IB Biology Topic 3.1-3.6

carbon, oxygen, and hydrogen

nitrogen, calcium, phosphorous, iron, and sodium

found mainly in proteins

involved in muscular contractions, makes bones hard

found in hemoglobin, which transports oxygen in the blood

found in nucleic acids

needed for the transmission of nervous impulses

in some proteins

transmission of nervous impulses

• Water can be vaporized, or turned from a liquid to a gas by the heat of vaporization
• heat of vaporization- the quantity of heat a liquid must absorb for 1 gram to be converted to a gaseous state
• The molecules of water can absorb a lot of heat energy (high specific heat capacity before it changes from one phase to another
• Water has a very high melting point and boiling point

• Cohesion: the attractive forces between molecules of the same type
• hydrogen bonding between water molecules results in cohesion
• Water binds to itself due to polarity of its molecules

Water is usually the dissolving agent of a solution because ionic and polar compounds can dissolve in water because it is also polar.

Water acts as a coolant in organisms when they sweat. Because water has a high amount of vaporization when organisms sweat, it takes heat with it when it evaporates. This makes the organism cooler.

• Water can act as a transport medium because it is cohesive. Because the water can bind to itself, and all the molecules are bonded to one another, it alows for the transport of water against gravity
• ex) transpiration or water being drawn up the xylem, water up a straw

Water is a universal solvent because it can dissolve polar and ionic bonds. In order for reactions to occur, the molecules have to be dissolved. The dissolved molecules can react in the cell because the cell is mainly made up of water, which acts as a medium of metabolic reactions.

occurs when the atoms involved have different electro-negativites (one sides is -, the other is +)

A bond formed by the charge attractions when a hydrogen atom covalently bonds with one electronegative atom, and is attracted to another electronegative atom

• results in high specific heat and high heat of vaporization
• allows for cohesion
• allows for evaporative cooling
• allows for transportation of water against gravity

amount of heat that must be absorbed or lost for one gram of a substance to change temperature by one degree Celsius

quantity of heat a liquid must absorb for one gram to be converted to a gaseous state

cooling of a liquids surface when a liquid evaporates

• Hydrophilic molecules are polar, and capable of hydrogen bonding. Because of this, it can dissolve in water
• Hydrophobic molecules are non polar, and cannot dissolve in water

organic compounds contain carbon, inorganic do not contain carbon

• Glucose: no amino acid or carrboxyl group, hexagon
• 

• Ribose: Pentagon shaped
• 

Amino acids: has amino and carboxyl group

Fatty Acids: carboxyl group @ one end, and liner sequence of carbons

• Monosaccharides: glucose, galactose, fructose
• Disaccharides: maltose, lactose, sucrose
• Polysaccharides: starch, glycogen, cellulose

• IN ANIMALS
• Glucose: used in cellular respiration as a source of energy
• Lactose: Energy source found in milk, nutrition for babies
• Glycogen: an energy storage polysaccharide
• IN PLANTS
• Fructose: makes up sucrose and is produced by photosynthesis
• Sucrose: plats transport carbohydrates from leaves to the roots in the form of sucrose
• Cellulose: reinforces plants wall, structural support

• Condensation: a type of polymerization where monomers are covalently bonded with the release of water
• In condensation reactions, two molecules work together and form one big molecule along with water, because water is released during this reaction.
• Through condensation, monosaccharides bond to form disaccharides and polysaccharides, amino acids join to form dipeptides and polypeptides, and fatty acids join to glycerol to form triglycerides
• Hydrolysis: chemical reaction that breaks covalent bonds between monomers with the addition of water.
• Water molecules are used to make a large molecule into a small molecule
• Through hydrolysis, disaccharides and polysaccharides break down to monosaccharides, polypeptides and dipeptides break down to amino acids, and triglycerides are broken apart from glycerol to form fatty acids.

• 1) Serve as long term energy storage
• 2) Insulate the organism against heat loss
• 3) Act as padding in places such as the hands and feet
• 4) Cushion the organs

• Lipids and Carbohydrates are both used to store energy in living things
• Carbohydrates: easy to make and breakdown
• contain loss energy per gram than lipids, so they are heavier
• plants store their energy as carbohydrates because they are not concerned about weight because they don't move
• Exception= airborne seeds, which use lipids
• Lipids: harder to make and breakdown
• contain more energy per gram than carbs (2x more), so they are lighter
• Lipids are more economical for animals because they can have more energy for less weight, thus making it easier to move around
• takes twice as much energy to break down carbohydrates

• Sugar is deoxyribose, which has one less sugar than ribose
• Phosphate group is the PO₄^-3 group
• Base is nitrogenous, of which there are 4 different kinds (adenine, guanine, cytosine, thymine)
• 

adenine, guanine, cytosine, thymine

• A nucleic acid polymer results from joining nucleotides together by covalent bonds called phophodiester linkages. The bond is between the phosphate of one nucleotide and the sugar of the next
• results in a backbone with a linear pattern

the protein unravels, changing of the shape of the enzyme of its active site, making it nonfunctional

An enzyme is a biological catalyst that speeds up a reaction. And active site is a region of the enzyme where the substrate fits into

Only a certain key fits into a certain lock, much like a certain substrate can only fit into a certain enzyme. The active site is usually only a pocket or groove, so the shape specificity of the substrate is crucial.

