Part 1 Flashcards
Tissues
A group of cells that are similar in structure and function
Cells
fundamental unit of life; can be capable of independent existence or part of a tissue with a specific function
organelles
specialized compartments of a cell that perform a specific function
Molecules
chemical structure consisting of two or more atoms
What are the three domains of life?
bacteria, eukarya, archaea
DNA storage in eukaryote vs. prokaryote?
In eukaryote, DNA is stored in nucleus, away from the rest of the cell. In prokaryote, there is no nucleus and DNA is stored in cytoplasm .
Organelles in eukaryote vs. prokaryote?
eukaryotes have organelles, prokaryotes don’t
Metabolism in eukaryote vs. prokaryote?
In eukaryotes, most metabolism occurs in mitochondria. In prokaryotes, all metabolism occurs in cytoplasm
Size of eukaryote vs. prokaryote?
eukaryotes are large while prokaryotes are small
Chromosomes in eukaryote vs. prokaryote?
Eukaryotes have multiple linear chromosomes. Prokaryotes have a single circular chromosome.
What is the cell theory?
- started in 1839
- The cell is the fundamental unit of structure and function in all living organisms.
- All living things are made up of one or more cells.
- All living cells arise from pre-existing cells.
What is the central dogma of molecular biology?
DNA is transcribed to RNA which is translated to a chain of amino acids making a protein.
Elements
A simple chemical substance that cannot be reduced to smaller chemical parts
What are atoms composed of?
neutrons, protons, and electrons
Covalent bond
a strong chemical bond where pairs of electrons are shared between atoms
valence shell
the outermost shell of electrons
electronegativity
- elements attract electrons to varying degrees, this level of attraction is electronegativity
- the more electronegative an atom, the stronger it pulls electrons towards itself
Non-polar covalent bond
- between two atoms of the same element
- in a bond between two atoms of the same, there is a standoff in terms of electronegativity, resulting in a non-polar covalent bond
Ionic bonds
-sometimes differences in electronegativity can be so great that some atoms strip electrons from their bonding partners
-the two resulting oppositely charged atoms or molecules are called ions
-these ions attract each other: this attraction is called an ionic bond (weaker than covalent bonds)
What makes H2O a polar molecule?
the high electronegativity of oxygen
- water has a polar-covalent bond
Polar covalent bond
one atom is more electronegative and the atoms do not share the electron equally; causes partial positive and partial negative
hydrogen bond
the attraction between partial (+) charge of the hydrogen atom and (-) charge of another atoms is called hydrogen bond
solvent
the dissolving agent of a solution
solute
the substance that is dissolved
solution
a liquid that is a completely homogenous mixture of substances
hydrophilic
describes any substance that has an affinity for water, such as ionic or polar substances
hydrophobic
substances that repel water because they are nonionic or non polar
carboxyl
-COOH
What are the four protein-protein interactions?
- hydrogen bonds
- electrostatic (between + and - ions)
- van der Waals attraction (proximity attraction due to fluctuating charge) ‘
- hydrophobic interactions (strongest)
amino
-NH2
sulfhydryl
-SH
phosphate
-PO4
Carbonyl
-COH, -CO-
What is the build up and breakdown of polymers?
condensation then hydrolysis
- condensation: energetically unfavorable
-hydrolysis: energetically favorable
What type of bonds are sugar monomers joined by?
glycosidic bonds
types of sugar polymers?
monosaccharide (1), disaccharide (2), oligosaccharide (3-15), polysaccharide (16+)
Glycogen
- a macromolecule used for energy storage (storage of extra sugar)
- glycosidic bonds can form between different carbons with hydroxyl groups
Lipids
- composed of fatty acids
- long hydrocarbon chain (hydrophobic)
- carboxyl group (hydrophilic)
Amphipathic
a molecule having both hydrophilic and hydrophobic regions
What determines saturation of fatty acids?
how saturated the fatty acid is with hydrogens
triagcylglycerols
glycerol + 3 fatty acids = triacylglycerol
Fatty acid storage in cells
fatty acids are stored in cells as a energy reserve (fats and oils) through an ester linkage to glycerol to form triacylglycerols
What alters the properties of fats?
tail length and degree of saturation
Phospholipids
the major structural component of cell membranes
- 2 fatty acids +glycerol + phosphate+ polar group
- Naming convention= phosphatidyl-X (X=name of the polar head group)
saturated fatty acid tails
straight
unsaturated fatty acid tails
bent
Parts of a Phospholipid
- Hydrophilic Head: polar group + Phosphate
- glycerol
- Hydrophobic Tail: two fatty acid tails
What do enzymes do?
catalyze reactions
Catabolism
- food molecules broken down into the many buildings blocks for bio synthesis
-breaks things down
-Through catalysis we get useful forms of energy and the many building blocks for biosynthesis
-In catabolism a major portion of the energy stored in the chemical bonds of food molecules is dissipated as heat. But some of this energy is converted to the useful forms of energy that are needed to drive the synthesis of new molecules in anabolic pathways
Anabolism
the many building blocks for biosynthesis become the molecules that form the cell
- builds things
metabolism
the sum of all chemical reactions needed for a cell to survive
How do cells create order, but increase disorder in their surroundings?
