Категории: Все - enzyme - chemical - cellular - intermolecular

по Maya Collins 1 день назад

105

Unit 1: Cells

The topic covers the concepts of chemical bonds, distinguishing between intermolecular and intramolecular bonds. Intermolecular bonds include hydrogen bonding, dipole-dipole interactions, ion-dipole interactions, and London dispersion forces.

Unit 1: Cells

Unit 3: DNA Replication

Replication Fork: Y-shaped structure where replication occurs.

Okazaki Fragments: Short DNA fragments on the lagging strand
Template Strand: The parental strand used to synthesize a complementary strand.

Telomeres: Protective ends of linear chromosomes.

Semi-conservative The two strands of the parental molecule separate, and each functions as a template for synthesis of a new, complementary strand.

Conservative The two parental strands reassociate after acting as templates for new strands, thus restoring the parental double helix.
Dispersive Each strand of both daughter molecules contains a mixture of old and newly synthesized DNA

Helicase- Unwinds the double helix by breaking hydrogen bonds between bases.

Topoisomerase- Relieves supercoiling ahead of the replication fork.
Single-Strand Binding Proteins (SSBs)- Prevent reannealing of separated strands.

Primase- Synthesizes RNA primers to initiate DNA synthesis.

DNA Polymerase DNA Polymerase III: Adds nucleotides in the 5′ to 3′ direction. DNA Polymerase I: Replaces RNA primers with DNA.

Ligase- Seals nicks in the sugar-phosphate backbone, especially on the lagging strand.

Initiation Origin of replication-Specific DNA sequence where replication begins. -Helicase unwinds the DNA. -Primase lays down RNA primers

Elongation Leading strand: Synthesized continuously in the 5′ to 3′ direction. Lagging strand: Synthesized discontinuously as Okazaki fragments
Termination Replication ends when replication forks meet or reach termination sequences. Ligase joins Okazaki fragments

Concept Map 3

Gene Expression

Transcription

The creation of mRNA from DNA genes to further go onto be a protein in translation
Eukaryotic Transcription

The Nucleus of a Eukaryotic cell

Prokaryotic Transciption

The Cytoplasm of a Prokaryotic cell

Subtopic

ADD PHOTOSYNTHESIS TO THE SECOND MAP

Enzyme active site ( a spacious pocket for bindng)

Enzyme-Substrate complex that weakens the substrates bonds for reactions to occur easier

Every energy transfer or transformation increases the entropy or disorder of the universe!

Makes ATP as energy is needed to make ADP into ATP with the addition of a phosphate group

Exergonic reactions as they are th only reaction that allows cells to do work. REACTIONS NEED TO END UP NEGATIVE

Second Law: (Principle of entropy increase)

Example: Food allows animals to run and release heat which increases disorder/entropy. There would be more order than normal but there is still order. For Biology, we need order.

First Law: (Principle of conservation of energy)

Example: Consuming food, there is stored energy in the bonds we are eating! potential->kinetic

Energy can be transformed and transferred but cannot be created or destroyed.

ATP; the energy coupler or currency of the cell.

3 phosphates with negative charges

hydrolysis occurs on inorganic phophate
Heat is released so high free energy is left

ATP acts as a Endergonic and exergonic coupler

Unit 2: Cell Membranes

Types of Transport

Functions of Selective Permeability

maintains internal environment
Receptor proteins bind signaling molecules

Barrier against harmful substances

Cell Membrane Structure

Cholesterol- Provides membrane fluidity and stability
Carbohydrates -help with cell recognition and protection, which are important for selective permeability of the cell membrane
Channel Protein- facilitate the transport of substances across a cell membrane through a process called facilitated diffusion. This process moves molecules from high to low concentration without using energy
Carrier Proteins- transmembrane proteins that move molecules and ions across cell membranes. They are responsible for transporting small molecules from areas of low concentration to areas of high concentration, against a biochemical gradient

Receptor Proteins- a special class of proteins that function by binding a specific ligand molecule. When a ligand binds to its receptor, the receptor can change conformation, transmitting a signal into the cell.

