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Biochemistry I

Page history last edited by Darrell Sharp 9 years ago


Ribosome, mRNA, tRNA image by Sanbonmatsu Team, Los Alamos National Laboratory 


3.1 Chemical elements and water 


Homework Questions 


Notes the Open Door web site


Notes Click4biology






State that the most frequently

occurring chemical elements in

living things are carbon, hydrogen,

oxygen and nitrogen.



Most common elements in living things:

C, H, O, N 




State that a variety of other elements

are needed by living organisms,

including sulfur, calcium, phosphorus,

iron and sodium.



Other common elements:

S, Ca, P, Fe, Na 




State one role for each of the elements

mentioned in 3.1.2.



Examples of functions:

  • Sulfur - holds some proteins together with covalent bonds.
  • Calcium - component of bones and teeth; co-factor of enzymes.
  • Phosphorus - component of the backbone of DNA
  • Iron - part of hemoglobin, the protein that carries oxygen in the blood.
  • Sodium - part of the electrical impulse of neurons.





Draw and label a diagram showing the

structure of water molecules to show

their polarity and hydrogen bond formation.


Water Notes 



Diagram of Water Molecules showing polarity (+/-) and Hydrogen Bonding.









Outline the thermal, cohesive and solvent

properties of water.



Thermal Properties of Water

  • Water changes temperature slowly compared to other compounds.
  • The hydrogen bonds in water control vibrations due to heat.
  • Water absorbs excess heat in cells so cells don't get too hot.
  • Water releases heat slowly so cells don't get too cold.


Cohesive Properties of Water

  • Cohesion is the attraction between the same kinds of molecules due to hydrogen bonding.
  • Example: water molecules "stick" to other water molecules.
  • Adhesion is the attraction between different kinds of molecules due to hydrogen bonding.
  • Example: water "sticks" to cellulose in plants to move up from the ground to the leaves.


Solvent Properties of Water

  • Because water is a polar molecule, it dissolves other polar molecules and ions easily.
  • "Dissolve" means to mix thoroughly with another substance.
  • A solution is a solute mixed in a solvent (vocabulary).
  • Salt (NaCl) dissolves in water because water molecules surround the charges of the ions.
  • Salt is the solute; water is the solvent.
  • Water cannot dissolve nonpolar molecules.
  • Example: oil and water do not mix 


Diagram of Ammonia dissolved in Water - Note the NH3+ molecules







Explain the relationship between the

properties of water and its uses in living

organisms as a coolant, medium for

metabolic reactions and transport medium.


Water as a coolant in organisms:

  • Blood is mostly water and can absorb heat and carry it to other parts of the body like the skin.
  • Humans sweat to cool their bodies down.


Water as a medium for metabolic reactions:

  • Metabolic reactions means all the chemical reactions that happen in a cell or organism.
  • The medium is the substance through which the reactions happen.
  • Cells are mostly water.
  • Most of the chemical reactions in cells happen in water.
  • Everything is dissolved in water.


Water as a transport medium:

  • Substances can be dissolved in water and moved around an organism by moving the water.
  • Water carries other compounds be dissolving them. 






3.2 Carbohydrates, lipids and proteins 


Homework Questions 






Molecular Images


Amino Acids






Distinguish between organic and inorganic compounds.



Organic compounds are based on carbon atoms and are found in living things. Some carbon compounds are not considered organic, such as CO2 and  HCO3-  


Inorganic compounds are all other compounds that are not organic compounds.





Identify amino acids, glucose, ribose and fatty acids from diagrams showing their structure.




                Monosaccharides (simple sugars)

       Glucose                    Ribose



       Amino Acid                      





       Fatty Acids




(Extra Information: All 20 Amino Acids)









List three examples each of monosaccharides, disaccharides and polysaccharides.




  • glucose
  • ribose
  • deoxyribose
  • fructose
  • galactose 
  • dextrose



  • sucrose
  • maltose
  • lactose 



  • starch (amylose)
  • glycogen
  • cellulose 





State one function of glucose, lactose and glycogen in animals, and of fructose, sucrose and cellulose in plants.




