BRAINSCAPE GAG Flashcards
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Hydroxyl
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Carbonyl
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Carboxyl
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Amino
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Sulfhydryl
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Phosphate
Properties: Hydroxyl
polar
Properties: Carbonyl
polar
Properties: Carboxyl
polar, acidic
Properties: Amino
polar, basic
Properties: Sulfhydryl
slightly polar
Properties: Phosphate
polar
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Ionized Phosphate
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Ionized Carboxyl
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Ionized Amino
Definition: Monomer
The smallest repeating unit of a polymer
Definition: Polymer
A large molecule composed of repeating monomers
Definition: Monosaccharide
A simple sugar; a carbohydrate composed of 3-7 carbon atoms
Definition: Disaccharide
A carbohydrate composed of two monosaccharides joined by a covalent bond
Definition: Polysaccharide
A carbohydrate polymer composed of many monosaccharides joined by covalent bonds
Definition: Glycosidic Linkage
A covalent bond between monosaccharides
Formula: Glucose/Fructose/Galactose
C6H12O6
Compare: Alpha Glucose vs Beta Glucose
Alpha glucose has a hydroxyl in the down position on its first carbon, beta has a hydroxyl in the up position
Compare: Glucose vs Galactose
Glucose has a hydroxyl in the down position on its fourth carbon, galactose has one in the up position
Which reaction releases a water molecule?
Dehydration synthesis/condensation
Which reaction uses up a water molecule?
Hydrolysis reaction
What is maltose made of?
Alpha Glucose + Alpha Glucose
What is sucrose made of?
Alpha Glucose + Beta Fructose
What is lactose made of?
Beta Glucose + Beta Galactose
Which carbons link in the formation of maltose?
alpha 1:4 linkage
Which carbons link in the formation of sucrose?
alpha 1:2 linkage
Which carbons link in the formation of lactose?
beta 1:4 linkage
Rank the three common polysaccharides from least branched to most branched
Cellulose, starch, glycogen
What is the use of glycogen?
Short-term energy storage in animals
What is the use of starch?
Short-term energy storage in plants
What is the use of cellulose?
Structural support in plants
How often does glycogen branch?
Approximately every ten residues
How often does starch branch, and where?
Approximately every 30 residues, in the amylopectin
Which carbons link in cellulose, and of which monomer?
1:4 beta glucose linkage
What is chitin made of?
A carbohydrate with a nitrogen-containing functional group
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Alpha glucose
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Galactose
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Fructose
Which carbons link in glycogen, and of which monomer?
alpha glucose 1:4 linkage
Which carbons link in amylopectin, and of which monomer?
alpha glucose 1:4 linkage
Which carbons link in branches, and of which monomer?
alpha glucose 1:6 linkage
Functions: Triglycerides
long-term energy storage, twice the energy per grams compared to carbohydrates/proteins, provide insulation, components of cell membranes
Features: Saturated Fatty Acids
no double bonds, saturates with hydrogen atoms, straight chain, solid at room temperature
Features: Unsaturated Fatty Acids
One or more double bonds, not saturated with hydrogen atoms, liquid at room temperature
Features: Cis Fats
Very bulky, liquid at room temperature
Features: Trans Fats
Pack together, solid at room temperature, unhealthy
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Glycerol
<img></img><br></br><br></br>Is this saturated or unsaturated?
Saturated
<img></img><br></br><br></br>Is this saturated or unsaturated?
Unsaturated
What are the two main types of linkages?
Ester linkages and ether/glycodic linkages
How many water molecules are produced during the creation of triglyceride?
Three
<img></img><br></br><br></br>What type of linkage is this?
Ester linkage
<img></img><br></br><br></br>What type of linkage is this?
Ether linkage
Definition: Valence
The number of chemical bonds that each atom of a chemical element typically form
What is the valence of: Carbon, Oxygen, Phosphorus, Nitrogen, Sulphur, Hydrogen?
4/2/5/3/2/1
Definition: Isotope
Atoms with the same number of protons but a different number of neutrons
Definition: Radioisotope
An unstable isotope that emits radiation and decays over time while becoming more stable
How are radioisotopes used in medicine?
Radioisotope tracing, a process where radioactive material is injected into the body and traced using a positron emission topography (PET) scan to locate tissues with higher levels of activity (higher activity indicates cancer)
Definition: Biochemistry
The study of the chemical processes within living organisms
Definition: Intramolecular Forces
The forces that hold atoms together within a molecule
Definition: Intermolecular Forces
The attractive and repulsive forces between the molecules of a substance
Definition: Electronegativity
The tendency of a nucleus to attract electrons towards itself
An electronegativity difference of less than __ results in a(n) __ bond
0.5, pure covalent
An electronegativity difference between __ and __ results in a(n) __ bond
0.5, 1.6, polar covalent
An electronegativity difference greater than __ results in a(n) __ bond
1.6, ionic
Definition: Hydrogen Bonding
The attraction of a slightly positively charged hydrogen atom to a slightly negatively charged oxygen, nitrogen or fluorine atom that is also connected to a hydrogen atom
Definition: Hydrophobic
Does not dissolve in water
Definition: Hydrophillic
Dissolves in water
Why is water described as polar?
The two hydrogen atoms have slightly positive charges while the oxygen atom has a slightly negative charge due to their electronegativity difference
State the 4 unique properties of water
Hydrogen bonding, special density properties, polarity, dissociation of intramolecular bonds
What property of water explains how water can travel within the xylem vessels of a tree?
Hydrogen bonding, more specifically cohesion/adhesion. Cohesion making the water molecules stick together, and adhesion making them stick to the xylem.
What property of water explains how belly flops hurt?
Hydrogen bonding, more specifically surface tension
What is surface tension?
The tension of the surface of a liquid caused by the attraction of the molecules on the surface to the bulk of the liquid.
What property of water explains how drinking lots of fluids can help reduce a fever?
Hydrogen bonding, more specifically water’s high specific heat capacity, which is explained by the high amount of energy needed to break these bonds, meaning it takes a lot of heat to make water molecules move faster and heat up
What property of water explains why lakes freeze from the top down?
Water becomes less dense as a solid, which causes ice to float to the top
What property of water explains how the products of digestion easily diffuse across the villi membrane?
Water’s polar nature makes it a solvent, dissolving the products of digestion, making it easier for them to diffuse as non-solids
Definition: Acid
Acids are substances with high concentrations of H+ ions. They donate protons, and they produce H+ ions when dissolved in water.
Definition: Base
Bases are substances with low concentrations of H+ ions. They accept protons, and they produce OH- ions when dissolved in water.
Definition: Buffer
A solution that resists changes in pH when an acid or base is added to it
Why are buffers important to biological systems?
They maintain acid-base homeostasis by releasing H+ or OH- ions. This prevents complications that can occur if the pH of the body is too high or too low
Formula: Maltose/Sucrose/Lactose
C12H22O11
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Phospholipid
What are the main component of cell membranes?
Phospholipids
Definition: Phospholipid
A lipid with a hydrophillic “head” and a hydrophobic “tail”
What is the structural difference between a triglyceride and a phospholipid?
One fatty acid is replaced with a phosphate group
Definition: Phospholipid Bilayer
A thin polar membrane formed in aqueous environments that allows for the cell to be selectively permeable
Definition: Steroids
Hydrophobic molecules composed of four linked carbon rings
Functions: Steroids
component of cell membrane in animals, sex hormones, used to reduce inflammation
Definition: Waxes
Diverse structures, solid at room temperature. Most have long chains of fatty acids or carbon rings.
