Chemical Bonds

DNA Replication Mechanism

Semi-Conservative

2 strands of the parental molecule separate and each functions as a template for synthesis of a new complementary strand

Dispersive

each strand both daughter molecules contains a mixture of old and newly synthesized

Conservative

2 parental strands reassociate after acting as templates for new strands, this restores the original parental double helix

Protein Pathway(s)

Transcription

Initiation Phase

Makes mRNA

Upstream

Promoter

TATA Box

DNA Sequence

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 cytosplasm

Main enzyme: RNA Polymerase

Reads 3' to 5'

Synthesizes 5' to 3'

Translation

Start Codon: AUG

Eukaryotes: Met

Prokaryotes: F- Met

Stop Codons

UAA, UGA, UAG

Forms polypeptide chains

Peptidyl Transferase

Makes peptide bonds

consists of amino acids

Formation of Proteins from mRNA

In cytoplasm

tRNA

Ribosomes

Prokaryotes

70's

Binding Sites

EPA

Eukaryotes

80's

Amino Acyl tRNA Synthetase

Adds amino acids to 3' of tRNA

DNA & RNA Monomers

RNA

Uracil

STRUCTURE: 4 hydrogen, 4 carbon, 2 nitrogen, and 2 oxygen. It's atoms that are bonded together, gives a ring shape.

FUNCTION: Uracil (RNA) replaces Thymine (DNA) in RNA. It helps carry out enzyme synthesis that's necessary for cells to function through bonding with the riboses and phosphates

DNA

Thymine

STRUCTURE: Composed of a single ring consisting of carbon (4), hydrogen (5), nitrogen (2), and oxygen (2).

FUNCTION: Helps stabilize nucleic acid structures. Paired with Adenine. (2/4)

Both

Adenine

STRUCTURE: Made of carbon, nitrogen, and hydrogen atoms. It's chemical formula is C5H5N5. When it attaches to ribose and phosphate, it forms a nucleotide.

FUNCTION: A nitrogenous bases for the nucleic acid synthesis. 1/2 purine nucleobases, it's job is to produce nucleotides for nucleic acids. It's typically paired with Thymine. Belongs to nucleotide group called purines (1/4)

Guanine

STRUCTURE: Composed of 2 nitrogen, 3 carbon, 4 hydrogen, and 1 oxygen. It's 2 rings attached to each other, 5 membered ring and a 6 membered ring.

FUNCTION: A building block of DNA which encodes information. It's also used for energy in G proteins. Paired with Cytosine. (3/4)

Cytosine

STRUCTURE: a single heterocyclic aromatic ring, a keto group of C2 and an amino group at C4c. It's molecule is a planar shape. Cytosine can form 3 hydrogen bonds with guanine

FUNCTION: codes genetic information that molecules carry. It can be made into different bases to carry epigenetic information. Energy carrier and cofactor of CTP. Paired with Guanine(4/4)

Cells

Prokaryotic Cells

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.

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.

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.

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)

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.

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.

Ribosomes

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

Structure: The main part of the structureis the phospholipid bilayer which forms a stable barrier between 2 compartments. Inside the plasma membrane, these compartments are the in and outside of the cell.

Function: Manages the transport of materials entering and exiting the cell. They keep toxic substances out of the cell. They contain receptors and channels that allow specific molecules (ions, nutrients, wastes, and metabolic products), mediate cellular and extracellular activities passing between organelles. Lastly, they maintain cell mobility, secretions, and absorptions of substances.

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

Nucleus

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.

Mitochondria

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.

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

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.

covalent bonds

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.

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

Hydrogen Bond

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.

Ionic 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.

Cell Membranes as Permeable Barriers

Selectively Permeable

Allows positive, and necessary substances to pass through while also preventing unnecessary substances from entering.

Achieves through combination of factors including the bilayer and various other proteins embedded within the membrane.

Regulating Homeostasis

Cells must control the passage of ions and molecules to maintain the proper concentration of substances inside and out.