  • Glucose: substrate for cellular respiration (used for producing energy)
  • Lactose: milk sugar for mammals to feed their young
  • Glycogen: polymer of glucose for storing energy



  • Fructose: sugar reward in fruit for seed dispersing animals
  • Sucrose: inactive form of sugar for moving around in plants
  • Cellulose: strength and rigidity to cell walls



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 and polypeptides.



Condensation Reactions

  • Join two smaller molecules together
  • Produces water
  • Two monosaccharides are joined by a condensation reaction to form a disaccharide
  • Polysaccharides are formed by many condensation reactions with simple sugars
  • Fatty acids are joined to glycerol to form a triglyceride by condensation reactions
  • Amino acids are joined by condensation reactions to form polypeptides


(a) Two molecules of glycine, side by side, showing how a water molecule can be formed using OH from one and H from the other. (b) The two glycine molecules are linked together to form a dipeptide.

From: http://labspace.open.ac.uk/mod/resource/view.php?id=388779



Hydrolysis Reactions

  • Break apart large molecules in to smaller molecules
  • Uses water
  • Poly- and disaccharides are broken into monosaccharides
  • Triglycerides are broken into glycerol and fatty acids
  • Polypeptides are broken into individual amino acids 





State three functions of lipids.



Lipid Functions

  • store energy
  • thermal insulation (heat)
  • electrical insulation around neurons
  • buoyancy - help some organisms float on water



Compare the use of carbohydrates and lipids in energy storage.


Comparison of Carbohydrates and Lipids

Carbohydates provide about 4 Calories per gram.

Lipids provide about 9 Calories per gram.


Carbohydrates are more easily broken down than lipids.

Lipids require more oxygen to be broken down.


Carbohydrates are soluble in water, and lipids are not.

Carbohydrates are easy to move around in solution, lipids are not.




File:ADN animation.gif                                     


3.3 DNA structure 

Homework Questions 


Notes Click4biology 








Outline DNA nucleotide structure in terms of sugar (deoxyribose), base and phosphate.



A nucleotide consistes of three parts:

  1. phosphate PO43-
  2. sugar (ribose or deoxyribose)
  3. base (4 kinds in DNA: A, T, G, C)


Insert alt text



State the names of the four bases in DNA.










Outline how DNA nucleotides are linked together by covalent bonds into a single strand. 



Nucleotides are covalently bonded from the sugar of the first nucleotide to the phosphate of the second nucleotide.


A simple diagram of two nucleotides joined together:


Insert alt text



Note: below is a lot more detail than you need to know.


In a deoxyribose sugar the carbons are numbered from 1' to 5'



In a nucleotide, the phosphate is bonded to the 5' carbon, and the base is bonded to the 1' carbon.


The phosphate of the next nucleotide is covalently bonded to the 3' carbon.


The "backbone" of DNA is often referred to as a phosphate-sugar backbone going from 5' to 3'.


Note: when speaking, 5' is said as "five prime"



Explain how a DNA double helix is formed using complementary base pairing and hydrogen bonds.



Hydrogen bonds form between pairs of bases:


  • Adenine and Thymine
  • Cytosine and Guanine 


The base pairs hydrogen bond in only this arrangement.

The sizes of the bases and the hydrogen bonds will not fit together in any other arrangement. 


This is called complementary base pairing.

  • A complements T and vice versa
  • C complements G and vice versa


File:DNA chemical structure.svg




DNA has a double helix structure.


  • It is double because it has two strands of nucleotide polymers.
  • When the complementary base pairs come together, the angles of the sugar and phosphate create a helix shape (or spiral shape).


Sometimes it is called a "twisted ladder."



Draw and label a simple diagram of the molecular structure of DNA.






3.6 Enzymes 



Apoptosis simulation

Homework Questions


Lab Report Template


Enzymatic Activity Lab


Notes Open Door



(includes HL topics)


Notes Click4Biology




Define enzyme and active site.



An enzyme is a kind of protein that acts as a catalyst.

