Topic 2 Molecular Biology

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Topic 2 Molecular Biology

Topic 2.1 Molecules to Metabolism Essen%al idea: Living organisms control their composi?on by a complex web of chemical reac?ons.

Understandings:

•  2.1.U1 Molecular biology explains living processes in terms of the chemical substances involved.

•  2.1.U2 Carbon atoms can form four covalent bonds allowing a diversity of stable compounds to exist.

•  2.1.U3 Life is based on carbon compounds including carbohydrates, lipids, proteins and nucleic acids.

•  2.1.U4 Metabolism is the web of all the enzyme-catalyzed reac?ons in a cell or organism.

•  2.1.U5 Anabolism is the synthesis of complex molecules from simpler molecules including the forma?on of macromolecules from monomers by condensa?on reac?ons.

•  2.1.U6 Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers.

Applica?ons:

•  2.1.A1 Urea as an example of a compound that is produced by living organisms but can also be ar?ﬁcially synthesized.

•  2.1.S1 Drawing molecular diagrams of glucose, ribose, a saturated faQy acid and a generalized amino acid. [Only the ring forms of D-ribose, alpha–D-glucose and beta-D-glucose are expected in drawings.]

•  2.1.S2 Iden?ﬁca?on of biochemicals such as sugars, lipids or amino acids from molecular diagrams.

Skills:

I. Molecular biology

A.  Molecular biology explains living processes in term of the chemical substances involved-

1.  The structure of DNA was discovered in 1953, since then Molecular Biology has transformed our understanding of living processes

2.  The rela?onship between genes and the polypep?des they generate is at the heart of this science.

a.  The central idea can be simpliﬁed to

“DNA makes RNA makes protein”. The informa?on in this ﬂow cannot be reversed and the protein generated

cannot change the RNA or DNA. ^madprime

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I. Molecular biology

B.  Molecular biology is the study of the molecular basis of biological ac?vity in cells.

1.  Molecular biologists take a reduc?onist approach, breaking down processes into its component parts to improve our understanding of life.

a.  The processes of both photosynthesis and cellular respira?on were discovered using the reduc?onist approach.

biochemsoctrans.org; RegisFrey Some scien*st believe the reduc*onist approach is limited because it does not look at the “whole picture”.

II. Carbon Compounds

A.  Carbon atom can form four bonds allowing a diversity of compounds to exist-

1.  Carbon forms the backbone of every single organic molecule due to it’s proper?es:

a.  Carbon atoms has four electrons in their outer shell allowing them to form four covalent bonds with poten?al four other diﬀerent atoms.

2.  Covalent bonds are the strongest type of bond

between atoms. universetoday.com; tes.com

II. Carbon Compounds

3.  Because of the stability of covalent bonds large molecules with many bonds can be formed.

B.  The result of these proper?es is an almost inﬁnite number of diﬀerent possible molecules involving carbon.

Ti*n (connec*n) is the largest known protein and it contains 539,000 atoms (chemical formula C₁₆₉₇₂₃ H₂₇₀₄₆₄ N₄₅₆₈₈ O₅₂₂₄₃ S_912.). Ti*n gives muscle its elas*city.

ks.uiuc.edu

III. Classifying Carbon Compounds

A.  Life is based on carbon compounds including carbohydrates, lipids, proteins, and nucleic acids-

1.  Carbohydrates-

a.  Contain carbon, hydrogen and oxygen

b.  Consists of one or more simple sugars. Glycosidic bonds hold

monosaccharides together.

i.  monosaccharide = 1 ii.  disaccharide = 2 iii.  polysaccharide = many bbc.co.uk; shmoop.com; bankobiology.blogspot.com

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III. Classifying Carbon Compounds

c.  Monomers follow the general basic formula of (CH2O) i.e. glucose C6H12O6

d.  Monomers are commonly ring shaped molecules Can you recognize the

diﬀerence between the two glucose molecules?

These two molecules are anomers, a cyclic carbon molecule with a different configura*on at the C-1 carbon. This affects the way the molecules form bonds with other molecules

wikispaces.psu.edu; Talk I

III. Classifying Carbon Compounds

2.  Lipids-

a.  Contain carbon, hydrogen and oxygen b.  Lipids are insoluble in water but soluble in non-polar organic solvents

chemistry.about.com; hyperphysics.phy-astr.gsu.edu What do you no*ce about

the general structure of a triglyceride, a simple lipid?