Hydrophilic- water loving heads
Hydrophobic- water repelling tails

Cellular Respiration

Oxidative Phosphorylation

Citric Acid Cycle

Step 1: Acetyl coenzyme A enters the citric acid cycle and interacts with oxaloacetate to form citrate
Step 3: Isocitrate is oxidized and NAD+ is turned into NADH, while isocitrate is processed into ketoglutarate

Energy Production: 3 NADH, 1 ATP, and 1 FADH2

Gylcolysis

Step 1: A phosphorus from ATP is added to glucose with the help of Hexokinase to form glucose6P
Step 2: Glucose6P is turned into fructose6P with the help of phosphogluco-isomerase

Step 3: Fructose6P is converted into fructose1,6 bisphosphate by using a phosphate from an ATP and the help of phosphofructokinase

Steps 4/5: The enzyme aldose splits fructose1,6 bisphosphate into glyceraldehyde 3-phosphate (G3P) and DHAP and the molecules are differentiated

Step 6: G3P is oxidized and an electron is removed from the G3P and given to NAD+ to form NADH, while G3P becomes a byproduct that is given a phosphate group

Step 7: The byproduct from the previous reaction then gives ADP one of its 2 phosphate groups to form ATP and form another byproduct

Steps 8/9: An enzyme rearranges the byproduct to make another byproduct which is then processed by enolase to form phosphoenol-pyruvate(PEP)

Step 10: The phosphate group from PEP is transferred to ADP to make ATP and PEP is turned into pyruvate

Pyruvate Oxidation

Step 1: Pyruvate is taken from the glycolysis process and moved to the mitochondria and oxidized, giving electrons to to NAD+ to make NADH (requires O2)
Acetyl Coenzyme A: A byproduct of pyruvate losing an electron, but necessary for the citric acid cycle

Laws of Thermodynamics

GIBBS FREE ENERGY(G): A thermodynamic property that is used to predict the spontaneity of a process based on the principles of the second law.

Free energy Change (ΔG ): The difference between the free energy of the final state and the free energy of the initial state. ΔG = G ( final state) - G ( initial state)
Non-Spontaneous: When cell processes need energy to start a process in the cell it is non-spontaneous and ( ΔG < 0)

Endergonic Reaction: Since ΔG is positive (Products>Reactants), it needs to absorb energy to continue the cellular process and bond breakage.

Change = ΔG = ΔH - TΔS ΔH = Enthalpy (total potential of a system) ΔS = Entropy(measure of temperature)

Equilibrium: ΔG=0, no net change

Spontaneous Reactions: For cell processes to occur without additional energy and its initial state is more than the final state (ΔG > 0 )

Exergonic Reaction: Since ΔG is negative (Reactants>Products) is does not need energy to occur.

Cell Communication

Junctions

Plasmodesmata
The plant versions of Gap junctions, only present in plant cells
Tight Junctions
Junctions that try to prevent leakage and create a semi-permeable membrane which are more strict and selective on which ions get to pass
Desmosomes
Junctions that provide adhesion between cells and allow for more larger ions and molecules to pass through, is an intermediate between gap and tight junctions
Gap Junctions
Junctions on the cell membranes that allow cells to connect to each other and have molecules and substances to go in and out of the cells, resulting in the direct diffusion of ions

Critical Players:

Receptor
The receptor is present in the target cells that is receiving the signal

Intracellular receptor

Membrane Receptor

Signaling Molecule/Ligand
The molecule that is released by the cell which is usually received by another cell

Types of signaling

Long distance signaling
Hormonal signaling
Local Signaling
Synaptic signaling
Paracrine signaling

Enzymes

Enzymes are macromolecules that act as catalysts in chemical reactions in order to speed up reaction rate by lowering activation energy
Substrates

Reactant that enzyme binds to

Energy Payoff Phase: 4 ATP and 2 NADH made

Energy Investment Phase: 2 ATP is used during the processes

Anabolic Pathways

simpler molecules into complex molecules Ex. Photosynthesis 6CO2 +6H20 + light → C6H1206 + 6O2 Need light energy to create sugar and oxygen

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Catabolic pathways

complex molecules into simpler ones Ex. Cell respiration C6H1206 + 6O2→6CO2 +6H20 + ENERGY

Feedback Inhibition

prevents a cell from wasting chemical resources by synthesizing more product than is needed.

the product acts as a noncompetitive inhibitor and inhibits the first enzyme of the pathway, causing the pathway to shut down and restrict the creation of more product.

Cooperativity

substrates to control the functionality of an enzymes. The binding of one substrate can active other enzymes subunits into their active forms

Allosteric regulation

enzymes and proteins with quaternary structures

active to inactive depending on the reactions needs

1,4 Glycosidic Linkage: A linkage between the first Carbon group of a monosaccharide and the fourth Carbon group of another monosaccharide

Starch: Used for storage and consists of Amylopectin, which creates branches, as well as Amylose which does not branch out

Inhibitors

Non-competitive

binds to the enzyme away from the active site , altering the shape of the enzyme so that even though the substrate can still bind, the active site functions much less effectively, if at all.

