IB Biology Topic 3.1-3.6
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What are the most frequently occurring chemical elements in living things?
carbon, oxygen, and hydrogen
What other elements are needed by living organisms?
nitrogen, calcium, phosphorous, iron, and sodium
What role does nitrogen play?
found mainly in proteins
What role does calcium play?
involved in muscular contractions, makes bones hard
What role does iron play?
found in hemoglobin, which transports oxygen in the blood
What role does phosphorous play?
found in nucleic acids
What role does potassium play?
needed for the transmission of nervous impulses
What role does sulfur play?
in some proteins
What role does sodium play?
transmission of nervous impulses
Draw and label a diagram showing the structure of water molecules to show their polarity and hydrogen bond formation.
Outline the thermal properties of water
- 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
Outline the cohesive properties of water
- 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
Outline the solvent properties of water
Water is usually the dissolving agent of a solution because ionic and polar compounds can dissolve in water because it is also polar.
Explain the relationship between the properties of water and its uses in living organisms as a coolant, medium of metabolic reactions and transport medium.
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.
What makes a molecule polar?
occurs when the atoms involved have different electro-negativites (one sides is -, the other is +)
Explain what a hydrogen bond 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
What is the importance of hydrogen bonding to life?
- results in high specific heat and high heat of vaporization
- allows for cohesion
- allows for evaporative cooling
- allows for transportation of water against gravity
What is specific heat?
amount of heat that must be absorbed or lost for one gram of a substance to change temperature by one degree Celsius
What is heat of vaporization?
quantity of heat a liquid must absorb for one gram to be converted to a gaseous state
What is evaporative cooling?
cooling of a liquids surface when a liquid evaporates
Compare hydrophobic and hydophillic
- 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
Distinguish between organic and inorganic compounds
organic compounds contain carbon, inorganic do not contain carbon
Identify amino acids, glucose, ribose, and fatty acids from diagrams showing their structures.
List three examples each of monosaccharides, disaccharides, and polysaccharides
- Monosaccharides: glucose, galactose, fructose
- Disaccharides: maltose, lactose, sucrose
- Polysaccharides: starch, glycogen, cellulose
State one function of each glucose, lactose, and glycogen in animals, and of fructose, sucrose, and cellulose in plants.
- 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
Outline the role of condensation and hydrolysis in the relationships between monosaccharides, disaccharides, and polysaccharides; between fatty acids, glycerol, and triglycerides; and between amino acids, dipeptides, and polypeptides
- 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.
State three functions of lipids
- 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
Compare the use of carbohydrates and lipids in energy storage.
- 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
Outline DNA nucleotide structure in terms of sugar, base, and phosphate
- 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)
State the names of four bases in DNA
adenine, guanine, cytosine, thymine
Outline how DNA nucleotides are linked together by covalent bonds into a single strand
- 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
Define enzyme and active site
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
Explain the enzyme-substrate specificity.
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.
Explain the effects of temperature, pH, and substrate concentration of enzyme activity
- TemperatureEnzyme 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.
- pHFor 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 ConcentrationIn 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
Explain the use of lactase in the production of lactose free milk.
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
Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds
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.
Draw and label a simple diagram of the molecular structure of DNA
Label: parts of nucleotide, covalent bond, hydrogen bond
Explain the significance of complementary base pairing in the conservation of the base sequence in DNA
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.
DNA replication is ______.
Compare the structure of RNA and DNA
- 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
Describe the genetic code in terms of codons composed of triplets of bases
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
Explain the relationship between one gene and one polypeptide
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
Describe the structure of DNA including the antiparallel strands, 3'-5' linkages and hydrogen bonding between purines and pyrimidines.
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.
Eukaryotic genes can contain ______ and _____.
introns and extrons
DNA ________ is initiated at many points in eukaryotic chromosomes
DNA replication occurs in the _______.
Explain DNA replication
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.
Eukaryotic RNA needs the removal of ____ to form mature mRNA
Explain that each tRNA molecule is recongnized by a tRNA activating enzyme that binds a specific amino acid to tRNA, using ATP for energy
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
Outline the structure of ribosomes, including protein and RNA composition, large and smalle subunits, three tRNA binding sites and mRNA binding sites
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)
Translation consists of ________, _________, _________, and ________.
initiation, elongation, translocation, and termination
Explain the process of translation
- 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.
Free ribosomes synthesize proteins for use primarily ____ the cell and bound ribosomes synthesize proteins primarily for _______ or for _________/
within, secretion, lysosomes.
Explain the four levels of protein structure, indicating each level's significance
- 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
Outline the difference between fibrous and globular proteins, with reference to two examples of each protein type.
- 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
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