Glossary of Cellular Chemistry - Chapter 2

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What is an Atom?
Smallest units of matter, the tiny building blocks of everything.
What are 3 types of particles in atoms?
Protons, Neutrons, Electrons
What is the nucleus?
The center of the atom where protons and neutrons are grouped.
Where are electons located?
In motion around the nucleus
What is charge of an atom?
No charge - protons - positively charged and electrons - negatively charged - cancel each other out.
What is mass of elements in an atom?
Proton - 1 Dalton
Neutron - 1 Dalton
electtron - insignificant
Atomic Number
Number of protons in an atom - determines its properties
Atoms with different numbers of protons - the different types of matter - Periodic table of elements
Periodic Table
Lists all the elements by atomic number (numbers of protons).
Atomic Mass
determined by the number or protons and neutrons atom has. - is the average of the masses for the different isotopes of the element and takes into account how common each isotope is.
Electron Shells
Various energy levels around the nucleus holding the electrons. Each shell holds a specific number of electrons - 2, 8, 8
Connections between atoms
Atoms joined together by bonds. Atoms of different elements can join together to form molecules.
Covalent Bond
The type of bond when atoms share electrons. If one pair of electrons is shared - single bond, two pairs - double bond.
What is a polar covalent bond?
An unequal sharing of electrons. Electrons spend more time orbiting one of the atoms than the other because the atom has more pull. Eg.. Oxgen and hydrogen - electrons orbit O more.
Hydrogen Bond
Weak electrical attraction resulting from the slight positive or negative charges of atoms with polar covalent bonds. Individually weak, but a bunch act like Velcro.
Atom that loses or gains an electron thus becomes charged. eg. Sodium ion (+ charge), chloride ion (-charge). These two can then combine via an ionic bond
Ionic Bond
Electrical attraction between two ions. (opposite charges attract)
Chemical Reactions
Result of molecules interacting with each other to form new molecules. Written as equations
molecules that interact
Molecules that are formed in a chemical reaction - shown on right side of equation
What happens in a chemical reaction?
Atoms are not created or destroyed, they just switch bonding partners. Energy is either released or used by the reaction.
Ph Scale
Measures the concentration of hydrogen ions (H+) in a solution.
PH < 7
indicates a solution that has a high concentration of H+ and is acidic.
PH > 7
indicates a solution low in H+ and is a basic.
Molecules that release H+ into a solution
Molecules that pick up H+ from a solution
Compounds that help keep pH from changing very quickly.
Chemical Equilibrium
Balancing on both sides of the reaction. Eg. In cells, dihydrogen phosphate (H2PO4-) and hydrogen phosphate (HPO4 2-). Hydrogen phosphate picks up and extra H+, Dihydrogen phosphate releases H+ as needed. This results in a balancing between the two constantly.
Four categories of molecules important to cells
lipids (fats and related molecules)
Nuclei acids (DNA and related molecules)
The four types of molecules important to cells. - because they are large and complex - all have a carbon backbone.
Functional Groups
The groups of atoms attached to the carbon background (of macromolecules) making the molecules different
Key functional groups
(see book for illustrations)
Long molecules made up of repeating building blocks called monomers. (proteins, carbohydrates, and nucleic acids)
Building blocks of polymers
Dehydration synthesis
Condensation - what holds monomers together in polymers. A bond is formed between the monomers as a water molecule is removed. An enzyme is required to combine the two.
Way to break apart a polymer - a water molecule is inserted between monomers. An enzyme catalyzes the breaking of a bond.
fats and related molecules - not polymers, but have smaller components joined together by dehydration synthesis.
List the polymers/monomers of Protein:
Polymer: polypeptide
monomer: amino acid
List the polymer/monomer of Carbohydrate:
Polymer: polysaccharide
monomer: monosaccahride
List the polymer/monomer of Nucleic Acid:
Polymer: plynucleotide
Monomer: nucleotide
Why are proteins important to cells?
They can be:
hormones, antibodies, enzymes, cytoskeletal proteins, membrane proteins, receptor proteins
What is antibody?
Defensive compounds
Helper in chemical reactions
Cytoskeletal Proteins
Structural components, or movement proteins
What are receptor proteins?
