IB Biology Topic 3.1-3.6.txt

carbon, hydrogen, oxygen

nitrogen, calcium, phosphorous, iron, and sodium

found mainly in proteins

found in bones, involved in muscle contractions

found in hemoglobin (transports oxygen in blood)

found in nucleic acids

needed for transmission of nervous impulses

found in some proteins

needed for transmission of nervous impulses

• Thermal: water can be vaporized, or turned from a liquid to a gas by the heat of vaporization
• Heat of vaporization: quantity of heat a liquid must absorb for 1 gram to be converted to a gaseous state
• Water molecules can absorb a lot of heat energy (has a high specific heat capacity)
• Takes a lot of heat energy to evaporate because of the hydrogen bonds
• it stays together because of high kinetic energy
• Water has a very high melting point and boiling point

• Cohesion: the attractive forces between molecules of the same type (hydrogen bonding in water molecules results in cohesion)
• Water binds to itself due to polarity of its molecules
• example: allows water to be drawn up the xylem of plants

• Water is a solvent or dissolving agent due to its polarity (water is polar)
• Both ionic and polar compounds can dissolve in water

Water acts as a coolant in organisms when they sweat. Because water has a high amount of vaporization, when organisms sweat, it evaporates and it takes the heat with it. Thus, making the organism cooler. Water in the body maintains a relatively normal body temperature to keep the proteins from losing their shape

• 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 allows for the transport of water against gravity
• Ex) Water up a straw, Water being drawn up the xylem of plants (transpiration)

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. In this way, water acts as a medium of metabolic reactions.

Occurs when the atoms involved have different electro-negativities (one side is negative, the other side is positive)

A bond formed by the charge attraction when a hydrogen atom covalently bonds with one electronegative atom is attracted to another electronegative atom.

• Results in high specific heat and high heat of vaporization
• allows for cohesion
• allows for evaporative cooling and transportation

• A hydrophilic molecule is one that is polar and capable of hydrogen bonding. Because of this, it can dissolve in water
• A hydrophobic molecule is on that is non polar, and cannot dissolve in water.

Organic molecules contain carbon, Inorganic do not.

Glucose: no amino or carboxyl group, hexagon shaped





Amino Acids: Has amino and carboxyl group

• Ribose: Pentagon
• 

• Fatty Acids: Carboxyl group @ 1 end, and linear sequence of carbons
• 

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

• In Animals
• Glucose: used in cellular respiration as a source of energy
• Lactose: energy source found in milk (for nurturing babies)
• Glycogen: an energy storage polysaccharide
• In Plants
• Fructose: makes up sucrose and is produced by photosynthesis
• Sucrose: plants transport carbohydrates from leaves to the roots in the form of sucrose
• Cellulose: reinforces plant walls

• Condensation: type of polymerization where monomes are covalently bonded with the release of water
• In a condensation reaction, two molecules work together and form one big molecule along with water, because water is released during this reaction. So two amino acids could join together and form a dipeptide, and this would be a condensation reaction. The same applies for monosaccharides becoming disaccharides.
• Fatty acids join to glycerol in condensation to form triglycerides
• Hydrolysis: chemical reactions that break down covalent bonds between monomers with the addition of water.
• Water molecules are used to make a large molecule into a smaller molecule
• So...
• polypeptides and dipeptides can be broken down into amino acids
• polysaccharides and disaccharides can be broken down into monosaccharides
• triglycerides are broken apart from glycerol in hydrolysis to form fatty acids

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

• Lipids and Carbohydrates are used to store energy in living things
• Carbohydrates: are easy to make and break down
• they don't contain as much energy per gram, so they are heavier than lipids
• Plants store their energy as carbs because they're not concerned about the weight because they do not move (exception= airborne seeds, which use lipids as storage)
• Lipids: harder to make and harder to breakdown
• contain more energy per gram, thus lighter (2x more than carbs)
• Lipids are more economical for animals because they get more energy for less weight

adenine, guanine, cytosine, thymine

• Phosphate group is connected to the sugar of the next nucleotide
• Condensation forms DNA
• A nucleic acid polymer results from joining nucleotides together by covalent bonds called phopodiester linkages
• bond is between phospahe of one nucleotide to the sugar of the next
• results of backbone with a repeating linear pattern
• 

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

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

• An enzyme is a biological catalyst that speeds up a reaction
• An 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 of 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 because the chance that a substrate will encounter the correct active site increases. Reaction rate levels off after awhile because the active sites saturate

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

DNA helicase determines where replication begins. It separates 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 two strands being made, there are going to be two leading strands and two lagging strands. Because you can only add to the 3 prime end, this causes there to be only two ways to replicate. The leading strand starts at the origin, and continues on. With the two lagging strands, it has to wait for the DNA to separate, and then it lays down RNA primers and DNA polymerase II works backward toward the origin where they separated. The lagging strands compose the Ozaki fragments. Each separate strand has a leading and lagging strand. DNA polymerase I replaces RNA primer with the correct complementary DNA bases. DNA ligase connects the Ozaki fragments. Both the lagging and leading strands have a point in which they stop. The DNA ligase makes the final connection between the nucleotides of the Ozaki fragments. Deoxynucleoside triphosphates 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.

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 DNA.

semi conservative

Where DNA has two strands forming a double helix, RNA has one strand. Where DNA has the base thymine, RNA has the base Uracil. Where DNA has the sugar deoxyribose, RNA has the sugar ribose

Both consist of nucleotides. Both have the bases adenine, guanine, and cytosine

Genetic code is for determining the sequence of amino acids in a polypeptide chain. To code for 20 different amino acids, you need a unique sequence of 3 bases, or a triplet

RNA polymerase locates the promoter region on the DNA and recognizes that this is where it needs to stop. RNA polymerase separates the two 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 it 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 each other at the 3 prime end.

• Translation is made up of three stages: initiation, elongation, and translocation.
• Initiation
• mRNA and the small subunit come together such that the 5 prime 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 1st tRNA
• Elongation
• The next tRNa comes into the A site such that the anticodon matches the codon in the A site. The Polypeptide chain breaks off the tRNA in the P site and forms a dipeptide bond with the new amino acid
• Translocation
• The mRNA moves with the attached tRNA. The P site moves to the E site, and the A site moves to the P site. The one in the E site breaks off. After translocation, the whole cycle continues, until finally the stop codon on the end of the mRNA is reached. When the stop codon reaches the A site, it causes everything to separate, leaving the final completed polypeptide chain.

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.