Molecular Biology and Biochemistry
7 multiple choice
1 written response
1 written response
a. Demonstrate understanding that a small subset of elements (C, H, O, N, P, S) makes up most of the chemical compounds in living organisms by combining in many ways
The elements, C (carbon), H (hydrogen), O (oxygen), N (nitrogen), P (Phosphorous), and S (sulfur) are the most common elements found in living organisms.
Because carbon contains four valence electrons, it can form four covalent bonds. Molecules containing carbon can form straight chains, branches, or rings. This allows many possibility to generate a range of molecular structures and shapes. Carbon always wants to hold onto four other atoms or groups of molecules. This allows for tremendous diversity and variety of molecules based on the C atom attached to other atoms. Pretty much all living things are built around carbon-based molecules.
b. Recognize and differentiate the structure and function of molecules in living organisms, include carbohydrates, lipids, proteins, and nucleic acids.
Macromolecule- there are four classes of macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Macromolecules are polymers which are molecules built by linking together a large number of small, similar chemical subunits. For example, complex carbohydrates are polymers of simple ring-shaped sugars. Proteins are polymers of amino acids. Nucleic acids (DNA and RNA) are polymers of nucleotides. Macromolecules are grouped into four major categories: carbs, proteins, lipids, and nucleic acids.
Carbohydrates- made up of one simple subunit called monosaccharide which are then joined together to form disaccharides (sucrose and lactose) and polysaccharides (cellulose and starch). Carbs are comprised of carbon, hydrogen, and oxygen with a ration of 1:2:1. Carbohydrates are essential for energy storage and structural support.
Lipids- made up of glycerol, fatty acids, phosphate, long carbon chains, etc. This is a group of esters including fats and waxes found in living tissue. Lipids are insoluble in water but soluble in organic solvents. The most familiar lipids are fats and oils. They have a very high proportion of nonpolar carbon-hydrogen bonds, as a result these long-chain lipids cannot fold up like a protein. When placed in water, many lipid molecules will cluster together and expose the polar groups to the surrounding water while hiding away the nonpolar parts of the molecules together within this cluster. This setup is very important to cells as it underlies the structor of cellular membranes. Lipids are a source of energy, chemical messengers, insulation and crucial elements of membranes.
Proteins- subunit are amino acids, joined together in a peptide chain. There are only 20 amino acids, each with a Hydrogen, an amino group, a carboxyl group, and an R group (composed of varying molecules). Provides structure, catalyst in biological systems, provides support, movement, growth, and repair.
Nucleic acids- subunits are nucleotides. Two different acids called DNA and RNA that are found in the cells' nuclei (RNA is also found in the cytoplasm). There are five nitrogenous basis: adenine, guanine, uracil (found only in the RNA), thymine (found only in the DNA), and cytosine. There are three components: a five carbon sugar, a phosphate group, and a nitrogenous group. The nucleic acid is comprised of chains of 5-carbon sugars that is linked by phosphate bond, which an organic base protruding from each sugar. If the sugar is deoxyribose, then the polymer is a DNA, and if the sugar is a ribose, then the polymer is a RNA. Nucleic acids carry the genetic code in DNA and RNA. Their function is to encode genes and gene expression.
c. Describe the process of protein syntheses, including transcription and translation
Protein synthesis involves DNA and RNA (a type of nucleic acid RNA sugar are ribose as compared to DNA's deoxyribose. Because of the difference, RNA does not bind to the nucleotide base Thymine (T). Instead, RNA contains the nucleotide base Uracil (U) in place of T.
Transcription- in the first step of protein syntheses (which takes place in the cell nucleus), the two strands in the a gene that codes for a protein unzip from each other. The mechanism of transcription has parallels in that of DNA replication. Unlike DNA replication, in this process only one strand is transcribed. The strand that contains the gene is called the sense strand. The complimentary strand is called the antisense strand. The mRNA produced in transcription is a copy of the sense strand, but is is the antisense strand that is transcribed. Ribonucleotide triphosphates (NTPs) aligns with the antisense strand. RNA polymerase joins the ribonucleotides together and forms a pre-messenger RNA molecule. This is complementary to a region of the antisense DNA strand. Transcription is complete when the RNA polymerase enzyme reaches the end where it signals it to stop.
Translation- After mRNA is manufactured it leaves the cell nucleus and travels to a cellular organelle called the ribosome. In the ribosome, the mRNA code is translated into a transfer RNA (tRNA) code which, in turn, is transferred into a protein sequence. In this process, each set of 3 mRNA bases (codon) will pair with a complimentary tRNA base triplet (anticodon). Each tRNA is specific to an amino acid, a tRNA's are added to the sequence, amino acids are linked together by peptide bonds, eventually forming a protein that is later released by the tRNA using the mRNA strand.
