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UNL / Biology / MBIO 111 / what is an atom?

what is an atom?

what is an atom?


School: University of Nebraska Lincoln
Department: Biology
Course: Microbiology
Professor: Kenneth nickerson
Term: Spring 2016
Tags: Biology and General Biochemistry
Cost: 25
Name: BIOS 111-Chapter 2
Description: I did make one mistake with the pH information I mixed them up!...a lower pH# is more acidic, and a higher pH# is more basic.
Uploaded: 01/15/2016
7 Pages 13 Views 19 Unlocks

Key chapter 2 concepts to aid in your understanding of microbiology!  

what is an atom?


Atoms: smallest component of a pure substance w/ properties of that  substance

-can’t be divided w/o losing those properties

-combine to form molecules 

Parts of an atom: nucleus (protons +, neutrons 0), electron field  (electrons,e-)

If # protons=# electrons, no net charge

Atomic number: # protons

Atomic Weight: # protons+# neutrons

Isotope: # of neutrons differ in atoms of same element

Electron configuration: outermost (valence) energy level has to  have 8 e

to be stable.  

**This is why atoms react with other atoms; to achieve 8  valence e- When they react, they form

Chemical Bonds: 

Ionic: One atom takes electrons from another atom, and they  become charged particles called ions (ionic bond forms ions) Covalent: electrons are shared between atoms. One atom usually “wants” electrons more than the other one, resulting in polarity. These bonds are stronger and more common.  

what are chemical bonds?

Hydrogen bonds: Hydrogen (H) atom is bonded covalently to a  larger Oxygen or Nitrogen atom. However, the sharing is unequal  (polar), and a slight positive charge forms on the H atom while a slight  negative charge forms on the larger O or N atom. Positive and negative charges attract, but since the charge is only partial, a bond doesn’t  form. Rather a “bridge” forms.  

-Clear diagrams of this concept can be found online (I can’t put them in the notes for copyright reasons!)

**Hydrogen bonds and polarity are responsible for giving water its  distinct properties!**

Distinctive Properties of Water 

65-75% all cells are H20! (So we are basically cucumbers with anxiety)Don't forget about the age old question of What are the Related Principles of Classical and Operant Conditioning?

But water is the universal solvent for many molecules, and the  medium in which almost all biological reactions occur!!*  So what makes it special?

1. Polarity- remember those Hydrogen bonds? A water molecule has a slightly negatively charged part (the O atom)and two slightly  positively charged parts (the H atoms). Therefore, water can  form hydrogen bonds with itself.  

what are lipids?

2. It takes a great deal of energy to separate water molecules  thanks to these H bonds, so water is a great temperature buffer,  meaning it resists change in temperature. This is why our body  temperature remains so constant.  

3. Because of its polarity, it is the universal solvent for any  molecule that would dissociate into ions.  

 4. Density: when it gets colder, it expands (becomes less dense). It  is most dense in its liquid form. This is why ice floats! The ice on  top of a frozen lake insulates the organisms below. It is because  of ice that aquatic life is able to survive the winter.  

5. It plays a part in just about every chemical reaction that takes  place in an organism, either as a reactant (actively reacting) or  as a product (what’s produced).  

Chemical reactions: Endothermic and Exothermic Endo=in



-requires energy input to form bonds, and energy is released when  bonds break

**can also be called exergonic or endergonic, but meaning is the  same**

Making bonds=absorbs energy=endothermic If you want to learn more check out marketing communicating delivering and exchanging

Breaking bonds=releases energy=exothermic  


Atomic #= # of protons. Can be found on periodic table. Atomic weight= # of protons + # neutrons in an atom (measured in  amu’s-atomic mass units)

Molecular weight=sum of atomic weights of all atoms in a molecule  (amu)

A mole of a substance is that substance’s molecular weight expressed  in grams  

Ex. Glucose molecule molecular weight is 180 amu

1 mole of glucose is 180 grams

1 M=1 mole of solute/Liter

solute=what’s dissolved in the solvent (example: salt dissolved in  water)

Acids and Bases 

Acids: substances that dissociate into H+ ions in water  Ex. HCl  into H+ and Cl- ions

Bases: Substances that dissociate into OH- (hydroxide) ions in water Ex. NaOH into Na+ and OH- ions Don't forget about the age old question of medical terminology mizzou

Salts: still dissociates into ions when dissolved in water, but these ions  are not H+ or OH

Ex. NaCl Na+ and Cl

pH: “potential of Hydrogen”

pH scale: shown below

higher #= more acidic

lower #=more alkaline (basic)

The pH scale diagram can be found online very easily! (sorry I can’t put it in the notes because of copyright reasons, but I recommend looking  it up!)  

-organisms are EXTREMELY SENSITIVE to even small changes in pH So…many biological systems use buffers! 

Buffers: prevent drastic pH changes by replacing strong acids and  bases with weaker ones that don’t break into as many H+ or OH- ions

Organic Molecules 

*-contain carbon, hydrogen, oxygen and nitrogen

-the carbon forms a “skeleton”, which the other atoms  are covalently bound to.