Example: A wax produced in plants
Carnauba wax
Example: A wax produced in animals
Beeswax, earwax
Functions: Waxes
Hydrophobic, waterproof protection
What are protein monomers called?
Amino Acids
What bond is present in proteins?
Peptide bond
What are protein polymers called?
Polypeptides
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Amino Acid
Definition: Zwitterion
A molecule that contains an equal amount of positively or negatively charged functional groups
Visualize: Peptide Bond
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__ structure is the linear sequence of amino acids
primary
__ structure is the amino acids hydrogen bonding and either forming coils or folds
Secondary
What are the two secondary structures of proteins?
Alpha helix and beta pleated sheets
What do helixes and sheets in a polypeptide arrange themselves by in tertiary structures?
Hydrophobic/philicness, hydrogen bonding, electrostatic charges and molecular chaperones
__ structure is when various polypeptides join together to form multi-polypeptide proteins
Quaternary
How are alpha helixes created?
Hydrogen bonding between every fourth amino acid within a strand
Example: Alpha helix
In keratin
How are beta pleated sheets created?
Hydrogen bonds forming between two parts of the polypeptide chain layered on each other
Example: Beta pleated sheet
Inside spider webs
R-group interactions create __ structure
Tertiary
Definition: Denaturation
The breaking of stabilizing bonds within a protein molecule that disrupt its shape
What causes denaturation?
Changes in pH, heat, exposure to alcohol, high salt concentrations
What are are nucleic acid monomers called?
Nucleotides
What is a sugar-phosphate backbone made of?
Nucleotides bonded by phosphodiester bonds
What are the two types of nucleic acids?
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA)
How do DNA and RNA differ in their sugars?
RNA contains Ribose, a sugar with 5 oxygens, while DNA contains deoxyribose, a sugar with 4 oxygens (lacking one on the second carbon)
What is DNA’s purpose?
It contains the genetic information of organisms, which are decoded into the particular amino acid sequences of proteins
What is RNA’s purpose?
It contains the genetic information for some virus particles, and it assists DNA to make proteins
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Deoxyribose
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Ribose
What is a nucleotide made of?
A sugar, a nitrogenous base and a phosphate group
What are the two pairs of nitrogenous bases in DNA
Adenine and Thymine; Guanine and Cytosine
What are the two pairs of nitrogenous bases in RNA
Adenine and Uracil; Guanine and Cytosine
List the purines of DNA and RNA
Adenine and Guanine
List the pyrimidines of DNA and RNA
Thymine, Uracil, and Cytosine
How many hydrogen bonds are present in Guanine-Cytosine pairings?
Three
How many hydrogen bonds are present in Adenine-Thymine pairings?
2
Definition: Enzyme
A protein with catalytic purposes due to its power of specific activation
Enzymes have a __ shape
Globular
How much faster do enzymes allow reactions to occur?
10^6 times faster
What is the active site?
A specifically shaped site on an enzyme with a unique chemical environment that permits a chemical reaction to proceed more easily
What is activation energy?
The energy that chemical reactions need to begin
What state are molecules in during the initial input of energy?
Transition state
Why are enzymes necessary instead of just raising body temperature?
Biological systems are very sensitive to temperature changes
How do enzymes increase the rate of reactions?
They lower the activation energy
Definition: Cofactor
A metal ion or mineral that is needed by some enzymes to help the reaction
Definition: Coenzymes
Organic molecules/vitamins that assist the reaction
Definition: Substrate
The reactants activated by the enzyme, specific to an enzyme
The __ cycle refers to the lock and key mechanism
Catalytic
__ may be used more than once
Enzymes
What is the induced fit hypothesis?
When a substrate combines with an enzyme it changes the active site in order to create a precise conformation. Reduces activation energy by stretching the bonds of the substrate.
__ enzymes catalyze hydrolysis reactions
Hydrolase
What are some factors that affect enzymes?
Substrate concentration, pH, temperature, and inhibitors
How does substrate concentration affect enzymatic reactions?
The reaction velocity increases as substrates become more concentrated, but when all enzyme molecules are occupied this velocity reaches a maximum.
How does enzyme concentration affect enzymatic reactions?
As enzymes become more concentrated, more enzymes are available to bind with substrates, increasing the maximum reaction velocity.
__ are chemicals that reduce the rate of enzymatic reactions
Inhibitors
What is competitive inhibition?
Inhibitors that resemble the substrate compete with the substrate for the active site. If more inhibitor is present compared to substrate it will successfully bind with the active site.
What is non-competitive inhibition?
Inhibitors bind to the allosteric site, which regulates enzyme activity. They prevent the enzyme from working.
What is negative feedback in biochemical pathways?
The last reaction of a pathway produces a non-competitive inhibitor that prevents the enzyme that started the pathway from working again, ensuring cell products are not produces unnecessarily.
Rank the three proteins used in the Proteins Lab by how sensitive they were to HCl
Albumin, Casein, Gelatin
How do strong acids and bases affect protein denaturation and solubility?
They both denature proteins due to their extreme placement on the pH spectrum, lowering solubility and producing a precipitate
Which metal salt (CuSO4 and AgNO3) caused the most albumin denaturation in the Proteins Lab?
AgNO3 showed a stronger denaturing effect due to the fact that silver salts are more toxic than copper salts
Does isopropyl alcohol work well as a disinfectant? Why or why not?
Yes, it denatures the proteins in bacteria as proven by the fact that it made albumin clear and transparent.
Why is heat an effective form of sterilization?
Heat effectively denatures proteins, which are present in bacteria.
How does heat affect enzyme activity?
It weakens the hydrogen bonds within the enzyme by increasing their movement, causing the enzyme to lose its shape and ability to function properly.
How does cold affect enzymatic activity?
The cold slows down the movement of molecules which results in less collisions, and it renders the bonds within the enzyme inflexible which does not let the subtrate bind properly.
How does pH affect enzymatic activity?
Enzyme active sites are denatured when not in optimal pH levels which slows reaction rate
How do acids and bases specifically affect hydrogen bonds?
Excess H+ ions bond with negatively charged carboxyl groups, and OH- ions remove H+ from positvely charged amino groups.
How does enzyme surface area affect enzymatic activity?
If enzyme surface area is larger, the substrates can interact with more active sites.
Definition: Isoelectric Point
The pH at which a molecule has no electrical charge
What happens to solubility at the isoeletric point?
At the isoelectric point a molecule is at its minimum solubility because there is no polarity repelling it or attracting it to other particles in its environment.
Describe the first step of glycolysis in detail
Glucose converted into glucose 6-phosphate by a hexokinase. This adds a phosphate group to glucose’s sixth carbon. This uses 1 ATP. This is irreversible.
Describe the second step of glycolysis in detail
Glucose 6-phosphate converted into fructose 6-phosphate by an isomerase. This is reversible.
Describe the third step of glycolysis in detail
Fructose 6-phosphate converted into fructose 1,6-bisphosphate by a kinase. This adds a phosphate group to fructose 6-phosphate’s first carbon. This uses 1 ATP. This is irreversible.
