cell compounds and biological...
TRANSCRIPT
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Cell Compounds and Biological Molecules
Biology 12Unit 2 – Cell Compounds and Biological Molecules
Inquiry into Life pages 20 - 44
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Basic Chemistry
Matter – anything that has mass and volume
Element – comprises all matter, living or non-living
Atom – the smallest unit of matter to function in chemical reactions; composed of 3 subatomic particles
Isotope – atoms with the same atomic number but different atomic mass
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Basic Chemistry
SubatomicParticle
Charge Relative Mass
electron – 1 0
proton + 1 1
neutron no charge 1
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Basic Chemistry
6 12.0107
CCarbon
atomic number
atomic mass
element symbol
element name
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Basic Chemistry
Isotopes are different forms of the same atom
The only difference is the number of neutrons present
Neutrons only add mass and do not change chemical properties
Some isotopes are unstable and emit radiation radioactive isotope
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Molecules vs Compounds
A molecule is any chemical unit that contains more than 1 atom. They can contain the same atom or different atoms
A compound is any chemical unit that contains more than 1 atom, but the atoms cannot be the same.
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Ionic Compounds
Ionic compounds are formed when a metal and a non-metal are attracted resulting in the transfer of electrons from metal to non-metal
Ionic compounds require ions or charged atoms
Ions can be positive or negative, but never neutral
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Ionic Compounds
Positive ions are metals and have lost electrons
Negative ions are non-metals and have gained electrons
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Ionic Compounds
Because electrons are negative particles, having more electrons means the ion is more negative
Fewer electrons means more positive
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Ionic Compounds
This represents electron shells
1st shell = 2 e-
2nd shell = 8 e-
3rd shell = 8 e-
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Ionic Compounds
C
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Ionic Compounds
Remember, ionic bonds transfer outer shell electrons from the metal to the non-metal
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Covalent Compounds
Covalent reactions occur between two non-metals
Electrons are shared in covalent compounds instead of transferred
The shared outer shell electrons spend equal time between the two atoms
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Covalent Compounds
Each pair of electrons form a single covalent bond
When two pairs of electrons are shared, they form a double bond
When three pairs of electrons are shared, they form a triple bond
The more bonds between atoms, the more difficult it is to separate them
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Covalent Compounds
Electrons in the overlapping regions are shared
Each H shares 1 e- with the carbon
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Covalent Compounds
The hydrogens share their electron with each other, forming a molecule of hydrogen gas
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Water
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OH H
Water
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Water
Water is a polar molecule
Since oxygen has a larger nucleus, the shared electrons spend slightly more time near the oxygen nucleus than the hydrogen nuclei
This differential in time gives water a slight + and – charge at its poles
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OH H
–
+
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Water
Polar covalent molecules form weak bonds between compounds called hydrogen bonds
A hydrogen bond occurs when the slight positive charge of a bound hydrogen attracts the slight negative charge of a neighbouring atom
It is represented by a dashed line
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Water
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Water
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Properties of Water
1. Liquid at room temperature
2. Facilitates chemical reactions
3. Molecules are cohesive
4. Changes temperature slowly
5. Has a high heat of vapourization
6. Solid water is less dense than liquid water
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Roles of Water in Living Organisms
1. Temperature Regulator
2. Lubricant
3. Solvent
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Acids and Bases
Water spontaneous breaks up into two component ions, H+ and OH –
Acids are compounds that release H+ when dissociated in water
Bases are compounds that release OH – when dissociated in water
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Acids and Bases
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Acids
Strong acids are characterized by the amount of H + ions that dissociate
The more complete the dissociation, the stronger the acid
The more H + added to the water, the more acidic the solution
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Bases
Strong bases are characterized by the amount of OH – ions that dissociate
The more complete the dissociation, the stronger the base
The more OH – added to the water, the more basic the solution
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pH Scale
This scale is used to indicate the acidity or the alkalinity of a solution
Values range from 0 – 14
The lower the value, the more acidic the solution
The higher the value, the more basic the solution
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pH Scale
pH is a logarithmic scale:
pH 1 is 10X more acidic than pH 2
pH 1 is 100X more acidic than pH 3
pH 2 is 1000X more acidic than pH 5
pH 8 is 10X more basic than pH 7
pH 12 is 10 000X more basic than pH 8
pH 14 is 100 000 000 000 000X more basic than pH 0!
