Biology 1107 Exam 1 Study Guide

What is Element?

I) Molecules and Interactions:

∙ Parts of an atom:  

o Protons (positive charge)

o Neutrons (neutral charge)

o Electrons (negative charge)

o Protons + neutrons = mass

o Protons + electrons = charge

∙ Electronegativity – an atom’s ability to attract electrons to itself when bonded to  another atom

o Electrons are shared equally in nonpolar bonds, and are shared unequally in  polar bonds

o How to find a bonds polarity? – look at the difference in electronegativity  Nonpolar bonds have an electronegativity difference of 0.4-0.5, while  polar bonds have an electronegativity of >0.5

∙ Element – a form of matter with chemical and physical properties that cannot be  broken down into smaller substances

∙ Ion – a charged atom or molecule

o Cation = positive ions formed by losing electrons

o Anion = negative ions formed by gaining electrons

What are the chemical bonds between the six most common elements?

∙ Isotope – a form of the same element that contains the same number of protons as the original element, but a different number of neutrons

o For example, C-12 and C-14 are isotopes of carbon, but respectively have 6  neutrons and 8 neutrons

∙ Chemical bonds:

o Ionic bonds → formed between ions with opposite charges

o Polar covalent → one side of the molecule is more positively charged, while  the other side is more negatively charged If you want to learn more check out poll everywhere ucr

o Non-polar covalent → bonds between two atoms that share electrons equally ∙ What are the chemical bonds between the six most common elements? o Hydrogen likes to form single bonds with other atoms

 Bonds between hydrogen and other elements tend to be polar

o Carbon likes to form 4 bonds

 Because carbon forms 4 bonds to fill its octet, molecules bonded with  carbon tend to be nonpolar

What is the difference between the chemical bonds between a hydrogen and oxygen atom in a single water molecule and hydrogen in one water molecule and oxygen in another?

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o Oxygen likes to form 2 bonds

 Tends to be polar because of the negative charge on the oxygen atom o Nitrogen likes to form 3 bonds

o Sulfur

 Normally founds 2 bonds

 Tends to be nonpolar because its electronegativity is about the same  as that of carbon

o Phosphorous

 Can form up to 5 covalent bonds

∙ Polar bonds make it easier for compounds to dissolve in water

o If a molecule contains multiple polar bonds, it is highly likely that molecule  will be able to dissolve in water

∙ Nonpolar bonds make it difficult for compounds to dissolve in water o If a molecule contains many nonpolar bonds, that molecule will most likely  not dissolve in water

∙ Intermolecular interactions:

o Ionic bond – bonds formed between ions of opposite charges, in which the  opposite charges are attracted to one another We also discuss several other topics like lab practical biology

o Hydrogen bond – attractions between a polar hydrogen and an  

electronegative atom such as N or O

o Van der Waals Interactions – very weak interacts that occur anytime atoms  are close together Don't forget about the age old question of ribosomes Why are cells small?

 Formed due to an induced dipole, where part of an atom will take on a  partial positive charge while another part will take on a partial negative charge Don't forget about the age old question of mgf1106 uf

o Hydrophobic effect – hydrophobic molecules clump together to avoid  disrupting hydrogen bonds between water molecules

II) Water and Solutions:

 ∙     What is the difference between the chemical bonds between a hydrogen and  oxygen atom in a single water molecule and a hydrogen in one water molecule and an oxygen in another? 

o Bonds between a hydrogen and oxygen atom in a single water molecule → covalent bonds

o Bonds between a hydrogen in one water molecule and an oxygen in another  → hydrogen bonds

 ∙     Why do interactions between water molecules differ in its different states? o Ice – the water molecules are packed close together, preventing it from  changing shapes

 Water is the only element where the solid form is less dense than the  liquid form

 When the temperature decreases and water freezes, the molecules  space out and become crystallized

o Liquid water – liquid water molecules are constantly forming and breaking  bonds with one another Don't forget about the age old question of static electricity study guide

o Water vapor – as the temperature of water increases, the hydrogen bonds  are broken, allowing water molecules to escape into the gas phase and move freely

∙ Evaporation – the process in which some surface water molecules can escape the  liquid phase and vaporize into the gas phase

o Heat is used as the hydrogen bonds holding together water molecules break, cooling the surrounding environment

∙ Condensation – the process in which vapor is converted from a gas to a liquid,  caused by a change in pressure or temperature  

∙ Hydrophobic → polar molecules that interact and dissolve in water

∙ Hydrophilic → nonpolar molecules that are unable to interact or dissolve in water

∙ For a substance to dissolve in water, the attraction between the solvent and solute  particles must be greater than the forces holding the individual solute particles  together

III) Carbon, Functional Groups, and Polymers:

 ∙    What are the physical properties of the following chemical bonds? 

o C-C → nonpolar

o C-H → nonpolar

o C-S → nonpolar

o C-N → polar

o C-O → polar

∙ What are the major functional groups and their properties?