Competitive

mimics and competes with the substrate to try and bind with the active site. Overall prevents the substrate from binding.

Enzymes Ex. sucrose

Biomolecules: Nucleic Acids + Lipids

Lipids

Large biomolecules that include fats, phospholipids, and steroids
Phospholipid

made of glycerol with two fatty acids and a phosphate group; they can form bilayers and function as a membrane

Fat

triglyceride: 3 fatty acids that are linked to a glycerol molecule, fatty acids have long carbon skeletons with a functional group and non-polar C-H bonds in the hydrocarbon chains

Steroid

contains carbon skeleton with four fused rings containing a variety of chemical groups attached

Nucleic Acids

Ribonucleic Acid (RNA)
Single stranded polynucleotide where each nucleotide monomer with a ribose sugar and nitrogenous base

Nitrogenous bases include: -Adenine (A) -Guanine (G) -Cytosine (C) -Uracil (U)

Pyrimidines: -one six-membered ring of carbon and nitrogen atom Members include: -Cytosine -Thymine -Uracil

Deoxyribonucleic Acid (DNA)
Genetic material inherited from parents. Each chromosome from the long DNA molecule contains several hundreds of genes

DNA helps provide instructions for the cell to develop and reproduce by providing the genetic material for all of the proteins that the cell may need.

Double stranded helix where each polynucleotide strand has monomers with deoxyribose sugar and nitrogenous base

Nitrogenous bases include: -Adenine (A) -Guanine (G) -Cytosine (C) -Thymine (T)

Purines: -a six-membered ring fused to a five-membered ring Members include: -Adenine -Guanine

Bio-molecules

Carbohydrates

Cellulose: Found in plants exclusively and provides structure, does not branch at all
Beta glucose: The OH on the first Carbon group is above the center of the molecule
Glycogen: Used for storage and branches extensively

Proteins

Quaternary level:
Tertiary level:

Secondary level:

Primary Level:

Unit 1: Chemical Bonds

Intramolecular (Bonds in-between atoms/element) (Ex. O-H in H2O)

Covalent (Sharing of electrons)
Polar

Occurs when there is an unequal sharing of electrons between atoms, within a molecule. They are still willing to share though!

Example: C-O( 1.0 EN difference), O-H(1.4 EN difference), N-H (0.9 EN difference).

Non-polar

Occurs when electrons are shared equally between atoms, within a molecule.

Example: C-H(Hydrocarbon, 0.4 EN difference), CO2(linear molecular shape).

Ionic (The attraction of opposite charges, cations and anions)
Occurs when electrons are taken rather than shared between atoms, within a molecule.
Example: Na+ and Cl- make NaCl (table salt) - The 1 electron in Na+ valence shell if taken by the Cl- to fill its octet.

Intermolecular (Ex. Bond between H20 + H20)

Dipole-Dipole Interactions
London Dispersion Forces (Van Der Waals)
Ion-Dipole
Hydrogen Bonding

Unit 1: Cells

Prokaryotic

Archaea
Bacteria

Eukaryotic

Plant
Chloroplasts- Site of photosynthesis, where light energy is converted into chemical energy. Double membrane-bound organelle with internal stacks of membranes called thylakoids (containing chlorophyll), surrounded by fluid called stroma

Cell Wall- Provides structural support, protection, and regulates cell growth. Rigid outer layer made of cellulose

Large Central Vacuole- Stores water, nutrients, and waste products; provides turgor pressure for maintaining cell structure. Large membrane-bound sac (larger in plant cells)

Animal
Lysosomes- Membrane-bound vesicles containing hydrolytic enzymes. Digests and recycles cellular waste, worn-out organelles, and foreign substances

Centrosomes- Centrosomes consists of two centrioles (in animal cells), which are cylindrical structures composed of microtubules. Involved in organizing microtubules during cell division (mitosis) and forming the mitotic spindle.

Both
Mitochondria- Double-membrane organelles with an inner membrane folded into structures called cristae, and a fluid-filled space called the matrix. The site of aerobic respiration, producing ATP (energy) through the oxidation of glucose and other substrates. Also involved in metabolic processes and apoptosis

Nucleus- A membrane-bound organelle containing chromatin (DNA and proteins) and a nucleolus, surrounded by a double membrane (nuclear envelope) with pores. Function: Acts as the control center of the cell, housing genetic material (DNA) and regulating gene expression, growth, metabolism, and cell division