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(5/16/24) hope everyone did well!! will be fixing definitions and questions for next year folks 🫡
Water is composed of two main elements. What are they, and in what ratio are they composed?
Oxygen and hydrogen in a 1:2 ratio
Is oxygen or hydrogen more electronegative?
Oxygen
What is a covalent bond?
A chemical bond that is formed when two or more atoms share electrons
Covalent bonding can result in ____________ when there are differences in atomic electronegativities.
Polarity
What is a hydrogen bond?
The attraction between a hydrogen atom with a partial positive charge and another atom with a partial negative charge
Where are hydrogen bonds found in water?
Between the hydrogen atom of one water molecule and the lone pair of electrons on an oxygen atom of a neighboring water molecule
How many hydrogen bonds are formed between each complementary base pairing?
Adenine and Thymine = 2, Cytosine and Guanine = 3
What is the structure of an amino acid?
A central carbon atom attached to a hydrogen, an acidic carboxyl group (−COOH), an amino group (−NH2) and an organic side chain (also called an R group)
What are the three options for the R group?
A hydrophobic group, a charged polar group, and an uncharged polar group
For a hydrophobic R group, what its polarity? Justify your response.
Nonpolar. Hydrophobic R groups are characterized by their lack of affinity for water and inability to form hydrogen bonds between water molecules. This is due to the absence of partial charges in these groups, making them nonpolar
For a charged polar group, what its polarity? Justify your response.
Polar. These groups have full electric charge, either positive or negative, due to the loss or gain of electrons. This charge creates strong electrostatic attraction with water molecules, making them highly polar and soluble in water
For an uncharged polar group, what its polarity? Justify your response.
Polar. Although these groups do not carry a full electric charge, they have areas of partial positive and negative charges due to uneven distribution of electrons in their chemical bonds. This allows them to form hydrogen bonds with water, making them polar but without a net charge
What are the three properties of water?
High specific heat, cohesion, and adhesion
How does hydrogen bonding allow for high specific heat?
Hydrogen bonding allows for water's high specific heat because a large amount of energy is required to break these strong intermolecular bonds, meaning water can absorb or release large amounts of heat with only a small temperature change, providing stability to the environment and living organisms
How does hydrogen bonding allow for adhesion?
Hydrogen bonding allows for adhesion by enabling water molecules to form attractions with other substances or surfaces, facilitating the clinging of water to different materials through the polar interactions between hydrogen and electronegative atoms in those surfaces
How does hydrogen bonding allow for cohesion?
Hydrogen bonding allows for cohesion by enabling molecules, particularly water molecules, to attract and stick to each other due to the polarity created by the difference in electronegativity between hydrogen and other atoms like oxygen or nitrogen
What is the main difference between adhesion and cohesion?
Adhesion refers to the attraction between different substances, while cohesion refers to the attraction between molecules of the same substance
Define surface tension.
The property of a liquid's surface that allows it to resist external force, due to the cohesive forces between liquid molecules
What causes surface tension?
Hydrogen bonds between water molecules
Water's cohesive property allows for unique hydrogen bond interactions to occur when water is in a solid state, making ice (solid water) _____ dense than liquid water.
Less
Describe why water is considered a polar molecule?
It has a bent shape with two hydrogen atoms bonded to an oxygen atom, creating a partial positive charge on the hydrogens and a partial negative charge on the oxygen, resulting in an uneven distribution of charge across the molecule
Using the properties of water, describe how water can move up a capillary tube to move from the roots to the leaves in a plant.
As water evaporates from the leaf, hydrogen bonds cause the water molecules leaving the veins to tug on the molecules further down, pulling the water up through the plant. This is made possible by cohesion as the water attempts to stick together, and also adhesion as the adhesion of water to cell walls by hydrogen bonds helps counter the downward pull of gravity as water moves up the capillary tube
Using the properties of water, describe how a water strider can walk on water.
Due to hydrogen bonds allowing water to exhibit cohesive behavior, water has high surface tension. Because the water has high surface tension, it allows a water strider to walk on it without breaking
Law of Conservation of Energy
States that energy cannot be created or destroyed but can be changed from one form to another
What are the four macromolecules?
Carbohydrates, lipids, proteins, and nucleic acids
What are the elements in a carbohydrate?
C, H, O
What are the three functions of carbohydrates in living organisms?
The primary source of energy (cellular respiration), structural support in plants (cellulose) and animals (chitin in exoskeletons), and cell-to-cell recognition and signaling
What are the elements in proteins?
C, H, O, N, and sometimes S
What are the functional groups found in all amino acids?
Carboxyl (-COOH) and amino groups
What are three functions of proteins in living organisms?