HYDROXYL:

-polar

-forms hydrogen  

bonds

-increase water  

solubility

CARBOXYL:

-charged

-makes molecules

more acidic

AMINO:

-charged

-make molecules  

more basic

PHOSPHATE:

-charged

-make molecules  

more acidic

SULFHYDRYL:

-polar

-can form  

covalent bonds

CARBONYL:

-polar

-increase water  

solubility

METHYL:

-non-polar

-makes  

compounds more  

hydrophobic

∙ Monomers are small subunits that covalently bond to form polymers, which are  larger molecules, in a process known as dehydration synthesis

o When monomers combine with one another, they release a water molecule o Hydrolysis is the process of rehydrating a polymer by adding a water  molecule, thus breaking up the polymer into monomers

o Polymers are important because they make up many materials within living  organisms and provide basic structural materials

∙ Molecules may have the same physical properties but different shapes o A molecule’s shape allows the body to recognize it

o Enzymes bind with certain chemical reactants known as substrates, which  are specifically designed for particular enzymes

 An enzyme must be the proper shape to bond with its substrate

IV) Carbs and Lipids:

∙ Monomers of carbohydrates → monosaccharides

∙ Monomers of lipids → glycerol and fatty acids

∙ Carbs are polar and hydrophilic, meaning they soluble in water

∙ Lipids are very non-polar and hydrophobic, meaning they are insoluble in water o Most membrane lipids are amphipathic, meaning they have a polar and a  non-polar end

∙ Saturated lipids – consist of single bonds, where each carbon is bonded with two  hydrogen atoms, allowing the molecule to be “saturated” with hydrogen ∙ Unsaturated lipids – consist of are least one double bond, giving them a bent  orientation

∙ Triglycerides – lipids consisting of one glycerol molecule bonded with three fatty  acids

∙ Cholesterol – the most common sterol; a lipid made up of four interlocked carbon  rings known as steroids

∙ Both triglycerides and cholesterol are insoluble in water and can be produced  within the body

∙ Phospholipids – lipids consisting of a glycerol molecule, two fatty acids, and a  phosphate group

o Amphipathic (the polar ends face the water, while the nonpolar ends face  each other)

 Because of this property, phospholipids can form certain structures  

when added to water to help lipids dissolve in water

 Phospholipids can form different structures to transport lipids  

throughout the body

∙ Bilayer – a two-layered

arrangement of phosphate

and lipid molecules that

form a cell membrane,

where the hydrophilic

heads face outwards and

the hydrophobic tales face

inwards

∙ Liposome – the lipid bilayer

curls around on itself to

form a sphere

∙ Micelle – a single layer of

phospholipids forms an

even smaller sphere

o As lipids are transported throughout the body they are surrounded by  phospholipids bilayers that form a protective covering around the lipid,  separating it from the surrounding water and helping it dissolve

 ∙     Why does your body choose one molecule over another even though the two  molecules have the same chemical formula? 

o Even though compounds may have the same chemical formula, they can  have different molecular structures and shapes

V) Proteins and Nucleic Acids:

∙ Monomers of proteins → amino acids

∙ Monomers of nucleic acids → nucleotides

o Nucleotides have 3 parts: phosphate, pentose sugar, nitrogenous base o 5 different nitrogenous bases = adenine, thymine, guanine, cytosine, and  uracil

 In DNA, adenine bonds with thymine and cytosine bonds with guanine  In RNA, thymine is replaced with uracil

 ∙    What are the levels of protein folding? 

o Primary protein structure – a sequence of a chain of amino acids o Secondary protein structure – local folding of a protein chain

 Alpha helix (spiral shape)

 Beta sheet (folding sheets)

o Tertiary protein structure – folding of the whole protein chain

o Quaternary protein structure – multiple protein chains interacting ∙ Nucleic acid molecules have distinct ends known as 5’ and 3’ ends (refers to the  ends of the molecule and its polarity)

o The carbon atoms of the pentose sugar molecule are numbered 1’-5’  Phosphodiester bond – linkage between the 3’ carbon of one sugar  molecule and the 5’ carbon of another sugar molecule

o Must be anti-parallel to one another (3’s must connect to 5’s and vice versa) ∙ Whether a protein is polar depends on its R group:

o If the R group is nonpolar than the amino acid will not interact with water o If the R group is polar than the amino acid will interact with water o If the R group is charged than that molecule with interact with other charged  molecules

 ∙    How can the category an amino acid belongs to influence the structure and  behavior of a protein? 

o The R group (a side chain attached to the amino acid) determines the  characteristics of a protein, such as size, polarity, and pH

o The four main characteristics are non-polar, polar, acidic, and basic

VI) Water, pH, and Buffers:

∙ pH – a measure of the strength of the acid or base of a substance o pH chemically represents the power of hydrogen in a solution and can be  determined by the following formula:

+¿H¿ 

¿¿

pH=−log ¿

o pOH chemically represents the power of hydroxide in a solution and can be  determined by the following formula:+¿