Describe the fourth step of glycolysis in detail
Fructose 1,6-bisphosphate converted into dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (G3P) by aldolase. This is reversible.
Describe the fifth step of glycolysis in detail
Dihydroxyacetone phosphate (DHAP) is converted into glyceraldehyde 3-phosphate (G3P) by an isomerase. Glyceraldehyde 3-phosphate can also be turned into dihydroxyacetone phosphate by this isomerase, but that is not important in glycolysis. This is reversible.
Describe the sixth step of glycolysis in detail
Both glyceraldehyde 3-phosphates (G3P) are oxidized into 1,3-bisphosphoglycerates by glyceraldehyde 3-phosphate dehydrogenases. Two redox reactions occur during this step, with NAD+ being reduced into NADH and H+. It also adds an inorganic phosphate (no ATP spent) to each glyceraldehyde 3-phosphate. This is reversible.
Describe the seventh step of glycolysis in detail
Both 1,3-bisphosphoglycerates are converted into 3-phosphoglycerates by a kinase. This removes a phosphate, and adds it to ADP, producing 1 ATP (actually two). This is reversible.<br></br><br></br>
Describe the eighth step of glycolysis in detail
Both 3-phosphoglycerates are converted into 2-phosphoglycerates by a mutase. This moves the phosphate from the 3rd carbon to the 2nd carbon. This is reversible.
Describe the ninth step of glycolysis in detail
Both 2-phosphoglycerates are converted into phosphoenolpyruvates by enolase. This releases a water molecule. This is reversible.
Describe the tenth step of glycolysis in detail
Both phosphoenolpyruvates are converted into pyruvates by a kinase. This removes the phosphate, and adds it to ADP, producing 1 ATP (actually two). This is irreversible.
Function: Kinase
Adds a phosphate group to a molecule
Function: Dehydrogenases
Catalyze oxidations by transferring hydrogen
Function: Isomerases
Alter the physical structure of molecules
Function: Mutases
Isomerases that rearrange functional groups
What is the net reaction of glycolysis?
Glucose + 2ADP + 2Pi + 2NAD+ –> 2 Pyruvate + 2 ATP + 2 NADH + 2H2O
What is the net reaction of pyruvate oxidation?
1 Pyruvate + NAD+ + HS-CoA -> 1 Acetyl-CoA + NADH + H+ + CO2
Formula: Cellular respiration
C6H12O6 + 6O2 –> 6CO2 + 6H2O + ATP
Describe the first step of the Krebs cycle in detail
Acetyl-CoA (2C) and oxaloacetate (4C) are fused into citrate (6C) by citrate synthetase. This releases the CoA.
Describe the second and third steps of the Krebs cycle in detail
Citrate (6C) is rearranged into isocitrate (6C) by aconitase.
Describe the fourth step of the Krebs Cycle in detail?
Isocitrate (6C) is rearranged is converted into alpha-ketoglutarate (5C) by isocitrate dehydrogenase. 1 CO2 is released. NAD + is converted to NADH and H+.
Describe the fifth step of the Krebs cycle in detail
Alpha-ketoglutarate (5C) is converted into succinyl-CoA (4C) by alpha-ketoglutarate dehydrogenase. 1 CO2 is released. NAD + is converted to NADH and H+. CoA gets added to the molecule.
Describe the sixth step of the Krebs cycle in detail
Succinyl-CoA (4C) is converted into succinate (4C) by succinyl-CoA synthetase. It also creates GTP from GDP + inorganic phosphate. GTP lends a phosphate to ADP to produce 1 ATP. The CoA is released.
Describe the seventh step of the Krebs cycle in detail
Succinate (4C) is converted into fumarate (4C) by succinate dehydrogenase. FAD is covnerted into FADH2.
Describe the eighth step of the Krebs cycle in detail
Fumarate (4C) is converted into malate (4C) by fumarase. This adds 1 H2O to the molecule.
Describe the ninth step of the Krebs cycle in detail
Malate (4C) is converted into oxaloacetate (4C) by malate dehydrogenase. It also creates NADH and H+ from NAD+.
What enzyme is used in pyruvate oxidation?
Pyruvate dehydrogenase complex
What is the maximum ATP yield of a glucose molecule in a prokaryote?
38 ATP
What is the maximum ATP yield of a glucose molecule in heart, liver and kidney cells?
38 ATP
What is the maximum ATP yield of a glucose molecule in most cells of a eukaryote?
36 ATP
Where does glycolysis take place?
Cytosol
Where does the Krebs cycle take place?
Matrix
Where does oxidative phosphorylation take place?
Mitochondria
Where does pyruvate oxidation take place?
Matrix
What is the H+/ATP ratio in oxidative phosphorylation?
2
How many protons are pumped out of the matrix for each NADH?
6
How many protons are pumped out of the matrix for each FADH2?
4
How many ATP does each NADH make?
3
How many ATP does each FADH2 make?
2
Name the folds of the inner mitochondrial membrane
Cristae
How many carbons does Acetyl-Coa have?
2
What is the waste product of cellular respiration?
CO2
Definition: Chemiosmosis
The use of the H+ ion gradient to phosphorylate ADP to ATP
What is the first protein in the electron transport chain called?
NADH Dehydrogenase
What is the third protein in the electron transport chain called?
bc1 complex
What is the fourth protein in the electron transport chain called?
Cytochrome c oxidase
What is the final electron acceptor?
O (NOT O2)
What enzyme creates ATP in the electron transport chain?
ATP synthase
What are the products of the Krebs cycle per pyruvate?
1 ATP + 3 NADH + 1 FADH2 + 2 CO2
What are the products of the Krebs cycle per glucose?
2 ATP + 6 NADH + 2 FADH2 + 4 CO2
What are the important products of glycolysis?
2 pyruvate + 2 NADH + 2 ATP
What are the products of pyruvate oxidation per pyruvate?
1 Acetyl-CoA + 1 NADH + 1 CO2
What does pyruvate break down into?
Acetyl + CO2
Why is the maximum ATP produced by eukaryotic cells that aren’t heart, liver or kidney cells only 36?
The mitochondrial membrane is not permeable to the 2 NADH produced in glycolysis, and the 2 NADH must be shuttled in at the cost of 2 ATP
Galactose is phosphorylated outside of glycolysis and enters as __
Glucose-6-phosphate
Fructose is phosphorylated outside of glycolysis and enters as __
Fructose-6-phosphate
Glycerol enters glycolysis as __
Glyceraldehyde-3-phosphate
What is the maximum ATP yield of a glycerol molecule in most cells of a eukaryote?
20 ATP
What is the maximum ATP yield of a glycerol molecule in a prokaryote?
22 ATP
What is the maximum ATP yield of a glycerol molecule in heart, liver and kidney cells?
22 ATP
Where does beta oxidation take place, and for what?
Mitochondrial matrix, for fatty acids to undergo catabolism
What is the outer part of the inside of the mitochondria called?
Intermembrane space
Build-up of __ will allosterically inhibit glycolysis
Pyruvate
What are the two types of fermentation?
Ethanol fermentation and lactic acid fermentation
In what organisms does ethanol fermentation take place?
Unicellular organisms
In what organisms does lactic acid fermentation take place?
Some bacteria and eukaryotic cells
Why does fermentation happen?
To regenertate NAD+ to keep glycolysis going to create ATP
What are the 4 organic compounds that can be produced by anaerobic respiration?