What are proteins made of?
Chains of amino acids. - 20 amino acids found in living organisms on Earth. Each has the same backbone, but structure of the functional group attached to the backbone may be different making different aminos.
What is the backbone of an amino acid?
A nitrogen containing amino group and a carboxyl group
(See book for illustration p. 23)
Polypeptide Chains
Primary structure of the protein - amino acids joined by dehydration synthesis.
Secondary Protein Structure
Local folds (distinctive shapes) which occur when the amino acids in the polypeptide chain are linked to each other by hydrogen bonds.
Tertiary Structure
Entire chain folds up into a 3 dimensional shape - held together by bonds between the variable groups in the amino acids.
Quarternary Structure
proteins which are made of more than one folded polypeptide chain - have quarternary structure
If a protein is exposed to a harsh environment, it may unfold and no longer be able to function.
source of energy (primary function)
Important part of the structure of some types of cells - part of cell wall of bacteria and plants.
Simple sugars - carbon backbone of 3-7 atoms. Hydroxyl groups are attached to all the carbons but one and that last one is double bonded to an oxygen atom. In water environment, they form a ring.
Name 3 monosaccharides
Glucose, Galactose, Fructose
Two monomers - joined by dehydration synthesis
Many monomers - referred to as complex carbohydrates. Eg. starch
Name 3 disaccharides
Maltose, Lactose, Sucrose
Dioxyribonucleic Acid is a nucleic acid. Contains the genetic information of the cell, a large part of which is the instructions for bulding all of the proteins a cell needs to function.
Ribonucleic acid
Complex structure of nucleic acids. Polymers of monomers.
What are 3 components of nucleotides?
A five carbon sugar
A phosphate group
A nitrogenous base
Differences between DNA and RNA
DNA - 5 carbon sugar is - deoxyribose
RNA - 5 carbon sugar is ribose
What are the 4 nitrogenous bases found in DNA
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)
What is thymine (T) replaced with in RNA?
Uracil (U)
How is DNA or RNA formed?
Nucleotides are linked via dehydration synthesis. In cells, RNA molecules are single polynucleotide strands. DNA requires two strands. The nitrogenous bases of the two strands are attracted to each other via hydrogen bonds. They twist slightly forming the double helix.
What does adenine bond with?
What does Cytosine bond with?
Any molecule that does not mix with water
What are 3 important groups of lipids?
Fats and oils (triglycerides)
What do fats and oils do?
They store energy and provide insulation.
What do phospholipids do?
They are important components o the outer boundaries of cells (called plasma membranes)
What do sterols do?
Some are found in plasma membranes, others are vitamins and hormones.
What do fat molecules consist of?
3 Carbon backbone - to which long hydrocarbon chains (fatty acids) have been attached. 3 carbon backbone made from a molecule of glycerol.
Explain saturated.
Fatty acid tails have single bonds between the carbons. Tails are straight.
Explain unsaturated
Fatty acid tails have double bonds between the carbons. Tails are bent.
Explain structure of a phospholipid
backbone is made of glycerol, but only two fatty acid chains attached.
Instead of the 3rd (for a regular fat), a phsphate containg a head group is attached.
Water loving - head of phospholipid
Water hating - tail of phospholipid
What happens when phospholipids are put in water?
They form a double layer called a bilayer, turning their heads toward the water and tucking their tails away.
Explain structure of sterols.
Made up of 4 carbon containing rings. Egs. cholesterol (component of plasma membranes), testosterone, estrogen (steroid hormones), some vitamins like vitamin D.
What are the distinctive features of proteins?
Contains nitrogen in amino group (-NH3)
What are the distinctive features of nucleic acids?
Contains nitrogen in ringed structures called nitrogenous bases.
Contains phosphate.
What are the distinctive features of carbohydrates?
Short carbon chains (3-7 carbons)
Hydroxyl groups (-OH) on all carbons but one.
What are distinctive features of lipids: (fatty acids)
Long carbon chains
One hydroxyl (-OH) group
Lots of carbon-hydrogen bonds
What are distinctive features of lipids (phospholipids)
Phosphate in head group
No ringed structures

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