After the process of transcription and translation are complete, we are left with a protein that consists of the chain: Apartic Acid-Leucine. Proteins normally consist of hundreds or thousands of amino acids.
d. Compare anaerobic and aerobic respirations
Anaerobic Respiration-this is a type of internal respiration which does not use free oxygen. Anaerobic respiration takes place in the cells of organisms and releases a small amount of energy. In most organisms, a chemical reaction called glycolysis (glyco=sugar, lysis= breaking) breaks down glucose into pyruvic acid. All life on earth undergoes glycolysis and this process takes place in the cytoplasm. Normally aerobic respiration then takes place to break down this poisonous acid in the presence of oxygen, which releases a bulk of energy. Sometimes, aerobic respiration does not follow and instead the acid undergoes further anaerobic reactions that coverts it to lactic acid. Lactic acid fermentation occurs in mammals, is toxic, and is the "burn" you feel after an intensive activity. The goal of this fermentation process is to covert NADH to NAD+ (which is used in glycolysis). As this builds up, an organism acquires an “oxygen debt” which is paid off” later by taking in much more oxygen than normal. The latter process occurs in microscopic creatures, providing enough energy without the use of oxygen. The end products of glycolysis is 2 (it produces 4, but uses 2, with a net of 2 ATP) ATP molecules, pyruvate, and NADH.
Aerobic respiration- a type of internal respiration that takes place in the presence of free oxygen. Most organisms obtain the majority of their energy through aerobic respiration. Oxygen is carried by the blood and taken into the cell and reacts in the mitochondria with the pyruvic acid produced in anaerobic respiration. Carbon dioxide and water are the products of this reaction. Chemical energy is stored as “ATP”. This process is an example of oxidation where a substance is broken down in the presence of oxygen.
Krebs cycle: the goal is to take the pyruvate and produce NADH and FADH2. This process takes place in the mitochondria and has two steps. First is the conversion of pyruvate into Acetyl CoA, the second is the Krebs Cycle proper. Carbons, hydrogens, and oxygens end up as CO2 and H2O. Chemiosmosis is the production of ATP in cellular respiration. The goal of chemiosmosis is to break down NADH and FADH2, pumping H+ into the outer compartment of the mitochondria. The Electron Transport Phosphorylation (ETP) creates a gradient which is used to produced ATP. The ETP typically creates 32 ATP's**. ATP is generated as it moves down the concentrated gradient through a special enzyme called ATP synthase. 32 molecules of ATP can be produced for each glucose molecule as a result of the Krebs cycle reactions (2 ATP's), the electron transport system, and chemiosmois. In addition, 2 more ATP molecules are produced through glycolysis, giving us a net total of 36 ATP molecules**. Each ATP molecule can release 7.3 kilocalories of energy per mole.
** Note, some science books will list that a net of 38 ATPs is produced. This number has more to do with plants as they do not spend some of the ATP. Also, these numbers are ideal, and the maximum number of ATP's won't always be produced from every glucose.
Some differences between plants and animals:
1) While both plants and animal cells contain mitochondria, animal cells contain much more
2) Animal cells get most of their ATPs from mitochondria
3) On the other hand, plant cells get most of their ATP from chloroplast
e. Describe the process of photosynthesis
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html
http://photoscience.la.asu.edu/photosyn/education/learn.html
http://www.esf.edu/pubprog/brochure/leaves/leaves.htm
Since most plants are autotrophs (all green plants) and have the ability to make their own food, the process by which the make their complex food substance from simpler substances is called photosynthesis.
Photosynthesis is the process of converting solar energy into chemical energy. Photosynthesis mainly takes place in the palisade cells. Plants take in carbon dioxide and combine it with water, along with the energy taken in from the sun by the chloroplasts. Products of photosynthesis are oxygen and energy in the from of carbohydrates). Plants actually produce quite a bit of food energy, more than they need to survive. This is great for us organisms, as we are able to consume this extra energy food source.
The process:
Energy from sun- electromagnetic waves that enters the plant via chloroplasts. It is a one time trip for this energy, so thank goodness energy is continuously coming in from the sun.
Within the plant, water and carbon dioxide is broken down and recombine. Hydrogen is added onto the carbon and oxygen. The left over oxygen atoms are combined to make oxygen.