Ethanol, lactate, acetone, butanol
Definition: Oxygen debt
The amount of oxygen required to remove lactic acid and replace the body’s oxygen
How does oxygen debt get repaid?
Increased respiration after exercise
Where does anaerobic respiration take place?
Cyotosol
What are the end products of anaerobic respiration in humans?
Lactica acid and NAD+
What does the term “eukaryotic cell” mean?
A type of organism that contains a membrane-bound nucleus
What does the term “prokaryotic cell” mean?
A type of organism that lacks a nucleus and other membrane-bound organelles
Definition: Organelle
A specialized structure within a cell that performs specific functions
What is the purpose of the important macromolecule found in the nucleus?
The purpose of DNA is to carry the genetic information of organisms
Definition: Nucleoplasm
The gel-like substance within the nucleus that contains chromatin and other nuclear components
Definition: Nuclear Matrix
A network of proteins that provides structural support to the nucleus and organises the chromatin
Definition: Nucleolus
A dense region within the nucleus where ribosomal RNA (RNA) is synthesised and ribosome assembly begins
Definition: Nuclear Envelope
A double membrane that surrounds the nucleus, separating it from the cytoplasm
Definition: Nuclear Pore Complex
<b><span>Protein channels embedded in the nuclear envelope that regulate the passage of molecules between the nucleus and the cytoplasm</span></b>
Function: Nucleus
Stores the cell’s hereditary material and co-ordinates the cell’s activities
What is the endoplasmic reticulum made of?
<b><span>A complex system of channels and sacs composed of membranes enclosing a lumen; made up of the rough and smooth ER</span></b>
What are the 2 types of endoplasmic reticulum and what are their functions?
<b><span>Smooth and rough; smooth is used for the creation/storage of lipids and steroids, while rough is used for the synthesis of various proteins</span></b>
What unique fact about ribosomes allows antibiotics to help fight infection and not kill the host cells?
<b><div><span>Ribosomes of eukaryotes are structurally different from bacterial ribosomes</span></div></b><br></br>
What are the two parts of a ribosome called?
The large subunit and the small subunit
Definition: Endomembrane system
Group of interconnected organelles in a eukaryotic cell that modify, package and transport lipids and proteins. Involved in processes like synthesis, transport, and recycling cellular materials
What is the general type of enzyme found in lysosomes? What do they catalyze?
Hydrolytic enzymes; these enzymes catalyze hydrolysis of macromolecules into smaller molecules, and allow for digestion of these macromolecules<br></br>
Definition: Peroxisomes
Membrane-enclosed sacs that contain enzymes. They break down biological molecules and some toxic molecules
What type of enzymes are found in peroxisomes? What is their function?
The enzymes found in peroxisomes are known as oxidases; they catalyze redox reactions. They also contain catalase which breaks down H2O2, a common product of reactions in peroxisomes, into water and oxygen gas
Definition: Photosynthesis
The process by which green plants and some other organisms convert carbon dioxide and water into glucose and oxygen through the use of light energy
What are the two sequential processes of photosynthesis?
the light reactions and carbon fixation
What are the 3 parts of the light reactions?
photoexcitation, electron transport, and chemiosmosis
Electrons in chlorophyll molecules are initially at __?
ground state
Definition: Photosystem
A cluster of chlorophyll molecules associated with proteins that absorb light inside of chloroplasts
Definition: Antenna complex
An array of protein and chlorophyll molecules that gather light energy
Definition: Reaction centre
A complex that initiates the light reactions
Definition: Primary electron acceptor
A molecule in the thylakoid membrane that traps a high energy electron donated from the reaction centre (redox reaction)
Describe how photosystems work in detail
Pigment molecules known as the antenna complex gather photons and pass them to the reaction centre, which donates its excited electron to a primary electron acceptor
How many photosystems do chloroplasts in plants and algae have?
2
Describe photosystem I
Contains a specialized molecule known as P700 since it best absorbs light with an average wavelength of 700 nm
Describe photosystem II
Contains a specialized molecule known as P680 since it best absorbs light with an average wavelength of 680 nm
Where does cyclic photophosphorylation take place?
photosystem I
What is the purpose of cyclic phosphorylation?
Allows chloroplasts to make more ATP to drive the light-independent reactions
What is the Calvin cycle?
When chemical energy captured in ATP and NADPH is used to “fix” carbon dioxide in the light-independent reactions
CO2 is fixed into a ___?
3 carbon sugar
Calvin cycle also referred to as __?
C3 photosynthesis
What enzyme catalyzes the calvin cycle?
ribulose 1,5-bisphosphate carboxylase (rubisco)
What is the importance of the Calvin cycle?
Removes 200 billion tons of CO2 from the air every year
Where does the Calvin cycle occur?
Stroma
ATP and NADPH from light reaction used to reduce __ into __ molecules
CO2, carbohydrate
What are the 3 stages of the Calvin cycle?
carbon fixation, reduction reactions, Ribulose 1,5-bisphosphate (RuBP) regeneration
Describe phase 1 of the Calvin cycle in detail
CO2 joins to RuBP (5C) to form a 6C intermediate. This reaction is catalyzed by rubisco. Intermiediate 6C molecule immediately splits into 3C molecules called PGA (3-phosphoglycerate). This reaction occurs 3 times, therefore 3 CO2 are used and 6 PGA are produced.
Describe phase 2 of the Calvin cycle in detail
6 PGA molecules are phosphorylated by ATP to produce 6 molecules of 1,3-bisphosphoglycerate. 6 1,3 BPG are then reduced by NADPH to produce 6 G3P (a sugar). One G3P exits the cycle as a final product and the remaining 5 are used in RuBP regeneration. G3P that exited is used to synthesize larger sugars.
Describe phase 3 of the Calvin cycle in detail
5 G3P are rearranged to form 3 molecules of RuBP. 3 ATP are used in this process. The RuBP is now available to join with the next CO2 in the next cycle.
What would happen to Co2 and O2 levels if a plant was enclosed in a sealed container, and a light was switched on?
CO2 falls as it is consumed by photosynthesis, and O2 increases as it is made.
What would happen to Co2 and O2 levels if a plant was enclosed in a sealed container, and no light was present?
No photosynthesis occurs, but CO2 increases while O2 decreases due to respiration
As light intensity increases, the rate of ___ increases to a maximum
photosynthesis
What resources that benefit us are products of photosynthesis?
Food and fossil fuels
What is chlorophyll a’s R group?
-CH3
What is chlorophyll b’s R group?
-COH
Definition: Porphyrin ring
Mg ion in centre, surrounded by hydrocarbon ring. This ring contains the electrons that absorb light energy.
Definition: Phytol chain
Hydrocarbon tail anchors the molecule to a membrane
What were the first organisms to use sunlight in the production of organic compounds from water and CO2?
Cyanobacteria
Cyanobacteria contain chlorophyll _ to carry out photosynthesis
a
Cyanobacteria contain d: photosynthetic pigments called __
phycobilins
What are the prokaryotic autotrophs?
Cyanobacteria
What are the eukaryotic autotrophs?