They can act as enzymes for catalyzing biochemical reactions for metabolism and other processes, provide structural support (collagen), and play a role in cell signaling and regulatory processes
How does the R group affect the folding of the protein? (include polar and nonpolar R groups)
Nonpolar (hydrophobic) groups fold inward, avoiding water, while polar (hydrophilic) groups form bonds with water and each other, guiding the protein into its functional shape
What are the elements found in nucleic acids?
C, H, O, N, P
What are parts found in all nucleotides?
All nucleotides are composed of three parts: a five-carbon sugar, a phosphate, and a nitrogen-rich structure called a nitrogenous base
What are three functions of nucleic acids in living organisms?
Genetic information storage as DNA is the blueprint for all genetic information, protein synthesis, and regulating gene expression
What are the elements found in a lipid?
C, H, O
How are the three different types of lipids different?
Triglycerides store energy and provide insulation, phospholipids form cellular membranes with their hydrophilic heads and hydrophobic tails, and steroids, like cholesterol, stabilize membranes and serve as precursors for hormones and vitamins
What are three functions of lipids in living organisms?
Lipids serve as long-term energy storage, form the structural basis of cell membranes, and act as hormones and signaling molecules in many biological processes
What is dehydration synthesis? Provide an example.
A chemical reaction in which two molecules are joined together with the removal of a water molecule. An example of this is the formation of a peptide bond between two amino acids. When the carboxyl group of one amino acid reacts with the amino group of another, a molecule of water is released, and a peptide bond is formed, linking the two amino acids together
What is hydrolysis? Provide an example.
A chemical reaction where a water molecule is added to a substance, causing it to split into two parts. An example is the breakdown of a disaccharide like sucrose into its monosaccharide components, glucose, and fructose. During this process, a water molecule is used to break the glycosidic bond between glucose and fructose, resulting in the separation of these two sugars
What type of bond is found in carbohydrates, and where specifically, is this bond located?
Glycosidic bonds are covalent bonds found in carbohydrates, typically found between the hydroxyl groups of adjacent monosaccharides
What type of bond is found between protein monomers and where specifically, is this bond located?
Peptide bonds are found between protein monomers and are covalent bonds that form between the carboxyl group (-COOH) of one amino acid and the amino acid (-NH2) of another
What type of bond is found between nucleic acid monomers and where specifically, is this bond located?
Nucleic acid monomers (nucleotides) are linked by phosphodiester bonds, located between the phosphate group of one nucleotide and the 3' hydroxyl group of the sugar (either ribose or deoxyribose) of the adjacent nucleotide
What is the monomer of a carbohydrate? Identify the components of the monomer.
The monomer of a carbohydrate is a monosaccharide, consisting of carbon, hydrogen, and oxygen atoms in a structure that can form chains or rings
What is the monomer of a protein? Identify the components of the monomer.
The monomer of a protein is an amino acid, which includes an amino group, a carboxyl group, a hydrogen atom, and a variable side chain (R group) attached to a central carbon atom
What is the monomer of a nucleic acid? Identify the components of the monomer.
A nucleotide, composed of a phosphate group, a sugar molecule (ribose in RNA and deoxyribose in DNA), and a nitrogenous base
Identify the components of a phospholipid.
A phospholipid comprises a glycerol backbone, two fatty acid tails, and a phosphate group attached to one of several possible polar molecules
What type of bond is found in starch?
α-1,4-Glycosidic Bonds
What type of bond is found in cellulose?
β-1,4-Glycosidic bonds
What bond can be broken by animals?
Covalent bonds
How does a saturated and unsaturated fatty acid differ?
Saturated fatty acids have hydrocarbon chains connected by single bonds only. Unsaturated fatty acids have one or more double bonds. Each double bond may be in a cis or trans configuration
How does the level of saturation affect the function of the lipid?
Higher degrees of unsaturation lead to lower melting temperatures. This is because the double bonds add kinks to the fatty acid chains which prevent tight packing of lipid molecules. In general, the degree of saturation impacts the fluidity of the membrane to a greater extent than the chain length
Describe how a nonpolar to polar R group substitution changes the structure and function of a protein.
Depending on whether the R group is hydrophilic or hydrophobic interaction between hydrophobic amino acids with each other and hydrophilic amino acids with each other results in folding that gives the protein its 3D shape. Changing a nonpolar R group to a polar R group can change the 3D shape of the protein and therefore change its ability to function correctly
Describe how a cytosine to thymine substitution changes the structure and function of DNA. (pyrimidine-pyrimidine substitution)
They have a different number of bonds required to bind to their complementary base, so the connection between the guanine and the thymine would be unstable. Changing a C to a T changes the genetic code for a protein and can result in a nonsense or missense mutation that can lead to a nonfunctional protein/genetic disorder. ie A to T substitution in the hemoglobin gene results in sickle cell anemia
Describe how a cytosine to guanine substitution changes the structure and function of DNA. (pyrimidine-purine substitution)
A cytosine to guanine substitution in DNA, a pyrimidine-to-purine change, alters the base pairing, potentially causing distortions in the DNA structure and affecting the fidelity of genetic information transmission
Describe how a deoxyribose to ribose changes the structure and function of a nucleic acid.