Light-dependent reactions: Photons from the sunlight hit the pigments in the thylakoid (first part of photosyntheses process, aka light reaction). The pigments are light harvesting molecules. Each pigment absorbs a different type of light, which allows the plant to utilize a wide range of light. So, in green plants, the primary photosynthetic pigments are chlorophylls a and b. Electrons are knocked loose and energize the process of photosynthesis (the electrons. Photolysis of water break it down into oxygen and hydrogen. Hydrogen further breaks down into a positively charged ion and an electron. This electron replaces the missing electrons knocked loose by the photons. The hydrogen ion stays in the hydrogen reservoir of the thylakoid. They leave through special channels of the membrane during photosynthesis. This provides energy to the ATP syntheses enzymes where ATP molecules are made. ATP and NADPH power the dark reaction. Gas exchanges takes place in the stomas. The gas flowers into the roomy air passages of the spongy parenchyma region. These passages are all connected to each other and to the mesophyll cells.
Guard cells (part of the stomate) are open during the day and closed at night. Stromas may be closed on hot dry days but need to be careful because this slows down photosynthesis as carbon dioxide runs out. Guard cells can have some chloroplasts in them, like mesophyll cells. Each chloroplasts is one little carbohydrate factory. The membrane envelope of chloroplast controls the flow of necessary material and particles into and out of the chloroplast. After the thylakoids, the photosynthesis process moves out of its stroma. Here, enzymes take the carbon dioxide and combine it with hydrogen and oxygen to make simple carb molecules. This part of the process is called “light independence” reaction or “dark reaction” (sometimes called carbon fixing process because carbon from carbon dioxide is “fixed” into the beginning of simple sugar or carb molecule). Out in the stroma, enzymes use carbon dioxide and positively charged hydrogen ions to assemble sugar fragments, which are half of the glucose molecule. After photosynthesis, half of the glucose molecule passes through chloroplasts outer membrane into the cell. Here, more enzymes join the 3-carbon fragment with another 3-carbon fragment and you have glucose molecule. This becomes the building block for other carbs such as sucrose, lactose, ribose, and starch. If eaten by animals, it is used to make fats, oils, amino.
The elements, C (carbon), H (hydrogen), O (oxygen), N (nitrogen), P (Phosphorous), and S (sulfur) are the most common elements found in living organisms.
Because carbon contains four valence electrons, it can form four covalent bonds. Molecules containing carbon can form straight chains, branches, or rings. This allows many possibility to generate a range of molecular structures and shapes. Carbon always wants to hold onto four other atoms or groups of molecules. This allows for tremendous diversity and variety of molecules based on the C atom attached to other atoms. Pretty much all living things are built around carbon-based molecules.
b. Recognize and differentiate the structure and function of molecules in living organisms, include carbohydrates, lipids, proteins, and nucleic acids.
Macromolecule- there are four classes of macromolecules: carbohydrates, lipids, proteins, and nucleic acids. Macromolecules are polymers which are molecules built by linking together a large number of small, similar chemical subunits. For example, complex carbohydrates are polymers of simple ring-shaped sugars. Proteins are polymers of amino acids. Nucleic acids (DNA and RNA) are polymers of nucleotides. Macromolecules are grouped into four major categories: carbs, proteins, lipids, and nucleic acids.
Carbohydrates- made up of one simple subunit called monosaccharide which are then joined together to form disaccharides (sucrose and lactose) and polysaccharides (cellulose and starch). Carbs are comprised of carbon, hydrogen, and oxygen with a ration of 1:2:1. Carbohydrates are essential for energy storage and structural support.
Lipids- made up of glycerol, fatty acids, phosphate, long carbon chains, etc. This is a group of esters including fats and waxes found in living tissue. Lipids are insoluble in water but soluble in organic solvents. The most familiar lipids are fats and oils. They have a very high proportion of nonpolar carbon-hydrogen bonds, as a result these long-chain lipids cannot fold up like a protein. When placed in water, many lipid molecules will cluster together and expose the polar groups to the surrounding water while hiding away the nonpolar parts of the molecules together within this cluster. This setup is very important to cells as it underlies the structor of cellular membranes. Lipids are a source of energy, chemical messengers, insulation and crucial elements of membranes.
Proteins- subunit are amino acids, joined together in a peptide chain. There are only 20 amino acids, each with a Hydrogen, an amino group, a carboxyl group, and an R group (composed of varying molecules). Provides structure, catalyst in biological systems, provides support, movement, growth, and repair.