Algae, protists and plants
Definition: Cuticle
Water resistant and protective wax on a leaf
Definition: Upper epidermis
Single layer of cells containing few or no cloroplasts, allow light to pass to mesophyll
Definition: Palisade mesophyll cell
Cells with abundant chloroplasts, location of most photosynthesis
Definition: Guard cells
Create openings called stomata
Definition: Stomata
Regulate exchange of CO2 and O2, allow water to escape by transpiration
Definition: Transpiration
The evaporation of water from leaves
Definition: Transpiration pull
A force that helps to move water, minerals and other substances upward
Size and shape of guard cell changes with __
water concentration
In the morning, what does blue light do?
Activates receptors in guard cell membranes that stimulate proton pumps to actively drive protons out of guard cells. Establishes an H+ ion gradient, which causes K+ ions to diffuse into the guard cells. Water follows by osmsis, and guard cells swell and open.
Stomata are usually closed during the __
night
Process of stomata closing is regulated by __?
A decrease in sucrose in guard cells
When K+ ions diffuse into the guard cells, what happens?
Water also moves in by osmosis and the guard cells swell, causing stomata to open.
Stomata are usually open during the __?
day
Why should stomata be open during the day?
To make CO2 available at same time as sunlight for photosynthesis
Definition: Stroma
Protein-rich semiliquid material in the interior of chloroplast
Definition: Lamellae
Unstacked thylakoids between grana
Definition: Thylakoid
Membrane-bound, flattened sacs that stack to form grana
Where is chlorophyll embedded?
Thylakoid membrane
What is the name of the technique used to separate pigment compounds in leaves?
Paper chromatography
Why do leaves change colour in the fall?
There is less light and water in the fall, which trigger guard cells to close stomata (stops gas exchange). Plant can not go through photosynthesis, and chlorophyll breaks down
Formula: Photosynthesis
6CO2 + 6H2O + light energy -> C6H12O6 + 6O2
What wavelengths of light is maximally absorbed by chlorphyll a?
Purple and red
What wavelengths of light is maximally absorbed by chlorphyll b?
Blue and orange
What wavelengths of light is not absorbed by neither chlorphyll a nor b?
green
Why do plants appear to be green?
The chlorphyll can’t absorb green wavelengths
Define: Bundle-sheath cell
A leaf cell type that forms a tightly packed layer surrounding the veins
Definition: Xylem
Transports water and water-soluble nutrients
Definition: Phloem
Transports sugars, proteins, and other organic molecules
How might transpiration be harmful to a plant?
If water loss exceeds water intake, the plant will become dehydrated
How might transpiration be helpful to a plant?
Produces an evaporative cooling effect that prevents overheating and helps to move water, minerals and other substances upwards
Where is ADP phosphorylated in photosynthesis?
Stroma
What creates the proton gradient in photosynthesis?
b6f complex and the splitting of H2O
__ is the final electron acceptor in photosynthesis, it is reduced to __
NADP+, NADPH
For every two electrons that pass through the electron transport chain in photosynthesis, __ NADH and __ ATP are made by __
1, 1, ATP synthase
NADPH and ATP are used in light-independent reactions to fix __ into __
CO2, glucose
6 turns of the Calvin cycle needed to make __ glucose molecule
1
Definition: Photorespiration
The reaction of oxygen with ribulose 15-bisphosphate in a process that reverses fixation and reduces the efficiency of photosynthesis
What enzyme is involved in photorespiration?
rubisco
Describe the consequence of photorespiration in terms of photsynthetic efficiency in plants
all of the energy used to regenerate the ribulose 1,5-bisphosphate is wasted, thus reducing the efficiency of photosynthesis
C4 plants separate the initial uptake of __ from the __ into different __
CO2, Calvin cycle, types of cells
What happens in the mesophyll cells in C4 photosynthesis? What is the product of carbon fixation?
CO2 is added to phosphoenolpyruvate (C3) to create oxaloacetate (C4) which gives the plants their name. The oxaloacetate is converted into malate and transported into the bundle-sheath cells. There, the malate is decarboxylated, resulting in pyruvate, which is transported back into the mesophyll cells and converted into PEP. The CO2 released from this decarboxylation goes into the Calvin cycle, and it is the final product.
What is the role of bundle-sheath cells? How do they help to limit the degree of photorespiration?
They are impermeable to gases and have high concentrations of CO2, meaning that photorespiration does not occur
Describe the temporal adaptations in CAM plants and how the stomata are involved?
CO2 fixation is separated from the Calvin cycle by time of day. CAM plants thrive in hot, arid desert conditions. To prevent water loss, their stomata remain closed during the day and open at night. CO2 is fixed at night while the stomata are open. The reactions proceed until malate is formed, and then it is stored in a large vacuole until daytime, when the stomata close. When the light-dependent reacyions have produced enough ATP and NADPH to support the Calvin cycle, the malate exits the vacuole and is decarboxylated, freeing the CO2 which is then fixed again by rubisco and enters the Calvin cycle.
Definition: Photophosphorylation
The conversion of ADP to ATP using solar energy
What is created by photorespiration?
Phosphoglycolate and 3-phosphoglycerate
Fully explain Friedrich Miescher’s findings
Isolated nucleic acids from the nuclei of white blood cells obtained from pus-soaked bandages. Called this DNA “nuclein.” First person to discover DNA!
Fully explain Frederick Griffith’s findings Studied Streptococcus pneumoniae bacteria in mice. He used two strains: the pathogenic S-strain and the non-pathogenic r-strain. He injected mice with a combination of heat-killed S-strain and live R-strain. He discovered that the R-strain became pathogenic when exposed to the heat-killed S-strain
suggesting that somehow
genetic information was being transferred between the two strains.
Fully explain Oswald Avery’s findings Avery and his colleagues prepared identical extracts of the heat-killed S-strain
disrupted their cell membranes
and collected the contents of the cells. Then
one of three enzymes was added to each extract (either a protein-destroying enzyme
an rna-destroying enzyme
and a dna-destroying enzyme). Each-enzyme treated extract was then mixed with R-strain cells. The only extract that did not transform the R-strain cells into pathogenic S-strain cells was the extract exposed to the DNA-destroying enzyme. Also figured out how to isolate DNA.
Fully explain Rosalind Franklin’s findings Used X-ray diffraction to examine DNA fibers. She captured high-resolution images of DNA’s structure
particularly focusing on the helical shape of DNA. Her findings revealed that DNA is a double helix
with two strands cpiled around each other. Her data proved essential information for understanding DNA’s structure before Watson and Crick stole it.
Fully explain Martha Chase’s and Alfred Hershey’s findings Used bacteriophages
specifically T2 phages
to study whether DNA or protein was the genetic material transferred during viral infection. They labeled viral DNA with radioactive phosphorus and viral protein with sulfur to track the transfer to bacteria. After using a blender and centrifugation
it was evident that the bacteria was not radioactive when viral protein was cultured with bacteria
but it was when viral DNA was cultured with bacteria
meaning DNA was the genetic material.
Fully explain Francis Crick’s and James Watson’s findings Using Rosalind Franklin’s work
Watson and Crick built a 3D model of DNA’s structure. Their model proposed that DNA is made of two strands forming a double helix
with nitrogenous bases pairing specifically. They also wrote a paper on how DNA could replicate
revolutionizing molecular biology.