The change would cause the nucleic acid to function as a RNA molecule. The purpose of RNA is to develop proteins within our body through the process of protein synthesis. RNA is also single stranded whereas DNA is double stranded
Describe the structure of the nucleic acid polymer (DNA)
DNA has a double-helix structure The sugar (deoxyribose) and phosphate lie on the outside of the helix, forming the backbone of the DNA. The 2 strands run in opposite directions (antiparallel) The nitrogenous bases are stacked in the interior, like the steps of a staircase, in pairs. Adenine and Thymine/Cytosine and Guanine are bound to each other by hydrogen bonds
What are the ends of nucleic acids polymer called?
5' and 3' end
Number of hydrogen bonds between A and T
2 hydrogen bonds
Number of hydrogen bonds between C and G
3 hydrogen bonds
Primary Structure Proteins
The simplest level of protein structure, primary structure, is simply the sequence of amino acids in a polypeptide chain.
Secondary Structure Proteins
The secondary structure arises from the hydrogen bonds formed between atoms of the polypeptide backbone. The hydrogen bonds form between the partially negative oxygen atom and the partially positive nitrogen atom.
Tertiary Structure Protein
The tertiary structure of a protein refers to the overall three-dimensional arrangement of its polypeptide chain in space. It is generally stabilized by outside polar hydrophilic hydrogen and ionic bond interactions, and internal hydrophobic interactions between nonpolar amino acid side chains
Quaternary Structure Protein
A protein with a quaternary structure is composed of several complex subunits. These subunits are bonded together through non-covalent bonds, primarily via hydrogen bond
What are the ends of a protein called and what is found at each end?
C-terminus (COOH) and N-terminus
Which end is the location of the growing polypeptide strand?
C-terminus
Describe the structure of a carbohydrate polymer.
Organic molecules consisting of carbon, hydrogen, and oxygen atoms, typically in a 1:2:1 ratio. They also have an hydroxyl group.
What are the components of a fat molecule?
Glycerol and fatty acids. Glycerol is an alcohol with three carbons, five hydrogens, and three hydroxyl (OH) groups. Fatty acids have a long chain of hydrocarbons with a carboxyl group attached
Describe the structure of a steroid.
Steroids are composed of a backbone of four fused carbon rings and are formed from a cholesterol precursor in body cells.
What are the three components of a DNA or RNA molecule?
DNA and RNA are made up of three main components: nucleotide bases (adenine, cytosine, guanine, and either thymine in DNA or uracil in RNA), a sugar molecule (deoxyribose in DNA and ribose in RNA), and a phosphate group, which forms the structural backbone.
Identify main differences between DNA and RNA.
DNA contains the pentose sugar deoxyribose, whereas RNA contains ribose. The nitrogenous bases in DNA include adenine, cytosine, guanine, and thymine; in contrast, RNA contains uracil instead of thymine. DNA is double-stranded, forming a helical structure, while RNA is typically single-stranded. The directionality of DNA and RNA strands is from 5' to 3', with RNA usually being synthesized in this direction during transcription from the DNA template.
Scientists examined the folded structure of a purified protein resuspended in water and found that amino acids with non polar R groups were primarily buried in the middle of the protein, whereas amino acids with polar R groups were primarily on the surface of the protein. Explain the location of the amino acids in the folded protein.
Nonpolar R groups that cannot form hydrogen bonds with water are pushed into the middle of the protein.
How is DNA/RNA synthesis directionally oriented?
New nucleotides are added to 3’ hydroxyl
What is the structure and function of the ribosome?
A ribosome is made up of two subunits, a small subunit, and a large subunit. These subunits come together before the translation of mRNA into a protein to provide a location for translation to be carried out and a polypeptide to be produced.
How does the structure of the ribosome aid in the function?
The structure of the ribosome allows proteins to be made inside or outside the cell
What are the three types of RNA involved in the structure or function of the ribosome?
They are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA)
How does the ribosome demonstrate a common ancestry of all known life?
Ribosomes are not enclosed by a membrane and are subcellular components found in ALL forms of life, reflecting the common ancestry of all known life.
What is the structure and function of the rough ER?
The rough endoplasmic reticulum has on it ribosomes, which are small, round organelles whose function it is to make those proteins.
How does the structure of the rough ER aid in the function?
It allows for the production, folding, quality control and dispatch of some proteins.
What is the structure and function of the smooth ER?