Nucleic acids- subunits are nucleotides. Two different acids called DNA and RNA that are found in the cells' nuclei (RNA is also found in the cytoplasm). There are five nitrogenous basis: adenine, guanine, uracil (found only in the RNA), thymine (found only in the DNA), and cytosine. There are three components: a five carbon sugar, a phosphate group, and a nitrogenous group. The nucleic acid is comprised of chains of 5-carbon sugars that is linked by phosphate bond, which an organic base protruding from each sugar. If the sugar is deoxyribose, then the polymer is a DNA, and if the sugar is a ribose, then the polymer is a RNA. Nucleic acids carry the genetic code in DNA and RNA. Their function is to encode genes and gene expression.
c. Describe the process of protein syntheses, including transcription and translation
Protein synthesis involves DNA and RNA (a type of nucleic acid RNA sugar are ribose as compared to DNA's deoxyribose. Because of the difference, RNA does not bind to the nucleotide base Thymine (T). Instead, RNA contains the nucleotide base Uracil (U) in place of T.
Transcription- in the first step of protein syntheses (which takes place in the cell nucleus), the two strands in the a gene that codes for a protein unzip from each other. The mechanism of transcription has parallels in that of DNA replication. Unlike DNA replication, in this process only one strand is transcribed. The strand that contains the gene is called the sense strand. The complimentary strand is called the antisense strand. The mRNA produced in transcription is a copy of the sense strand, but is is the antisense strand that is transcribed. Ribonucleotide triphosphates (NTPs) aligns with the antisense strand. RNA polymerase joins the ribonucleotides together and forms a pre-messenger RNA molecule. This is complementary to a region of the antisense DNA strand. Transcription is complete when the RNA polymerase enzyme reaches the end where it signals it to stop.
Translation- After mRNA is manufactured it leaves the cell nucleus and travels to a cellular organelle called the ribosome. In the ribosome, the mRNA code is translated into a transfer RNA (tRNA) code which, in turn, is transferred into a protein sequence. In this process, each set of 3 mRNA bases (codon) will pair with a complimentary tRNA base triplet (anticodon). Each tRNA is specific to an amino acid, a tRNA's are added to the sequence, amino acids are linked together by peptide bonds, eventually forming a protein that is later released by the tRNA using the mRNA strand.
After the process of transcription and translation are complete, we are left with a protein that consists of the chain: Apartic Acid-Leucine. Proteins normally consist of hundreds or thousands of amino acids.
d. Compare anaerobic and aerobic respirations
Anaerobic Respiration-this is a type of internal respiration which does not use free oxygen. Anaerobic respiration takes place in the cells of organisms and releases a small amount of energy. In most organisms, a chemical reaction called glycolysis (glyco=sugar, lysis= breaking) breaks down glucose into pyruvic acid. All life on earth undergoes glycolysis and this process takes place in the cytoplasm. Normally aerobic respiration then takes place to break down this poisonous acid in the presence of oxygen, which releases a bulk of energy. Sometimes, aerobic respiration does not follow and instead the acid undergoes further anaerobic reactions that coverts it to lactic acid. Lactic acid fermentation occurs in mammals, is toxic, and is the "burn" you feel after an intensive activity. The goal of this fermentation process is to covert NADH to NAD+ (which is used in glycolysis). As this builds up, an organism acquires an “oxygen debt” which is paid off” later by taking in much more oxygen than normal. The latter process occurs in microscopic creatures, providing enough energy without the use of oxygen. The end products of glycolysis is 2 (it produces 4, but uses 2, with a net of 2 ATP) ATP molecules, pyruvate, and NADH.
Aerobic respiration- a type of internal respiration that takes place in the presence of free oxygen. Most organisms obtain the majority of their energy through aerobic respiration. Oxygen is carried by the blood and taken into the cell and reacts in the mitochondria with the pyruvic acid produced in anaerobic respiration. Carbon dioxide and water are the products of this reaction. Chemical energy is stored as “ATP”. This process is an example of oxidation where a substance is broken down in the presence of oxygen.
Krebs cycle: the goal is to take the pyruvate and produce NADH and FADH2. This process takes place in the mitochondria and has two steps. First is the conversion of pyruvate into Acetyl CoA, the second is the Krebs Cycle proper. Carbons, hydrogens, and oxygens end up as CO2 and H2O. Chemiosmosis is the production of ATP in cellular respiration. The goal of chemiosmosis is to break down NADH and FADH2, pumping H+ into the outer compartment of the mitochondria. The Electron Transport Phosphorylation (ETP) creates a gradient which is used to produced ATP. The ETP typically creates 32 ATP's**. ATP is generated as it moves down the concentrated gradient through a special enzyme called ATP synthase. 32 molecules of ATP can be produced for each glucose molecule as a result of the Krebs cycle reactions (2 ATP's), the electron transport system, and chemiosmois. In addition, 2 more ATP molecules are produced through glycolysis, giving us a net total of 36 ATP molecules**. Each ATP molecule can release 7.3 kilocalories of energy per mole.