Fully explain Matthew Meselson’s and Franklin Stahl’s findings Used E. coli bacteria grown in media with heavy nitrogen isotopes (N15) and light nitrogen (N14) to distinguish between parent and daughter strands. Grew bacteria in a liquid culture containing N15 and checked its density
noting that it was uniform. After one round of replication in the N14 media
the conservative model of replication was ruled out because all DNA’s density was midway between N14 DNA and N15 DNA (there was a single band after centrifugation). After a second round of replication
the DNA separated into two bands
N14 density and N15 density
proving dispersive wrong as only one band would have ever been observed.
Fully explain Craig Venter’s findings Led the sequencing of the human genome
mapping the entire human genome identifying every gene and their functions
Fully explain Francis Collin’s findings Directed the Human Genome Project
using sequencing technologies to map all 20
000-25
000 human genes. The completion of the Human Genome Project revealed the full sequence of human DNA
providing insights into human genetics
disease
and potential treatments through genomics.
What is Chargaff’s Rule Erwin Chargaff determined that the amount of adenine in DNA is always equal to the amount of thymine
and the amount of guanine is always equal to the amount of cytosine
What word describes the directionality of the sugar-phosphate backbones? Antiparallel
The 3’ end terminates with __? a hydroxyl group
The 5’ end terminates with __? a phosphate group
Definition: Genes The functional unit of DNA. They code for the production of specific proteins or RNA.
What is non-coding DNA? A large percentage of the DNA of an organism which regulate gene expression instead of coding for the synthesis of proteins or RNA.
Where is eukaryotic DNA contained? The nucleus
and a little bit is in chloroplasts and mitochondria
Where is prokaryotic DNA contained? The nucleoid region of the cytosol of the bacteria
which has no nuclear membrane
How does DNA coil? It wraps around proteins called histones to form nucleosomes
which coil into chromatin fibers before packing together to form chromosomes.
Definition: Supercoiling The condensing of loop-like structures of DNA controlled by topoisomerase I and II
Definition: Plasmid A non-nucleoid structure that carries extra genetic information. Very important tool in biotechnology as it is used for the genetic modification of organisms
“Which model of replication is this?<br></br><img src=”“paste-54d38c6618818685b85869557ac80d75aa85386c.jpg””>” Conservative
“Which model of replication is this?<br></br><img src=”“paste-f2732c2cd47dfb83f1edfcb1c0ba19a8d4440844.jpg””>” Semi-conservative
“Which model of replication is this?<br></br><img src=”“paste-0ef00398c5ee1cb0dd18945a750b92377f85986f.jpg””>” Dispersive
When does DNA replication take place? During the S (synthesis) phase of the cell cycle
Why does cell replication take place? It is crucial for cell division
ensuring that each daughter cell receives a complete set of the original parental genome
What are the three stages in the replication process? Initiation
elongation and termination
Definition: Initation stage Helix is unwound to exposes bases for new base pairing
Definition: Elongation stage (transcription) New strands are assmbled using parental DNA as template
Definition: Termination stage (transcription) Process stops and new DNA molecules coil into their double helix forms before separating. The replication machine is dismantled.
Function: DNA Helicase Unwinds the double helix by breaking the hydrogen bonds. Starts at a specific nucleotide sequence called the origin of replication. A replication fork and bubble is formed.
Function: DNA Gyrase Assists initation by making sure twists and knots don’t form ahead of the replication bubble. Helps to relieve strain at the replication fork.
Function: Single stranded binding proteins Keep DNA template strands separated
Definition: Topioisomerase Reesolve tenisions such as supercoiling ahead of the replication bubble by introducing cuts in DNA strands.
Function: DNA Polymerase III Catalyzes the addition of new nucleotides at the 3’ end of a growing polynucleotide strand. Can reverse and replace nucleotides during replication.
What is used to power DNA synthesis? The cleavage of two phosphates from a nucleoside triphosphate
What direction are DNA strands synthesized in? 5’ to 3’
Why must DNA be primed? DNA Polymerase III attaches nucleotides to free 3’ hydroxyl ends
which are not exposed after DNA is unwound.
Function: Primase Creates an RNA Primer
Function: RNA Primer Serves as a starting point for the addition of nucleotides because it ends with a 3’ hydroxyl group
Definition: Leading strand Strand that is synthesized toward the replication fork. Formed continuously from the 3’ end of the parent strand
Definition: Lagging strand Strand that is synthesized away from the replication fork. Formed discontinuously (in segments) from 5’ end. Creates Okazaki fragments
each beginning with an RNA primer.
Definition: Okazaki fragments Short DNA fragments generated during the synthesis of the lagging strand in DNA replication.
Function: DNA Polymerase I Removes RNA primer and fills gaps between Ozakazi fragments on the lagging strand. It also proofreads.
Function: DNA Ligase Catalyzes the joining of Okazaki fragments to avoid gaps
Definition: Replication machine Protein-DNA complex at each fork
Function: DNA Polymerase II Proofreads newly synthesized DNA
Definition: Mismatch repair A mechanism for repairing errors made during DNA replication
whereby a group of proteins recognize a mispaired nucleotide on the newly synthesized strand and replace it with a correctly paired nucleotide
Definition: Telomere A repetitive section of DNA near each end of a chromosome. Helps to prevent the loss of important genetic information during replication.
Why is information lost during DNA replication in eukaryotes and not prokaryotes? In eukaryotes
when the final RNA primer added closest to the 5’ end of the lagging strand is removed
there is no DNA or primer following it to provide a 3’ end
meaning the primer and any DNA that comes after it can not be synthesized into DNA/replicated and are lost. Prokaryotic DNA replication is circular
not linear
and as such every primer is in between two other primers
guaranteeing no information is lost.
Function: Telomerase Synthesizes telomeric regions and can replace lost sequences
Definition: Gene expression The transfer of genetic information in a cell that results in protein synthesis
What is often called the central dogma of genetics? The theory that genetic information flows from DNA to RNA to protein
What are the two phases of protein synthesis? Transcription and translation
Where does transcription occur? In the nucleus
Where does translation occur? In the cytoplasm at a ribosome
What did Beadle and Tatum determine in 1941? They determined that one gene codes for a specific polypeptide. This is known as the one gene/one polypeptide hypothesis.
Definition: Transcription Synthesis of RNA molecule from DNA template
Why is transcription necessary? DNA cannot leave the nucleus
Definition: Messenger RNA (mRNA) A copy of the DNA that can leave the nucleus
What are the four steps of transcription? Initiation
elongation
termination
and processing (post-transcription modification)
Definition: Promoter “A series of nucleotides with a high concentration of adenine and thymine bases adjacent to the start of the of the gene
on the coding strand. It orients RNA polymerase on the right strand
and DNA begins to be opened at the promoter. ““TATA box.”””
Definition: Transcription factors A set of proteins required for initiation of transcription; it is required for the RNA polymerase complex to bind to the promoter
Definition: Template strand Antisense strand
the strand with the gene to be transcribed
Definition: Sense strand Coding strand
not copied
Explain the elongation step of transcription RNA polymerase brings RNA nucleotides to the template strand
following complementary base pairing rules but replacing thymine with uracil for mRNA
Is the promoter region transcribed? No
How many primers are needed for the elongation step of transcription? None
What direction does RNA polymerase read the DNA template strand? 3’ to 5’
What direction does RNA polymerase build the mRNA? 5’ to 3’
Definition: Terminator A sequence of nucleotides that mark the end of a gene
which cease transcription and release mRNA when RNA polymerase reaches it
Definition: Precursor mRNA mRNA that requires processing before translation occurs
Definition: Mature mRNA mRNA that has been processed
with spliced exons
a 5’ cap and a 3’ poly-A tail
Definition: 5’ cap A modified guanine nucleotide added to the 5’ end of mRNA. It is recognized by protein synthesis machinery
Definition: 3’ poly-A tail A series of adenine nucleotides linked to the 3’ end of mRNA. Makes it stable so it can exist longer in cytoplasm.