III. Classifying Carbon Compounds

c.  Common lipids include

i.  triglycerides - a simple lipid, fats are solid at room temperature and oils are liquid at room temperature.

ii.  phospholipids - a compound lipid containing a phosphate group, the main component of cell plasma membranes.

iii.  steroids - derived lipids, important in membrane structure and communica?on as hormones.

Study.com; Pearson Educa?on; McGraw Hill

III. Classifying Carbon Compounds

Can you recognize the basic components of the diﬀerent groups of lipids?

Ibbioninja.com.au

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III. Classifying Carbon Compounds

3.  Proteins-

a.  Contain carbon, hydrogen, oxygen and nitrogen (addi?onally sulfur is common, but it is not present in all proteins).

b.  Proteins are large organic compounds made of monomers called amino acids, arranged into one or more linear chains.

i.  pep?de bonds hold amino acids together

ii.  dipep?de = 2

iii.  polypep?de = many Study.com; BCA Chemistry

III. Classifying Carbon Compounds

c.  There are 20 amino acids, each with a diﬀerent R group that give amino acids diﬀerent proper?es.

Pearson Educa?on You don’t need to memorize the structures of the 20 diﬀerent amino acids, but you will need to understand how the R groups play a role in the interac*ons a protein has with it’s environment.

III. Classifying Carbon Compounds

d.  Proteins have the most uses in the body, from structural to enzyma?c, and communica?on!

i-Biology.com

III. Classifying Carbon Compounds

4.  Nucleic acids-

a.  Contain carbon, hydrogen, oxygen, nitrogen and phosphorus.

b.  Nucleo?de monomers chain together to form a polynucleo?de.

c.  Nucleo?des consist of base, sugar and phosphate groups covalently bonded together d.  If the sugar is ribose then the

nucleic acid formed is RNA if the sugar is deoxyribose then DNA is formed.

dlc.dcccd.edu; Study.com

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III. Classifying Carbon Compounds

d.  If the sugar is ribose then the nucleic acid formed is RNA if the sugar is deoxyribose then DNA is formed.

Pearson Educa?on; Nature Educa?on

IV. Metabolism

A.  Metabolism is the web of all the enzyme catalyzed reac?ons in a cell or organism-

The IUBMB-Sigma- Nicholson Metabolic Pathways Chart aims to show all the metabolic pathways found in eukaryote cells. The chart in it's en*rety shows how complex the chemicals reac*ons needed to support life in a single cell unit.

IV. Metabolism

B.  Most (if not all) reac?ons are catalyzed by enzymes 1.  Enzymes are a class of proteins that are organic catalysts.

2.  Catalysts are substances that increases the rate of a chemical reac?on without itself undergoing any permanent change.

C.  Metabolism is made of two processes: anabolism and catabolism.

Bahamn Adam; tutorsglobe.com

V. Anabolism

A.  Anabolism is the synthesis of complex molecules from simpler molecules including the forma?on of macromolecules from monomers by condensa?on reac?ons-

1.  Anabolic – reac?ons that build molecules i.e. protein synthesis.

2.  Condensa?on reac?on – creates bonds by removing water between two or more molecules.

Wikipedia Commons; i-Biology.com

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Maltose synthase condenses two molecules of glucose into maltose forming a glycosidic bond

A ribosome condenses two amino acids into a dipep*de forming a pep*de bond The bonds formed are types of covalent bonds. Bonding monomers together creates a polymer (mono = one, poly = many).

Dehydra*on reac*on and condensa*on reac*on are not the same. In dehydra*on water is removed only from one molecule, while condensa*on take OH from one and an O from another molecule to form water..

Examples of anabolism by condensa?on

bioknowledgy.net

VI. Catabolism

A.  Catabolism is the breakdown of complex molecules into simpler molecules including the hydrolysis of macromolecules into monomers-

1.  Catabolic – reac?ons that break down molecules.

2.  Hydrolysis – breaks bonds by adding water and splimng two or more molecules apart.

Ross Whitwam; i-Biology.com

Lactase hydrolyses lactose into glucose and galactose breaking the glycosidic bond A protease hydrolyses a dipep*de into two amino acids breaking the pep*de bond

Examples of catabolism by hydrolysis

bioknowledgy.net