** Note, some science books will list that a net of 38 ATPs is produced. This number has more to do with plants as they do not spend some of the ATP. Also, these numbers are ideal, and the maximum number of ATP's won't always be produced from every glucose.
Some differences between plants and animals:
1) While both plants and animal cells contain mitochondria, animal cells contain much more
2) Animal cells get most of their ATPs from mitochondria
3) On the other hand, plant cells get most of their ATP from chloroplast
e. Describe the process of photosynthesis
http://www.emc.maricopa.edu/faculty/farabee/BIOBK/BioBookPS.html
http://photoscience.la.asu.edu/photosyn/education/learn.html
http://www.esf.edu/pubprog/brochure/leaves/leaves.htm
Since most plants are autotrophs (all green plants) and have the ability to make their own food, the process by which the make their complex food substance from simpler substances is called photosynthesis.
Photosynthesis is the process of converting solar energy into chemical energy. Photosynthesis mainly takes place in the palisade cells. Plants take in carbon dioxide and combine it with water, along with the energy taken in from the sun by the chloroplasts. Products of photosynthesis are oxygen and energy in the from of carbohydrates). Plants actually produce quite a bit of food energy, more than they need to survive. This is great for us organisms, as we are able to consume this extra energy food source.
The process:
Energy from sun- electromagnetic waves that enters the plant via chloroplasts. It is a one time trip for this energy, so thank goodness energy is continuously coming in from the sun.
Within the plant, water and carbon dioxide is broken down and recombine. Hydrogen is added onto the carbon and oxygen. The left over oxygen atoms are combined to make oxygen.
Light-dependent reactions: Photons from the sunlight hit the pigments in the thylakoid (first part of photosyntheses process, aka light reaction). The pigments are light harvesting molecules. Each pigment absorbs a different type of light, which allows the plant to utilize a wide range of light. So, in green plants, the primary photosynthetic pigments are chlorophylls a and b. Electrons are knocked loose and energize the process of photosynthesis (the electrons. Photolysis of water break it down into oxygen and hydrogen. Hydrogen further breaks down into a positively charged ion and an electron. This electron replaces the missing electrons knocked loose by the photons. The hydrogen ion stays in the hydrogen reservoir of the thylakoid. They leave through special channels of the membrane during photosynthesis. This provides energy to the ATP syntheses enzymes where ATP molecules are made. ATP and NADPH power the dark reaction. Gas exchanges takes place in the stomas. The gas flowers into the roomy air passages of the spongy parenchyma region. These passages are all connected to each other and to the mesophyll cells.
Guard cells (part of the stomate) are open during the day and closed at night. Stromas may be closed on hot dry days but need to be careful because this slows down photosynthesis as carbon dioxide runs out. Guard cells can have some chloroplasts in them, like mesophyll cells. Each chloroplasts is one little carbohydrate factory. The membrane envelope of chloroplast controls the flow of necessary material and particles into and out of the chloroplast. After the thylakoids, the photosynthesis process moves out of its stroma. Here, enzymes take the carbon dioxide and combine it with hydrogen and oxygen to make simple carb molecules. This part of the process is called “light independence” reaction or “dark reaction” (sometimes called carbon fixing process because carbon from carbon dioxide is “fixed” into the beginning of simple sugar or carb molecule). Out in the stroma, enzymes use carbon dioxide and positively charged hydrogen ions to assemble sugar fragments, which are half of the glucose molecule. After photosynthesis, half of the glucose molecule passes through chloroplasts outer membrane into the cell. Here, more enzymes join the 3-carbon fragment with another 3-carbon fragment and you have glucose molecule. This becomes the building block for other carbs such as sucrose, lactose, ribose, and starch. If eaten by animals, it is used to make fats, oils, amino.
© Science CSET: Free Prep Guides, 2008. Unauthorized use and/or duplication of this material without express and written permission from this blog’s author and/or owner is strictly prohibited. Excerpts and links may be used, provided that full and clear credit is given to Science CSET: Free Prep Guides with appropriate and specific direction to the original content.