• Temperature
• Enzyme reaction rate increases with increasing temperature. Optimal temperature allows for the greatest number of molecular collisions without denaturing the enzyme. Beyond optimal temperature, reaction rate slows due to denaturation.
• pH
• For an enzyme to be effective, it must have a certain shape so the substrate can fit into it. The pH of the system that an enzyme is found in can influence the folding of the polypeptide chains of the proteins, and the shape. As the pH increases or decreases from its optimum, enzyme activity is reduced.
• Substrate Concentration
• In general, the greater the substrate concentration, the faster the reaction. This is because the chance that a substrate will encounter the correct active site increases. Reaction rate levels off after awhile, because the active sites saturate

Most individuals produce an enzyme that can break down lactose, a disaccharide composed of galactose and glucose. Lactose intolerant people cannot. Biotechnicians artificially produce lactase and put it in dairy products. Lactase breaks down lactose intro galactose and glucose

A single strand is used to form the double helix. Complementary bases pair together with bases of the other strand to form a complementary strand. Adenine pairs with Thymine, and Cytosine pairs with Guanine. A covalent bond is formed between the new nucleotides. A hydrogen bond is formed between the complementary bases.

The new strand is formed such that it is complementary to the old strand, thus reforming the strand it was separated from. It is necessary to ensure that there is a way to replicate the DNA.

semi-conservative

• Both consist of nucleotides
• Both have the bases guanine, cytosine, and adenine
• Where DNA has two strands forming a double helix, RNA has one strand.
• Where DNA has the sugar deoxyribose, RNA has ribose
• Where DNA has the base thymine, RNA has uracil

Genetic code is for determining the sequence of amino acids in a polypeptide chain.To code for 20 different amino acids, a unique sequence of 3 bases is needed, which is why it is called a triplet

One gene determines one polypeptide. A gene consists of a linear sequence of bases where this series determines the series of amino acids in a polypeptide chain

DNA is double stranded. Each strand consists of a linear sequence of nucleotides covalently bonded to each other. The 2 stranded are bonded to each other through hydrogen bonding such that one strand there is a bases that is hydrogen bonded to a complementary base on the other strand. For the complementary base pairing, one base is a purine and the other is a pyrimidine. The two strands run in opposite directions. One runs in the 5'-3' direction, the other in the 3'-5' direction.

introns and extrons

initiation

5'-3' direction

DNA helicase determines where replication begins. It seperates the two strands at the origin of replication. RNA primase lays down a short segment of complementary RNA nucleotides. DNA polymerase III brings and links complementary DNA nucleotides. For each of the 2 strands being made, there are going to be 2 leading strands and lagging strands. Because you can only add to the 3' end, this causes there to be only two ways to replicate. THe leading strand starts at the origin, and continues on. With the lagging strand, it has to wait for the DNA to separate and then it lays down RNA primer and DNA Polymerase III fills in with nucleotides and works backward toward the origin where they seperated. The lagging strands compose the Ozaki fragments. Each separate strand has a leading and lagging strand. DNA polymerase I replaces RNA primer with correct complementary DNA bases. DNA ligase connects the Ozaki fragments. Both the lagging and leading strands have a point in which they stop. DNA ligase makes the final connection between the nucleotides of the Ozaki fragments. Deoxynucleoside triphoshates are nucleotides that have three phosphate groups on them. They are attached on the 3 prime end. They give off 2 phosphate groups for energy to be used to covalently bond nucleotides to the end of the strand.

RNA polymerase locates the promoter region on the DNA. It recognizes that this is where it needs to begin. RNA polymerase seperates the 2 strands, and begins to lay down complementary RNA bases, only using one of the two strands of DNA. WHen RNA polymerase reaches the terminator, or the sequence that RNA recognizes to stop), it breaks off and there is a completed RNA strand. The nucleotide triphosphate is an RNA nucleotide that is added to the 3 prime end. It looses two phosphate groups and the energy is used to covalently bond RNA nucleotides to eachother.

introns

A particular tRNA will only have a particular amino acid attached. There is a particular activating enzyme that binds a specific amino acid to a tRNA using ATP

Ribosomes are composed of protein and rRNA. THere is a small and large subunit. The small subunit has an mRNA binding site. THe large subunit has 3 tRNA binding site (E,P,A)

initiation, elongation, translocation, and termination

• Translation consists of initiation, elongation, translocation, and termination. During elongation, mRNA and the small subunit come together such that the 5' end of the mRNA would connect with the mRNA binding site on the small subunit. It has to recognize AUG, which is the start codon. The anticodon on one end is complementary to a specific codon on the mRNA. tRNA comes with an anticodon that matches AUG. THe large subunit comes to the P site, which fits into the first tRNA.
• During Elongation, the next tRNA comes into the A site such that the anticodon matches the codon in the A site. Polypeptide chain breaks of the tRNA in the P site and forms a dipeptide bind with the new amino acid.
• During translocation, the mRNA moves with the attached tRNA. The P site moves to the E site, A site to the P site. The one in the E site breaks off. After translocation, the whole cycle continues until finally termination occurs. This occurs when the stop codon is reached on the end of the mRNA. When the stop codon reaches the A site, ti causes everything to separate and you end up with the final polypeptide chain.

within, secretion, lysosomes.

• Primary Structure: unique linear sequence of amino acids in a polypeptide chain
• determined by the genes
• can be sequenced in a lab
• determines final structure
• Secondary Structure: Regula repeated coiling or folding of the helix or pleats in a polypeptide chain
• stabilized by hydrogen bonds
• protein's backbone
• Tertiary Structure: 3 dimensional large folding of the polypeptide chain
• 2 types of bonds= weak interactions and covalent linkages
• Quaternary Structure: structure that results from interactions between several polypeptide chains
• fibrous/globular proteins
• all proteins do not have quaternary

• Fibrous: Secondary structure is dominant (determines overall structure), long and thin, insoluble in water
• Ex) Collagen, spiders silk
• Globular: tertiary or quaternary structures are dominant, folding into round shapes
• soluble in water
• ex) hemoglobin, amylase