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Buffers and pH
A buffer is a chemical that keeps pH within certain limits
Buffers resist changes in pH by absorbing excess hydrogen and hydroxide ions
Buffers in human blood are carbonic acid and bicarbonate ions
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Organic Molecules
Characterized by the presence of carbon and hydrogen
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Organic Molecules
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Organic Molecules
Carbon molecules can link to other carbon molecules forming a hydrocarbon molecule
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Organic Molecules
Functional groups can be added to hydrocarbons to impart certain characteristics
Two important functional groups are:
carboxyl (COOH)
amine (NH3)
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Carbohydrates
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Carbohydrates
Short-term energy storage
Structural molecule in plants and bacteria
Cell membrane communication
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Carbohydrates
Monosaccharides are simple carbohydrates that can be characterized by having 5 or 6 carbons (pentose and hexose)
Common monosaccharides are:
glucose
fructose
galactose
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Carbohydrates
Disaccharides are links of two monosaccharides (di meaning two and mono meaning one)
Common disaccharides:
sucrose
lactose
maltose
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Polysaccharides contain many monosaccharides linked together
Polysaccharides are considered polymers
A polymer is a long chain of monomers
A monomer is a single unit
Carbohydrates
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Carbohydrates
monomer
polymers
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Carbohydrates
Polysaccharides are formed through a process called condensation synthesis
synthesis = making of
condensation = releases water
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Carbohydrates
Breaking apart polysaccharides involves a process called hydrolysis
hydro means water
lysis means to break apart
Hydrolysis reactions break down polysaccharides by adding water
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Carbohydrates
monomers polymer + H2O
http://www.biotopics.co.uk/as/disaccharidehydrolysis.html
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Carbohydrates
Starch and glycogen store glucose in plants and animals
Starch is a polymer of glucose with few side branches
GLYCOGEN is similar to starch except it is highly branched
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Carbohydrates
Cellulose is found only in plants
The glucose molecules are linked differently than in glycogen and starch
This linkage causes the greater strength of this molecule
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Lipids
Lipids are the greatest energy source in biological molecules
carbohydrates = 17 kJ/g
proteins = 17 kJ/g
lipids = 38 kJ/g
However, most lipids are not used as energy stores
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Lipids
Lipids have different structures and functions:
long-term energy storage
steroids (sex hormones)
membrane components
What links all lipids is that they are all insoluble in water
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Lipids
Fats and oils
usually of animal origin and is solid at room temperature
Fats have two functions:
long term energy storage
insulation and cushioning
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Lipids
Fats and oils form when one glycerol molecule react with three fatty acid molecules
Sometimes called trigylcerides
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Lipids
Emulsification is the process of mixing fat with water
Elmulsifiers are made of a polar molecules (polar head and nonpolar tail)
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Lipids
Fat globule Emulsifier
(bile)
(soap)
polar head
nonpolar tail
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Fat Emulsification
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Fatty Acids
A fatty acid is a hydrocarbon chain that ends with the acidic group -COOH
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Saturated Fatty Acids
Saturated fatty acids have no double bonds between carbon atoms, and it is saturated, or full of, all the hydrogens that can fit
Saturated fatty acids are solid at room temperature
Animal fats are often saturated
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Unsaturated Fatty Acids
Unsaturated fatty acids have double bonds somewhere within the carbon chain, often causing kinks in the chain
They occur where the carbon does not have two hydrogens attached to it
Unsaturated fatty acids are liquid at room temperature