  • A catalyst is a substance that speeds up the rate of a chemical reaction.
  • A catalysts lowers the activation energy needed to start the reaction.
  • Most biological reactions would not happen without enzymes helping them.


The active site is the place on the enzyme that holds the reactants.

  • The reactants are called substrates when enzymes are involved in the reaction.
  • The active site is where the chemical reaction happens.
  • The enzyme holds the substrates and changes shape to weaken the bonds of the substrates.
  • The enzyme releases the products, and the enzyme is ready to do the reaction again and again. 




Explain enzyme–substrate specificity.



Enzyme-Substrate Specificity

  • One enzyme usually catalyzes one reaction. 
  • The active site only fits with one kind of substrate.
  • There are lots of different enzymes to all the different chemical reactions in a cell.

The Lock and Key Model describes enzyme-substrate specificity.

  • The active site and teh substrate fit togther like a lock and a key.
  • Only one key fits one lock.
  • Only one substrate fits one enzyme. 





Explain the effects of temperature, pH and substrate concentration on enzyme activity.



Define denaturation.



Effect of Temperature on Enzyme Activity

  • As the temperature increases, enzyme activity increases.
  • At high temperatures, the heat energy makes the enzyme lose its shape and activity decreases.
  • Denaturation is the loss of structure and function of an enzyme. 
  • Enzymes have an optimum temperature at which they are most active.




pH and Enzyme Activity

  • Enzymes function best at an optimum pH level.
  • pH levels above or below the optimum level decrease enzyme activity.
  • Highly acidic or basic conditions affect the hydrogen bonds that hold the enzyme together.
  • The enzyme can be denatured by changes in the pH level away from the optimum level.
  • Different enzymes have different optimum pH levels depending on their evolution and function. For example, stomach enzymes like acidic pH levels.




Enzyme Activity and Substrate Concentration

  • As the substrate concentration increases, enzyme activity increases.
  • At high substrate concentrations, enzyme activity increases slower.
  • Eventually substrate concentration increases beyond the number of available enzymes.
  • The enzyme activity reaches a constant rate.
  • The enzymes are saturated or fully occupied, and cannot work any faster.
  • At this point, increasing the substrate concentration does not increase the enzyme activity any more.





Explain the use of lactase in the production of lactose-free milk.


Lactose-Free Milk


Lactose is a disaccharide made of a glucose and a galactose bonded together.

It is known as milk sugar because it is found in the milk of mammals.

  • Milk and milk products like yogurt and cheese have lactose in them.

Lactase is an enzyme that breaks down lactose into glucose and galactose.


Many humans are lactose intolerant - this means they cannot digest lactose and feel sick when they consume milk products.

Companies produce lactose-free milk for people who are lactose intolerant.

The commercial production begins with lactase taken from yeast.

The enzyme is attached to structural proteins so that it isn't lost in the process.

  • It usually looks like beads.

Milk is added to the beads and recirculated until all the lactose is broken down.

The lactose-free milk is ready for the consumer.

Enzymes are useful for this process and many others because:

  • they can be re-used.
  • they efficiently convert the lactose into glucose and galactose.
  • they make the process inexpensive.


See Click4Biology for a diagram of the industrial process.






3.4 DNA replication  





Homework Questions 


Notes Click4Biology






Explain DNA replication in terms of unwinding the double helix and separation of the strands by helicase, followed by formation of the new complementary strands by DNA polymerase.



Explain the significance of complementary base pairing in the conservation of the base sequence of DNA.



State that DNA replication is semi-conservative.



DNA Replication video


Watch the video and note these things:


1. Helicase

2. Replication fork

3. Leading strand

4. Lagging strand 

5. DNA polymerase III

6. Free nucleotides

7. Complementary base pairing

8. Template

9. Semi-conservative replication

10. Result






3.5 Transcription and translation  


Homework Questions 


Notes Click4Biology







Compare the structure of RNA and DNA.











  • DNA & RNA: polymer of nucleotides
  • DNA RNA5-carbon sugar
  • DNA & RNA: four possible bases        





  • DNA sugar is deoxyribose        
  • RNA sugar is ribose
  • DNA bases: adenine, thymine, cytosine, guanine
  • RNA bases: adenine, uracil, cytosine, guanine
  • DNA double-stranded    
  • RNA single-stranded




Uracil is very similar in shape and hydrogen bonding to thymine.

