.
Structure: Each ribosome consists of 2 separate RNA-protein complexes (aka small and large subunits). The ribosomes themselves are made up of RNA and proteins.
Function: The ribosome is the sole site for protein synthesis. They read the mRNA sequence and translate the genetic code into an amino acids string which lead to grow into long chains that fold to form proteins. Attaches itself to Rough ER when available (Only in Euk)
Cell membrane
Concept Map 3
Chromosomes
All body cells have same chromosomes
Regulating by turning on (inducing)
Regulating by turning off (repressing)
Activator and enhancer Region
7 different control points in eukaryotes
Regulatory genes (regulators) = affect transcription / translation in making final protein
In eukaryotes = gametes
Operon system depending on lactose and glucose
Transcription
Initiation Phase
makes mRNA
Pre mRNA in Eukaryotes
modified guanine 5' Cap
Recognition signal for Ribosomes to bind
Allows Translation to occur
Introns and Exons
Spliceosomes
Introns removed
mature mRNA
mRNA leaves the nucleus
Poly-A Tail on 3'
Uses ATP
Protects from degradation in cytoplasm
Upstream
Promoter
TATA Box
DNA sequence
Main Enzyme: RNA Polymerase
Reads 3'to 5'
Synthesizes 5' to 3'
Translation
Start Codon: AUG
Prokaryotes: F-Met
Eukaryotes: Met
Stop Codons
UAA, UGA, UAG
tRNA
Ribosomes
Binding Sites
EPA
Eukaryotes
80's
Prokaryotes
70's
Amino Acyl tRNA Synthetase
Adds amino acids to 3' of tRNA
Formation of Proteins from mRNA
In cytoplasm
Forms polypeptide chains
Peptidyl Transferase
Makes Peptide Bonds
Consists of Amino Acids
DNA Replication mechanism
conservative
2 parental strands reassociate after acting as templates for new strands, this restores the original parental double helix
This visualization is a lot easier because it can only have 2 options: 2 pure dna strands. 3 pure light blue DNA and 1 pure dark blue DNA
dispersive
each strand both daughter molecules contains a mixture of old and newly synthesized
A way to visualize the dispersed model is the result in the first replication being unpredictive and messy strands. very messy strands, unpredictable
semiconservative
2 strands of the parental molecule separate and each functions as a template for synthesis of a new complementary strand
A way to visualize in 1 pure strand separates and in the first replication you will end up with 2 strands of DNA equally dispersed into it. the 2nd replication could result in 2 equally split DNA strands together and 2 pure strands of DNA. 1 light blue and 1 dark blue strand combined and a pure light blue strand of DNA
Organic molecules
Oxygen is used as the electron acceptor
used for the ETC
cellular respiration formula
C6H12O6 + 6O2 = 6CO2 + 6H2O + ATP
Goes through 3 Stages
Glycolysis then converted to pyruvate
Krebs Cycle
Last step in cellular respiration
2 ATP and NADH made
Used in Cellular Respiration
Occurs in mitochondria
Produces ATP
Energy for the body
Metabolic Pathway
Protein Pathway (s)
Endoplasmic Reticulum allow newly made protein to enter the ER lumen
Carbohydrates attach through enzymes which result in a glycoprotein
Protein gets packed to a Transport Vesicle
Vesicle delivered to cis side of Golgi
Folded proteins get packed into secretory vesicle (specific type) on the Trana side of Golgi
Delivered to plasma membrane
undergo exocytosis if they are free floating
Secrete out of cell
Embed into membrane if they are membrane-embedded
Called "Membrane Protein"
Folded protein gets packed into another transport vesicle
Lysosomes
Can return to ER
Can travel to cytoplasm
Peroxisomes
Plastids
Nucleus
Chloroplasts
Mitochondria
concept map 2
Cell Membranes as Permeable Barriers
Selectively Permeable
Allows positive, and necessary substances to pass through while also preventing unnecessary substances from entering.
Regulating Homeostasis
Osmoregulation: defined as the control of water balance; nutrient uptake, waste elimination, and maintaining an electrochemical gradient across the membrane
Cells must control the passage of ions and molecules to maintain the proper concentration of substances inside and out.
Achieves through combination of factors including the bilayer and various other proteins embedded within the membrane.
Proteins
Receptor Proteins
Proteins in the cell membrane act as receptors for specific molecules, this allows the cell to detect and respond to environmental signals.
Represents the membrane as a dynamic and constantly changing structure, with lipids and proteins able to move within the bilayer, this further influences permeability.
Transport Proteins
These transport proteins that often require energy, in the case of active transport, or they will rely on the concentration gradients, this in the case of passive transport, to help move substances.
Glycoproteins + Glycolipids
Proteins and lipids with attached carbohydrate chains. They play the roles in cell recognition, adhesion, and signaling.
Cholesterol
Present in the cell membrane, they help regulate the fluidity and stability of the membrane.
They prevent the membrane from becoming too rigid. This dynamic adjustment of fluidity ensures that the membrane functions optimally under varying environmental conditions.
Interspersed within the lipid bilayer
Lipid Bilayer
Composed primarily of phospholipids
This is the basic structure of the cell membrane.
These lipids have hydrophobic tails (water repelling) and hydrophilic heads (water loving). These create a barrier to the passage of water-soluble substances, as they repelled by the hydrophobic core of the membrane.
The hydrophobic tails face towards the interior of the bilayer.
The hydrophilic heads face the aqueous environment both in and outside the cell.
Tyrosine Kinase
Inactive monomers with a ligand binding site
When signal molecules bond with receptor sites they create a dimer of two tyrosine kinase receptors
Dimerization activates phosphorylation
The active receptor is now recognized by multiple relay proteins
cellular responese
G Protein Coupled Receptor
cAMP is a second messenger in signaling pathway of a G protein
GCPR is activated with a first messenger bind
Then the now activated GCPR binds to the G Protein then activates GTP and activated G protein.
Attaches to Adenyl Cyclase which causes phosphatase to occur
Activated Adenyl Cyclase converts cAMP to ATP
Then second messenger cAMP activates another protein
cellular response
Glycolysis
Pyruvate oxudation
occurs in cytosol
Used: 2 ATP Formed: 4 ATP, 2 NADH Net: 2 ATP, 2 Pyruvate Molecules, 2 H2O, 2 NADH
Step 1: Glucose ---> Glucose 6 Phosphate
Step 2: Glucose 6 Phosphate --> Fructose 6 phosphate
Step 3: Fructose 6 phosphate --> Fructose 1, 6 biphosphate
Enzyme in use: Phosphofructokinase/PFK (transfers phosphate group from ATP to opposite end of sugar (using second molecule of ATP))
Step 4: Fructose 1,6 bisphosphate --> TWO glyceraldehyde 3 Phosphates (G3P)
ATP ---> ADP (using phosphate group from ATP)
Enzyme in use: Phosphoglucoisomerase (converts glucose 6P to fructose 6P
Enzyme in use: Hexokinase (Transfers phosphate group from ATP to glucose
ATP --> ADP (using phosphate group from ATP)
cell communication