- take in energy food
- use that energy to make macromolecules (increase order)
- but this process overall releases heat (increases disorder of surroundings)
Energy in cells
- cells can convert energy from one form to another
- energy cannot be created or destroyed, only change forms
Importance of the sun
- the ultimate source of energy for most living organisms
- plants, algae, etc used sunlight to produce organic molecules from CO2
- Animals obtain food by eating plants
Photosynthesis Stage 1
- Light reactions - energy from sun is captured and stored in activated carriers,
- Oxygen is produced by breaking down water to form O2
Photosynthesis Stage 2
Dark reactions: activated carriers are used to drive carbon fixation (building sugar from inorganic CO2)
Photosynthesis
converts energy from sunlight to chemical bonds
Carbon Fixation
building sugar from inorganic CO2
Oxidative pathways
catabolic reaction release energy by breaking down organic molecules, including foods through oxidative pathways
Catabolic reactions
provide the building blocks and energy required for anabolic reactions
Oxidation
losing electrons
- if you are being oxidized you are losing an electron
- in many reactions the thing being oxidized is organic molecules
Reduction
gaining an electron
- if you are being reduced you are gaining an electron
Free Energy (G in kJ/mol)
measures the energy of a molecule that could in principle be used to do useful work at constant temperature, as in a living cell
What bonds link amino acids?
peptide bonds
Peptides
shorter chains (usually less than 50 amino acids) of amino acids
Which amino acids have acidic side chains?
aspartic acid and glutamic acid
Which amino acids have basic side chains?
lysine, arginine, histidine
Which amino acids have uncharged polar side chains?
asparagine, glutamine, serine, threonine, tyrosine
Which amino acids have non polar side chains?
alanine, valine,mathionine, tryptophan, leucine, isoleucine, glycine, cysteine, proline, phenylalanine
disulfide bond
bond that forms between two cysteine side chains in proteins
What does a nucleotide consist of?
base, phosphate, sugar
Type of sugar in RNA?
beta-D-ribose
Type of sugar in DNA?
Beta-D-2-deoxyribose
Forms of nucleotide bases?
Pyrimidine (one ring) and purine (two rings)
What bonds hold nucleotides together?
phosphodiester bonds (bond between phosphate group of one nucleotide and the methyl group of another
Ends of nucleotide chains
starts with the 5’ end and goes to the 3’ end
ATP
Adenosine triphosphate
- as nucleoside di-and triphosphates, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds.
What is the bonds involved between lipids?
ester linkage
What are the types of carbohydrates?
monosaccharides, disaccharides, polysaccharides
What are the types of lipids?
triglycerides, phospholipids, steroids
Types of proteins?
fibrous and globular
What is the most abundant organic molecule in a cell?
macromolecules
Macromolecule Formation
- assemble in sequence by adding to one end of the molecule
- enzymes required: repetitive process
- energy required
- condensation reaction
(-)Delta G
- the disorder of the universe increases and y is converted to x
- this reaction can occur spontaneously
+Delta G
- the universe would become more ordered
- this reaction can occur only if it is driven by being coupled to a second energetically favorable reaction
How to enzymes catalyze reactions
by binding to particular substrates in a way that lowers the activation energy required for making and breaking specific covalent bonds
Example of coupled reaction
sucrose is made in a reaction driven by the hydrolysis of ATP
Effect of lowering activation energy?
increases reaction rates because more substrate molecules now have the energy to cross the barrier
What effect does a reaction have on an enzyme?
enzymes are not changed by the reaction
What does the Delta G for a chemical reaction depend on?
the concentrations of the reacting molecules
equilibrium
- no net charges in the conc. ratio of Y to X
- the G = 0 for both rxns
How do cells avoid equilibrium?
- bring in new molecules (nutrients)
- eliminate waste
- products siphoned off to become reactants in the next reaction in a chain
Standard Free Energy Change (delta G prime)
- allows us to compare the energetics of different reactions
delta G prime = free energy change based on fixed concentrations of 1mol/liter in aqueous solution
For Y—> X : K=[x]/[y]
K is the ratio of product to substrate when the reaction is in equilibrium (G=0)
(Y–>X is favorable)
- reactant of lower conc. is always on bottom (product divided by reactant)
- Ex: K=2 –> 8X/4Y= 2
“Random Walk”
molecules in a solution move in a random fashion due to the continual buffeting they receive in collisions with other molecules
What determines the rate at which an enzyme will encounter its substrate?
the concentration of the substrate
How do substrates bind to enzymes?
- non-covalent interactions allow enzymes to bind to specific molecules
- sum of many weak forces
- interaction must be strong enough to stay together long enough for chemistry
Enzymes effect on equilibrium
- enzymes cannot change the equilibrium point for a reaction
- enzymes accelerate the forward and backward reactions to the same degree
ATP vs. NADH and NADPH
- ATP: carries high-energy phosphate groups
- NADH and NADPH: carry high-energy electrons
Which activated carriers play a central part in coupled reactions in a cell?
ATP, NADH, NADPH
What do activated carriers do?
capture and store the energy from favorable reactions in order to drive unfavorable reaction in the cell
What is the most widely used energy carrier?
ATP
Why is ATP to ADP favorable?
- removes repulsion between adjacent negative charges on phosphate groups
- inorganic phosphate ion that is released is able to form hydrogen bonds with water (doesn’t always end up just interacting with water)
What can happen to the terminal phosphate in ATP hydrolysis?
it can be, and frequently is, transferred to another molecule
Step 1 of Biosynthesis
the Activation step: ATP transfers a phosphate to A-OH to produce a high energy intermediate
Biosynthesis Net Reaction
A-OH +B-H +ATP —>
A-B + ADP+ P
Step 2 of Biosynthesis
the condensation step: the activated intermediate reacts with B-H to form the product A-B, a reaction accompanied by the release of inorganic phosphate
NADH
oxidizing agent for catholic reactions
NADPH
reducing agent for anabolizing reactions