Definition: Introns Sections of mRNA that do not contain information needed to build the protein. They are extras and must be removed before the protein can be built.
Definition: Exons Sections of mRNA that contain the protein recipe and are joined to form the finished or mature mRNA. This process is called splicing
carried out by a spliceosome complex
Definition: Splicing The process by which introns are removed from precursor mRNA
Definition: Spliceosome complex A large ribonucleoprotein that carries out splicing
How does mRNA modification work in prokaryotes? There is none
as transcription and translation can occur simultaneously in prokaryotic cells (no nucleus) meaning mRNA can be used in protein synthesis as soon as it is made
Function: RNA Polymerase Synthesizes mRNA by following a strand of DNA during transcription
Definition: Gene A distinct sequence of nucleotides forming part of a chromosome
the order of which determines the order of monomers in a polypeptide
Definition: Alternative splicing The process by which only certain exons are spliced together
allowing a gene to code for more than one type of polypeptide. As a result
certain cell types are able to produce forms of a protein that are specific for that cell.
What are the three important characteristics of genetic code and what do they mean? Redundancy (more than one codon can code for the same amino acid
protecting us from mutations)
continuity (genetic code is read as a series of three-letter codons)
and universality (almost all organisms build the same proteins with the same genetic code)
How many amino acids are there? 20
Definition: Codon A series of three nucleotides that correspond to specific amino acids
Definition: Transfer RNA (tRNA) RNA that brings amino acids to the ribosomes and contains an anticodon with the three opposite nucleotides from the amino acid it carries
How are ribosomes involved in translation? They are the site of protein synthesis
What are ribosomes made of? Ribosomal RNA (rRNA) and proteins
Definition: Translation factors Proteins that assist with translation
What is the structure of transfer RNA? One end contains an anticodon loop
a 3’ to 5’ sequence of nucleotides that is complementary to a specific 5’ to 3’ mRNA codon. The opposite has an acceptor stem with an attached amino acid
complementary to the anticodon.
What enzyme attaches amino acids to transfer RNA molecules? Aminoacyl-tRNA synthetase
What are the four binding sites on ribosomes? P (peptide)
A (amino acid)
E (exit)
and mRNA binding site
Name the three steps in the translation process Initiation
elongation
termination
Explain the initiation phase of translation The small ribosomal subunit binds to the mRNA and moves across the transcript until it reaches the start codon AUG. The initiator tRNA with its UAC anticodon binds to the mRNA. Large subunit joins
forming the active ribosome. The ribosome moves forward one codon at a time. The initiator tRNA occupies the P site.
Explain the elongation phase of translation A second tRNA brings the second amino acid to the ribosome and enters the A site. A peptite bond is formed by a condensation reaction. Peptidyl transferase enzyme
found in the large subunit
catalyzes the synthesis. The ribosome moves over by one mRNA codon. The new polypeptide chain moves to the P site (emerges from the ribosome). The empty tRNA exits from the E site. Process is repeated rapidly.
Explain the termination phase of translation The process continues until the stop codon on the mRNA is reached. A protein called a release factor cleaves the newly synthesized polypeptide from the last tRNA.
How many different codons are there? 64
What direction is mRNA read in? 5’ to 3’
What direction is tRNA read in? 3’ to 5’
Definition: Mutation Any change to DNA
can affect how genes code for proteins
What are the three major types of mutations? Point mutations
frameshift mutations
and chromosomal mutations
Definition: Point mutation A mutation that involves a single change in the DNA nucleotide sequence. The change occurs when 1 base is substituted for another base.
Definition: Silent mutation A mutation that has no effect on the amino acid sequence
Definition: Missense mutation A mutation that changes the amino acid sequence
Definition: Nonsense mutation A mutation that creates a premature stop codon
Definition: Frameshift mutation Mutations that cause the reading frame of the codons to shift because of the addition or deletion of one or more nucleotides. Usually renders the protein nonfunctional.
What are the four types of chromosomal mutations? Deletion
duplication
inversion
translocation
Definition: Deletion mutation Loss of part of the chromosome
Definition: Duplication mutation Extra copy made of part of the chromosome
Definition: Inversion mutation Reverses direction of part of the chromosome
Definition: Translocation mutation Part of one chromosome attaches to another chromosome
What are some alternative ways mutations affect proteins besides determining the protein itself? Where and how much of a protein is made
and when a protein is made
<b><span>What are the roles of histones and methylation in regulating gene expression?</span></b>” “<b><span>Histones modulate chromatin structure through chemical modifications while DNA methylation serves as a heritable mechanism for silencing genes </span></b>
<b><span>What is an epigenetic tag?</span></b>” “<b><span>Epigenetic tags are heritable alterations that are not due to changes in the DNA sequence. Epigenetic tags such as DNA methylation and histone modification alter DNA accessibility and chromatin structure, regulating patterns of gene expression.</span></b>
<b><span>What are imprinted genes?</span></b>” “<b><span>Imprinted genes are an epigenetic phenomenon that cause genes to be expressed or not, depending on whether they are inherited from the male or female parent. Imprinted genes mean either the dad’s or the mom’s copy of a gene will be epigenetically silenced.</span></b>
<b><span>What are some environmental factors that can impact the epigenome?</span></b>” “<b><span>Stress, diet, activity level</span></b>
What are two different ways that changes in the epigenome can lead to cancer? “<b><span style=”“font-weight: 400;”“>Some genes have higher methylation levels (less active DNA)</b>
and some have lower levels (more active DNA). </span></b>Higher methylation levels can silence genes that keep growth in check
repair damaged DNA
and initiate programmed cell death. Lower methylation levels can activate genes that promote cell growth
it is more likely to be duplicated
deleted
and moved to other locations
and causes a loss of imprinting which can lead to two active or two inactive copies of a gene that should be imprinted.”
What is epigenome reprogramming? Reprogramming is the process by which epigenetic tags are erased from reproductive cells so that the fetus’s cells can specialize into any type of cell.
“<b><span style=”“font-weight: 400;”“>Summarize the challenges researchers face in trying to prove epigenetic inheritance.</span></b>” Inherited traits can occur from epigenetic inheritance
but also from extremely small mutations. It is very difficult to pinpoint these mutations
so the origin of such traits can not be proven. Additionally
when a woman is pregnant
the fetus
the mom
and the fetus’s reproductive cells are all exposed to the same environment. This means three generations may receive epigenetic tags directly. In order to prove actual inheritance
traits must carry on from the first generation to the fourth.
“<b><span style=”“font-weight: 400;”“>Summarize some possible implications of epigenetic inheritance on evolution.</span></b>” Evolution is known to be slow
with mutations and natural selection taking an extremely long time to drastically change a species. However
the epigenome can change rapidly and these rapid changes can be inherited by future generations
essentially “evolving” their epigenome much quicker than evolution that involves DNA alteration.