So, the complementary RNA nucleotide for A is U.




Outline DNA transcription in terms of the formation of an RNA strand complementary to the DNA strand by RNA polymerase.



Transcription: DNA --> RNA


  • DNA is an information molecule.
  • The information is written in "sentences" called genes.
  • A gene is a sequence of DNA nucleotides ("letters").
  • Each gene has information for making a protein.
  • Transcription is the process of converting the information of one gene into an RNA molecule.
  • The DNA gene is "transcribed" to make an RNA molecule with the same information.
  • DNA and RNA bases can make complementary pairs.
  • Transcription of information happens because of complementary base pairing.
  • Transcription happens in the nucleus 



  • DNA is unzipped by helicase to expose one gene.
  • Only one strand of the DNA is used for transcription.
  • Free RNA nucleotides base-pair with complementary DNA nucleotides,
  • The enzyme RNA polymerase catalyzes the bonding of a single strand of RNA.
  • At the end of the gene, the RNA is released and the DNA returns to its double helix shape.





Three kinds of RNA

  1. mRNA = messenger RNA has information for the sequence of amino acids in a protein.
  2. tRNA = transfer RNA bonds with one specific amino acid.
  3. rRNA = ribosomal RNA is part of the structure of a ribosome.


Ribosomes are structures in the cytosol of a cell and on the endoplasmic reticulum that build proteins. 




Transcription video 




Describe the genetic code in terms of codons composed of triplets of bases.



DNA is a book.

    A gene is a sentence.

        A nucleotide is a letter.

            What are the words?

                Triplets and Codons 

                     What do the words say?

                          "Put this amino acid in the protien."



A triplet is a three nucleotide sequence.

  • Often we write the sequence of nucleotides using the letters of their bases, for example:
  • A triplet has information for identifying one amino acid.
  • So the DNA sequence is divided into three letter words:
  • Each triplet would code for a different amino acid when building a protein. 


A codon is a triplet in mRNA. The DNA triplet is transcribed into an mRNA codon.

mRNA codons and their amino acids are identified in the genetic code.


In the genetic code below, the codon CAU is shown to code for the amino acid histidine.







Explain the process of translation, leading to polypeptide formation. 

Include the roles of messenger RNA (mRNA), transfer RNA (tRNA), codons, anticodons, ribosomes and amino acids.



Translation: RNA --> Proteins


How are the RNA codons translated into an amino acids in a protein?


Ribosomes use mRNA, tRNA, amino acids to build a new protein.

mRNA is a copy of a gene. It has the sequence of amino acids for making a protein coded in its nucleotide sequence.

tRNA has a triplet called an anticodon which is complementary to an mRNA codon.

The tRNA has a specific amino acid bonded to the other end. 



One mRNA codon matches one tRNA anticodon with one amino acid attached.

The ribosome holds the mRNA and the tRNA together.

Three mRNA codons fit inside the ribosome, and tRNAs can match their anticodons to the mRNA codons.

The ribosome acts like an enzyme and bonds the amino acids on the adjacent tRNAs together.

The ribosome moves down the mRNA and new tRNAs enter and their amino acids get bonded to the growing polypeptide.

At the end of the mRNA, the ribosome falls apart and releases the mRNA, tRNAs, and the polypeptide (protein).




Transcription and Translation video 


Transcription & Translation video 

from Shadowlabs


DNA Workshop - Interactive Shockwave Simulation


Transcription and Translation Model project 




Discuss the relationship between one gene and one polypeptide.



Historical Progression of the One Gene/One Polypeptide Hypothesis

1. one gene makes one enzyme - discovered in the 1940s

2. one gene makes one protein - DNA makes other kinds of proteins

3. one gene makes one polypeptide - some proteins have multiple subunits


4. one gene makes multiple polypeptides - mRNA can be modified after transcription to make different polypeptides from te same gene.









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