Plant fats are often unsaturated
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Phospholipids
Phospholipids are polar molecules containing a phosphate or a phosphate/nitrogen group attached to the lipid tail
They are found in cell membranes and will spontaneously form a bilayer with hydrophobic tails facing in and hydrophilic heads facing out
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Phospholipids
Lecithin is a common phospholipid found in soybeans and eggs
It is used to emulsify fats and is basis of mayonnaise, an emulsified fat
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Steroids
Steroids have the common stucture of 4 fused carbon rings
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Steroids
Steroids differ by their atom arrangement and the functional groups attached to them
Cholesterol is an important component in the cell membrane, adding to rigidity as well as the starting point for sex hormones like estrogen and testosterone
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Steroids
Examples of common steroids:
cholesterol
estrogen (estradiol)
testosterone
cortisol
vitamin D
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Proteins
Proteins have many functions, from movement to antibodies to enzymes to biological messengers
Proteins are polymers of amino acids monomers
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Proteins
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Proteins
The R group is what makes the 20 amino acids different from each other
R groups can be as simple as a single hydrogen (glycine) or as complex as a double benzene ring (tryptophan)
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Proteins
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Proteins
Amino acids combine through a peptide bond, which is a condensation synthesis reaction
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Proteins
A chain of amino acids is called a polypeptide
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Proteins
Four Levels of Organization (p. 39)
primary structure
the linear sequence of amino acids joined by peptide bonds
secondary structure
polypeptides form a 3-D shape
hydrogen bonds between peptide bonds keep the shape
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Proteins
Tertiary Structure
the final 3-D shape of proteins
this shape is maintained by different covalent, ionic, and hydrogen bonds between R groups, including the covalent disulphide bond between 2 cysteine amino acids
Quaternary Structure
two or more polypeptides arranged together (mostly enzymes)
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Proteins
Protein structure is extremely important because structure is related to function
If protein structure is changed (denatured) then the protein cannot function
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Nucleic Acids
Two types:
Deoxyribonucleic Acid (DNA)
Ribonucleic Acid (RNA)
Both are polymers of nucleotides
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Nucleotide
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Nucleotides
All nucleotides are composed of a sugar (either ribose or deoxyribose), a phosphate and a nitrogenous base
There are five bases:
Adenine
Thymine (DNA only)
Cytosine
Guanine
Uracil (RNA only)
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Nucleotide Chains
Nucleotides join via condensation synthesis – the same process as joining monosaccharides and amino acids!
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Nucleic Acids
Nucleic acids form strands made up of a sugar-phosphate backbone
Nitrogenous bases stick out of the sides
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DNA
DNA is double stranded, each twisting about the other
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RNA
RNA is a single strand of DNA
There are three types:
Messenger RNA (mRNA)
Ribosomal RNA (rRNA)
Transfer RNA (tRNA)
We will look more into DNA at a later time.
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ATP
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ATP
ATP (adenosine triphosphate) is composed of adenine (a nitrogenous base), a ribose 5-sided sugar and three phosphate groups. This structure is actually a modified nucleotide.
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ATP
ATP is the "energy currency" of the cell and is spent to drive chemical reactions
Glucose is converted into ATP in the mitochondria via cellular respiration.
Energy is derived from breaking the bond between phosphate 2 and 3, releasing energy stored in the bond.
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ATP
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ATP
Breaking this bond results in the production of ADP or adenosine diphosphate and a phosphate group.
These molecules can be recycled and used to produce more ATP in the mitochondria.