OH¿ 

¿¿

pOH=−log¿

+¿

H¿ 

∙

¿−¿

OH¿ ¿¿

∙ Strong acids and bases fully dissociate in water, while weak acids and bases only  partially dissociate

 ∙    What are reversible reactions? How are they related to weak acids and bases? o Reversible reactions – the reactants form the products, which in turn react to  reform the reactants

o Weak acids and bases result in reversible reactions and the formation of a  conjugate acid and a conjugate base

 The reaction is as follows:

∙   Acid + Base → Conjugate Base + Conjugate Acid

 ∙    Why can water act as both a weak acid and a weak base? 

o Water can act as both a weak acid and a weak base because it can both  donate and accept protons

∙ Buffer solution – a solution that resists any change in pH when a strong acid or  base is added to it

∙ A reaction is in equilibrium when both the forward reaction and the reverse  reaction occur at the same rate

∙ As the [H+] concentration increases the pH becomes more acidic, the carboxyl  groups accept protons and their charges increase

∙ As the pH [H+] concentration decreases the pH becomes more basic, the amino  groups donate protons and lose their charge

∙ Many molecules interact through ionic interactions between weak acids and weak  bases

VII) Endomembrane System:

∙ As a cube or sphere increases in size, its volume increases at a greater rate than  its surface area

o Changes in surface area and volume affect functions performed in organisms o Increased surface area means increased exposure to surroundings  ∙    How is membrane transport used to transport nutrients into the cell and waste out  of the cell? 

o Membrane transport involves the transportation of solutes through the lipid  bilayers within cells

o Nutrients are found in carbs, lipids, and proteins and they are absorbed into  our bodies through digestion, which involves breaking down complex  polymers into simpler monomers for easier absorption

o Cells also use chemicals obtained from the outside of the cell to get rid of  waste products

∙ To examine protein production, you could use an isotope of carbon, hydrogen,  sulfur, nitrogen, and oxygen, as these molecules are all present in protein  ∙     How does membrane function limit cell size? 

o Cell size can be limited by the stability of the cell membrane

o As cell size increases, the risk of damage to the cell membrane also  increases

 The cell membrane is very flexible, yet it is still fragile in regards to its  surroundings

o Another limitation on size is the fact that not all cells have a membrane bound nucleus  

 Some cells can overcome this by having more than one nucleus

∙ Secreted Protein Synthesis (in eukaryotes)

o Within the nucleus, DNA becomes translated into mRNA during transcription  so that it can exit the nucleus and enter the rest of the cell

o The mRNA then attaches to a ribosome on the rough endoplasmic reticulum  (ER) where it becomes converted into a protein via translation

o This protein travels through the rough ER and into the smooth ER, where it  pinches off within a vesicle so that it can travel to the Golgi body

o Once the protein travels through the Golgi body it becomes pinched off in  another vesicle so that it can travel to the cell wall

o Once attached to the cell wall, the protein exits both the vesicle and the cell  and is used for purposes outside the cell

∙ Cytoplasmic Protein Synthesis (in prokaryotes and eukaryotes)

o DNA is converted into mRNA during transcription

o The mRNA exits the nucleus and attaches to a free-roaming ribosome within  the cytosol

o Once attached to this ribosome, translation occurs and the mRNA is  translated into a protein

o Once protein synthesis is complete, the protein is used for purposes within  the cell

∙ “Pulse-chase” experiment – a two-phase technique used to examine cellular  processes that take place over time

o A specific amino acid is dyed so that it can be viewed as it goes through the  process involved in becoming a secreted protein

o Scientists can easily track this amino acid due to the dye

VIII) Cells:

Prokaryotes

Eukaryotes

∙ Only in bacteria and cyanobacteria ∙ Single circular chromosome

∙ One long DNA strand

∙ No membrane bound organelles ∙ Unicellular

∙ Small in size

∙ In plants, animals, and fungi

∙ Multiple linear chromosomes

∙ Large amount of repetitive DNA ∙ Membrane-bound organelles

∙ Multicellular

∙ Larger in size

∙ The cytoskeleton is a network of proteins that maintain the shape of the cell,  secure organelles, and allow cytoplasm, vesicles, and cells within multicellular  organisms to move

o What are the three types of fibers within the cytoskeleton?

 i) Microfilaments – smallest fiber; important in cellular movement and  cell structure

 ii) Intermediate Filaments – important in structure only; maintain the  shape of the cell and keep organelles in place

 iii) Microtubules – widest component; provide a track for the vesicles to move and pull replicated chromosomes to opposite ends of the cell  

during cell division

∙ Flagella – long, hair-like structures that extend from the plasma membrane to  move the cell

∙ Cilia – short, hair like structures that extend along the outer surface of the cell ∙ The extracellular matrix is a non-cellular component in all tissues and organs that  determines how a tissue looks and functions

o Made of collagen fiber that are interwoven with proteoglycans