Osmoregulation: defined as the control of water balance; nutrient uptake, waste elimination, and maintaining an electrochemical gradient across the membrane

Lipid Bilayer

Composed primarily of phospholipids.

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 hydrophilic heads face the aqueous environment both in and outside the cell.

The hydrophobic tails face towards the interior of the bilayer.

This is the basic structure of the cell 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

Fluid Mosaic Model

Energy Transfer

Cell Communication

Tyrosine Kinase

Inactive monomers with a ligand binding site

When signal molecules bond with receptor sites they create dimer of two tyrosine kinase receptors

Dimerization activates phosphorylation

The active receptor is now recognized by multiple relay proteins

Cellular Response

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

Hydrogen Bonds join these (G + C) together.

Hydrogen Bonds link adenine and thymine together in DNA

Hydrogen bonds link Uracil and Adenine together in RNA

Polar v Nonpolar Molecules

Polar Molecules (Glucose + Ions): Struggle to pass through the lipid bilayer because of their interaction with the hydrophobic region.

Nonpolar Molecules (O + CO2): they can easily diffuse the lipid bilayer because they are soluble in the hydrophobic interior.

Pyruvate Oxidation

This unique arrangement acts as a formidable barrier to the free passage if polar molecules and ions.

Aerobic Cell Respiration

Glycolysis

Hydrogen Bonds Link Adenine and Thymine together in DNA. And they line Adenine and Uracil in RNA

Enzyme in use: Hexokinase
What it does:Transfers phosphate group from ATP to glucose

Step 1: Glucose-->Glucose 6 Phosphate

ATP ---> ADP
(Using phosphate group from ATP)

Step 2:
Glucose 6-Phosphate--->Fructose 6 phosphate

Enzyme in use:
Phosphoglucoisomerase
What it does:Converts glucose 6P to fructose 6P

Step 3:
Fructose 6 phosphate--->Fructose 1,6 bisphosphate

ATP--->ADP
(Using phosphate group from ATP)

Enzyme in use:Phosphofructokinase/PFK
What it does:Transfers phosphate group FROM ATP to opposite end of sugar (USING 2ND MOLEC. OF ATP)

Step 4:
Fructose 1,6 bisphosphate--->TWO Glyceraldehyde-3-Phosphates(G3P)

USED: 2 ATP
FORMED: 4 ATP, 2 NADH
NET: 2 ATP , 2 Pyruvate molec. , 2 H2O , 2 NADH

Happens in Cytosol

2 Molec. of pyruvate from glycolysis

Subtopic

Organic Molecules

Oxygen is used as the electron acceptor

Used for the ETC

Used in Cellular Respiration

Metabolic Pathway

Produces ATP

Energy for the body

Occurs in mitochondria

Oxygen

Reduced

Glucose

Goes through 3 stages

Glycolysis then converted to pyruvate

2 ATP and NADH made

Krebs Cycle

Last step in cellular respiration

Cellular Respiration Formula

C6H12O6+6O2=6CO2+6H2O+ATP

Chromosomes

All body cells have same chromosomes

regulating by turning on (inducing)

regulating by turning off (repressing)

regulatory genes (regulators)= affect transcription/ translation in making final protein

In eukaryote= gametes

Operon system depending on lactose and glucose

7 different control points in eukaryotes

Activator and enhancer region

it limits the amount of mRNA that is produced from a particular gene

in bacteria= same operon system

depending on enviroment it is in

binding specific transcriptional regulatory proteins to enhancers

Endoplasmic Reticulum allows newly made protein to enter the ER lumen

Carbohydrates attach through enzymes
Results 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

Folded protein gets packed into another transport Vesicle

Can travel to Cytoplasm

Lysosomes

Can return to ER

Peroxisomes

Mitochondria

Plastids

Nucleus

Chloroplasts

Called "Glycosylation"

Further Modification Occurs

Protein folds into 3D shape

Called " Membrane Protein"

Amino Acids "Tell" proteins where they must go

IN ORGANELLES