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Quiz
Quiz on Lipids, Proteins, Nucleic Acids, and ATP
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This used to be Unit 6 – EnzymesTextbook Ch 6
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MetabolismMetabolism refers to the total of all chemical and
physical reactions that occur in a cell
Most of these activities are driven by ATP
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MetabolismMetabolism is controlled by thyroxine, a hormone
produced in the thyroid gland
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Metabolism
Thyroxine is made from the addition of iodine to the amino acid tyrosine
Thyroxine stimulates all cells to produce more ATP through cellular respiration resulting in overall increase in metabolism
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Metabolism
The level of thyroxine in the blood is determined by a negative feedback loop which goes like this:
Thyroxine levels drop causing hypothalamus to release TRH
TRH acts on the anterior pituitary to release TSHTSH acts on the thyroid causing it to produce more
thyroxineHigh levels of thyroxine cause the hypothalamus to
stop TRH production and anterior pituitary to stop TSH production
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Thyroxine Control Feedback Loop
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EnzymeEnzymes are protein molecules with particular shapes
(active sites) to bond with particular substrates
Enzymes are catalysts for cellular reactions, bringing substrates together where they can react and form new substances
http://highered.mcgraw-hill.com/sites/dl/free/0072421975/196646/lw03_enzymes_final.html
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SubstrateSubstrates are molecules that react to produce new
products with the help of an enzyme
Reactions can be hydrolysis (breaking down) or synthesis (building) reactions
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CoenzymeCoenzymes are smaller molecules that help enzymes
function properly and are often contain vitamins
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Activation EnergyActivation energy refers to the amount of energy
needed to make a reaction occur
Enzymes reduce the activation energy needed
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“Lock and Key” ModelEnzymes are locks. Locks can only be opened by a
specific key.
Substrates are keys. They only work on a specific lock.
Starch is the substrate, amylase is the enzymePeptides are the substrates, peptidase is the enzymeLipids are the substrates, lipase is the enzymeLactose is the substrate, lactase is the enzyme
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pH – enzymes work at specific pHs. Enzymes in the blood work at pH 7.4 while enzymes in the stomach work at pH 2.
Factors Affecting Enzyme Action
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Temperature – Enzymes in our bodies work efficiently at 37oC but their action starts to drop off dramatically after 40oC
Factors Affecting Enzyme Action
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Substrate Concentration – The higher the concentration the more reactions that can occur up to a certain point
Factors Affecting Enzyme Action
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Competitive Inhibitors – fight for active sites with the substrate and prevents them from binding.
Enzyme Inhibition – Products made by an enzymatic pathway prevent the binding of other substrates
Factors Affecting Enzyme Action
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Factors Affecting Enzyme Action
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Heavy Metals – Some metals act as enzyme cofactors (helps the enzyme function) but others (Hg and Pb) causes the enzymes to denature and no longer function
Factors Affecting Enzyme Action
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Factors Affecting Enzyme Actionhttp://highered.mcgraw-hill.com/sites/dl/free/0072421975/196644/feedback_inhibition.html
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Enzyme InhibitionEnzyme inhibition occurs when the enzyme
cannot bind substrate molecules
The purpose of this enzyme inhibition is to limit the amount of product made by the enzyme so levels do not rise too high
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Enzyme InhibitionAs product molecules are produced, their level or
concentration will rise
Eventually these product molecules will interfere or inhibit the enzymes producing them, by binding the active site on the enzyme or attaching to the enzyme in a manner that alters the active site on the enzyme.
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Enzyme InhibitionWhen the product molecules are used up or their
concentration lowers, the enzyme will no longer be inhibited by the product molecules
The enzyme active site will be available to bind with substrate and make new product once again
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Enzyme InhibitionEnzyme inhibition is controlled by a negative
feedback loop
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Enzymes Lab - CatalaseCatalase is an enzyme found in liver and catalyzes the
reaction decomposing hydrogen peroxide into oxygen and hydrogen
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Enzymes Lab - CatalaseIn this lab, you will combine the reactants in the test
tubes and record your observations
When you are finished your observations, you will explain your observations with respect to the factors affecting enzyme action.
The lab sheet is provided and all reactants are included
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Summary
Learn your basic chemistry
Water is a polar molecule and is the universal solvent – meaning lots of things can dissolve in it
Acids and bases dissociate into different ions and their strength can be measured using the pH scale
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Summary
Organic molecules contain C and H
Carbohydrates are composed of monosaccharides or polymers of them
Lipids are composed of gylcerol and 3 fatty acids and form fats and oils, phospholids, and steroids
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Summary
Proteins are composed of polymers of amino acids called polypeptides
There are 4 levels of protein organization
Protein function is dependent on maintaining proper structure
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Unit 2 Review
Reread textbook pages 20-41
Read section summaries on page 42
Answer all review questions on pages 42 – 43
Define all keyterms on page 44
Use the website listed on page 44 for extra practice
Test is on __________