Definition: Gene regulation The control of the level of gene expression in response to different conditions in the cell
Definition: Constitutive genes Genes that must be expressed all of the time and are involved in vital biochemical processes such as respiration
What are the three levels that gene regulation occurs at in prokaryotes? During transcription
during translation
and after protein synthesis
Definition: Operon A cluster of genes grouped together under the control of a single promoter in prokaryotic genomes
What is the lac operon? A cluster of three genes each involved in processing the sugar lactose
What sugar do bacteria with the lac operon prefer? Glucose
Definition: Operator A special DNA sequence that a repressor binds to to prevent transcription
Definition: Repressor protein Prevents transcription by binding to the operator to block RNA polymerase.
Definition: Activator protein A protein that increases transcription of a gene or a set of genes. It assists RNA polymerase.
Describe the events that occur when (-GLUCOSE
-LACTOSE) A repressor protein is continuously synthesized from a regulatory gene. It binds to and sits on the operator site
which is right in front of the lac operon. The repressor protein blocks the promoter site where the RNA polymerase settles so transcription does not occur.
Describe the events that occur when (-GLUCOSE
+LACTOSE) A derivative of lactose called allolactose is formed within the bacerial cell. This fits onto the repressor protein at an allosteric site. This causes the repressor protein to change its shape. It can no longer sit on the operator site. RNA polymerase can now reach its promoter site and genes are transcribed. An activator protein stabilizes RNA polymerase. The activator protein only works when glucose is absent.
Describe the events that occur when (+GLUCOSE
+LACTOSE) RNA polymerase can sit on the promoter site after allolactose removes it but it is unstable and it keeps falling off because no activator protein is produced to stabilize RNA polymerase.
Definition: Inducible operon Operons that can be turned on
Definition: Repressible operon Operons that can be turned off
Explain the trp operon 5 genes and a regulatory region. Under normal circumstances
tryptophan must be created
so the repressor does not bind to the operator. However
when trypotphan reaches a certain level in the cell
it binds to a repressor protein
and this makes it easier for the repressor to bind to the operator
reducing transcription
Explain pre-transcriptional and transcriptional control in eukaryotes Altering chromatin structures and loosening nucleosome structures so that proteins can gain access to the DNA
Definition: Enhancers A DNA sequence that increases the transcription of genes
Explain post-transcriptional and transational control in eukaryotes Alternative splicing
modifications of mRNA that do not include a 5’ cap or a 3’ poly-A tail so that it either degrades in the cell or does not leave the nucleus. Smll RNA molecules control gene expression through RNA interference
which inhibit gene expression by degrading mRNA or inhibiting translation by forming base pairs with mRNA.
Explain post-translational control in eukaryotes Many polypeptides that are synthesized in eukaryotic cells are not active immediately after synthesis. Activating them requires different modifications
for example insulin unfolding. Additionally
regulating how long a protein is available in the cell is a form of gene regulation. Adding a chain of ubiquitin molecules to a protein acts as a signal for the protein to be degraded.
Definition: Physical mutagen Physical agents such as radiation or heat
that cause damage to DNA by inducing structural changes.
Definition: Chemical mutagen Chemical substances that alter DNA by interacting directly with its bases or by inducing replication errors
Definition: Mutagen An event or substance that increases the rate of changes to the DNA sequence of an organism’s genome
Definition: Transposon A short segment of DNA capable of moving within the genome of an organism; also called a jumping gene
Definition: Photorepair A specific mechanism for repairing the thymine dimer structures.
Definition: Thymine dimer A structure that is created when two adjacent thymines covalently link together because of UV radiation.
Definition: Excision repair A non-specific repair mechanism that involves removing a damaged region of DNA and replacing it with the correct sequence.
Definition: Recombinant DNA A molecule of DNA that contains nucleotides from different sources
Definition: Exogenous Originating from outside of a specific organism
Definition: Restriction Endonucleases Cleaves DNA at specific sequences
found in bacteria
Definition: Methylases Enzymes that add methyl groups to specific DNA sites
which prevent restriction enzymes from cutting the DNA
How is DNA Ligase used in biotechnology? Used for gluing cut strands of DNA together
and it is isolated from a bacteriophage
What is gel electorphoresis? An electric current is used to separate DNA fragments according to their size. The negatively charged DNA fragments move to the positive side of the gel
and the smaller fragments move faster. A unique pattern is created which is used to analyze DNA and create a profile.
How does gene cloning work? Bacterial cells are mixed with a recombinant plasmid DNA
and a large amount of identical bacteria can be produced and studied after the non-modified bacteria die
Production site: Adrenocorticotropic hormone anterior pituitary gland
Target organ: Adrenocorticotropic hormone adrenal cortex
Effect: Adrenocorticotropic hormone “<b><span style=”“font-weight: 400;”“>Acts on the adrenals to produce cortisol and aldosterone. Cortisol raises blood sugar levels by releasing stored glucose</b>
and aldosterone increases blood pressure by increase salt absorption of the kidneys into blood which in turn makes them absorb more water</span></b>”
“Production site: <b><span style=”“font-weight: 400;”“>Thyroid-stimulating hormone</span></b>” Anterior pituitary gland
“Target organ: <b><span style=”“font-weight: 400;”“>Thyroid-stimulating hormone</span></b>” Thyroid
<b><span>Effect: Thyroid-stimulating hormone</span></b>” “<b><span>Stimulates the thyroid to increase the uptake of iodine from the blood to make thyroxine which controls metabolism and turns off tsh production which stops making too much thyroxine. </span></b>
“Production site: <b><span style=”“font-weight: 400;”“>Human growth hormone</span></b>” Anterior pituitary gland
“Target organ: <b><span style=”“font-weight: 400;”“>Human growth hormone</span></b>” Bones and muscle
“Effect: <b><span style=”“font-weight: 400;”“>Human growth hormone</span></b>” Increases Ca2 absorption and cell division and protein synthesis and lipid metabolism to grow muscle and bone.
“Production site: <b><span style=”“font-weight: 400;”“>Follicle-stimulating hormone</span></b>” Anterior pituitary gland
“Target organ: <b><span style=”“font-weight: 400;”“>Follicle-stimulating hormone</span></b>” Ovaries and testes
Effect: <b><span>Follicle-stimulating hormone</span></b>” “<b><span>In females, stimulates follicles on the ovary to grow and prepare the eggs for ovulation. In males, stimulates the production of sperm. </span></b>
“Production site: <b><span style=”“font-weight: 400;”“>Luteinizing hormone</span></b>” Anterior pituitary gland
“Target organ: <b><span style=”“font-weight: 400;”“>Luteinizing hormone</span></b>” Ovaries and testes
“Effect: <b><span style=”“font-weight: 400;”“>Luteinizing hormone</span></b>” In females
stimulates the production of estrogen and progesterone. In males
stimulates the producton of testosterone.
Production site: Prolactin Anterior pituitary gland
Target organ: Prolactin Mammary glands
Effect: Prolactin Promotes the growth of mammary alveoli and stimultates production of milk
Production site: Antiduretic hormone Posterior pituitary
Target organ: Antidiuretic hormone Kidney tubules
Effect: Antidiuretic hormone Acts on the kidneys to reabsorb water into the blood
Production site: Oxytocin Posterior pituitary
Target organ: Oxytocin Muscles of the mammary glands and uterus
Effect: Oxytocin Stimulates uterine muscle contractions and the release of milk by the mammary glands