-most C are bonded to H atoms, but other functional groups with  specific properties may be attached.  We also discuss several other topics like wiley company purchased new equipment for $60,000. wiley paid cash for the equipment. other costs associated with the equipment were: transportation costs, $1,000; sales tax paid $3,000; and installation cost, $2,500. the cost recorded for the equipment w
We also discuss several other topics like untstat

A table of these functional groups and what they are  found in can be found in the Tortora text, 11th edition on  page 36

Terms to know:

Monomer- (mono=one) the “building block” of an organic molecule,  the simplest unit that still contains the properties of that type of  molecule.  We also discuss several other topics like psych 110

If you were building a wall, the monomer would be one of the bricks.  

Polymer- monomers join to form polymers.  

using the wall analogy, the polymer would be the entire wall, made  out of all the bricks  

Dehydration synthesis: This is how monomers join to form polymers!  One monomer loses an H atom, and the hydroxyl group (OH) of  another monomer is lost and the two combine to form a water  molecule. Dehydration means water is being lost

Hydrolysis: the opposite of dehydration synthesis! A water molecule is  added to the polymer, and it separates the two monomers again.

Isomer: not related to the building of a molecule! It means: two or  more molecules that have the same chemical formula, but are  structured differently.  

An example of this is the carbohydrates glucose, fructose, and  galactose. Both have the same chemical formula C6H12O6, but  different physical structures and chemical properties.  

Carbohydrates-“hydrated carbon” 


-these are the sugars and starches

Functions: structural component of cell walls/membranes/DNA, fuel  cells with energy

-made of C, H, O atoms. **Ratio of H to O atoms is 2:1


Example: glucose

Disaccharide=2 monosac. bound together

Polysaccharide=multiple monosac. (can be 10’s or 100s!)  Ex. Glycogen, cellulose


Functions: structure and functional unit of cell membranes, energy  storage

**non polar and insoluble in water**

Simple lipids 

Triglycerides: glycerol molecule with 3 fatty acid chains attached  (Diglycerides/monoglycerides=2 or 1 fatty acid chain)

Fatty acid=carbon skeleton with attached hydrogen atoms Saturated=no double bonds, MAXIMUM amount of H atoms  possible

-solid at room temp., no “kinks”, stick together more easily Unsaturated=double bonds, liquid at room temp, “kinks” in the  chain so they can’t be as tightly packed

Complex lipids 

**Phospholipids-phosphate group+glycerol+sat. fatty acid  chain+unsat. fatty acid chain

-polar hydrophilic (water loving) head-phosphate group faces water -nonpolar, hydrophobic fatty acid “tails”

forms a bilayer (double layer) with tails facing in and heads facing out,  which is the main structural component of a cell membrane 

-other complex lipids are waxes and glycolipids, which are also found in cell membranes

Steroids (yes, these are lipids!) 

-interconnected carbon rings

-structural component of cell membranes (cholesterol) -keep the phospholipids from sticking together, preserves fluidity of membrane

Ex of steroid= Hormones (estrogen, testosterone)


-have nitrogen and sometimes sulfur as part of their chemical  structure! Unlike other org. molecules


1. enzymes-speed up biochem. Reactions

2. transport proteins

3. muscle contraction (actin and myosin)

4. some hormones  

5. antibodies- part of immune defense system

6. structural component of cell membranes  

Monomer=amino acid

 Stereoisomer= amino acids exist in either of 2 forms/configurations,  which are mirror images of each other.  

D and L- D is right handed, L is left handed

**amino acids found in proteins are most often the L form**  -D isomers occur in bacteria cell walls and antibiotics  

Amino acids “link” together via peptide bonds, forming a polypeptide  chain

( I will cover this more in my next posting of notes over ribosomes and protein  synthesis)

Protein structure-4 levels 

1. Primary structure=the sequence of amino acids (like beads on a  necklace)

2. Secondary= the folding and twisting of the polypep. chain into  either a helix or pleated sheet  

-held together by H bonds

3. Tertiary=the unique three-dimensional shape of the protein Most proteins stop here, but some have 

4. Quaternary=how 2 or more polypep. chains join to make one  functional protein

Shape=function. If a protein loses its shape (denatures) it  can no longer perform its function.  

Denaturation can occur w/ high temperatures, pH values,  or salt conc.  

Nucleic Acids 

DNA-deoxyribonucleic acid

RNA- ribonucleic acid


Nucleotide=simple sugar, phosphate group and nitrogenous base Bases form pairs:

-in DNA, bases are A, T, C, G



-in RNA, bases are A, U,C, G



DNA=genetic material of an organism.  

RNA=3 types-tRNA, mRNA, rRNA

(will be covered more in upcoming notes)

Adenosine Triphosphate(ATP) 

-the principal energy carrying molecule of all cells!

-3 phosphate groups=ATP

When ATP is “used”, the third phosphate group splits off and it  becomes ADP (what’s left) and Pi (the phosphate that splits off)  -The reaction goes in the reverse direction to replenish the ATP supply

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