The smooth endoplasmic reticulum has a tubular form. It participates in the production of phospholipids, the lipids in cell membranes and are essential in the process of metabolism. Smooth ER transports the products of the rough ER to other cellular organelles, especially the Golgi apparatus
How does the structure of the smooth ER aid in the function?
The reticulation (meshwork) of its structure increases the surface area of this organelle, providing more surface for synthesis, metabolism, detoxification, etc.
What is the relationship between the ribosome and the rough ER?
The ribosome that is synthesizing the protein is directly attached to the ER membrane. These membrane-bound ribosomes coat the surface of the ER, creating regions termed rough endoplasmic reticulum, or rough ER
What is the structure and function of the golgi bodies (also known as the golgi apparatus, or complex)?
The Golgi bodies (apparatus/complex), function as a factory in which proteins received from the ER are further processed and sorted for transport to their eventual destinations: lysosomes, the plasma membrane, or secretion.
How does the structure of the Golgi aid in the function?
The structure of the Golgi apparatus ensures that the proteins are sorted correctly, with each vesicle containing only the proteins that are destined for the same location.
Furthermore, the Golgi apparatus is not a static structure. Instead, it is dynamic and can change shape and size in response to the cell's needs. For instance, if the cell is producing a large amount of a particular protein, the Golgi apparatus can expand to help the increased workload.
What is the structure and function of the mitochondria?
Mitochondria are membrane-bound cell organelles (mitochondrion, singular) that generate most of the chemical energy needed to power the cell's biochemical reactions. Chemical energy produced by the mitochondria is stored in a small molecule called adenosine triphosphate (ATP). Mitochondria contain their own small chromosomes. Generally, mitochondria, and therefore mitochondrial DNA, are inherited only from the mother.
How does the structure of the mitochondria aid in the function?
The matrix is the name of the substance that fills the mitochondria. The internal surface area of the organelle is increased by the inner membrane's folding. The internal surface area of the organelle is increased by the inner membrane's folding. The increased surface area makes more room for chemical reactions to take place because the inner membrane is the site of numerous chemical processes.
What is the structure and function of the lysosome?
Lysosomes are membrane-enclosed organelles that contain an array of enzymes capable of breaking down all types of biological polymers—proteins, nucleic acids, carbohydrates, and lipids.
How does the structure of the lysosome aid in the function?
Structurally, lysosomes are like a floating garbage bag that contains enzymes capable of digesting molecules. Their external membrane is like a gateway that allows molecules inside of the lysosome without allowing the digestive enzymes to escape into the cell.
What is the structure of the vacuole?
They are surrounded by a thin membrane and filled with fluid and any molecules they take in.
What is the function of the food vacuole?
To ingest food particles using phagocytosis, a type of endocytosis. The food particles will then be broken down, or digested, when the lysosome fuses with the food vacuole.
What is the function of the central vacuole?
Among its roles in plant cell function, the central vacuole stores salts, minerals, nutrients, proteins, pigments, helps in plant growth, and plays an important structural role for the plant.
What is the function of the contractile vacuole?
A contractile vacuole works just the same as the name suggests, in that it expands and contracts. The point of the contractile vacuole is to pump water out of the cell through a process called osmoregulation, the regulation of osmotic pressure. It maintains the shape and internal pressure of the cell.
What is the structure and function of a chloroplast?
Chloroplast has a structure called chlorophyll which functions by trapping the solar energy and is used for the synthesis of food in all green plants.
How does the structure of the chloroplast aid in the function?
The chloroplast is surrounded by a double membrane, providing a distinct internal environment for photosynthesis to occur. Inside, it contains stacks of thylakoids, which are flattened sac-like structures. These thylakoids are where the light-dependent reactions of photosynthesis take place.
How does the endoplasmic reticulum provide mechanical support?
The endoplasmic reticulum gives additional mechanical support to the cytoplasm as it divides the fluid content of the cell into compartments.
How does the endoplasmic reticulum aid in protein synthesis?
The endoplasmic reticulum is the port of entry of the protein secretory pathway and an important part of protein synthesis. Due to all the ribosomes found on the RER, secretory proteins are synthesized here. Protein synthesis is composed of two major steps: transcription and translation.
How does the endoplasmic reticulum aid in intracellular transport?
The endoplasmic reticulum serves as a channel that proteins will pass through bound for their final destination. Outbound proteins from the endoplasmic reticulum will bud off into transport vesicles that travel along the cell cortex to reach their specific destinations.
How does the lysosome aid in intracellular digestion?
Lysosomes are organelles that contain digestive enzymes. They digest excess or worn out organelles, food particles, and engulfed viruses or bacteria.
How does the lysosome aid in recycling the cell's organic materials?
The lysosomes recycle the cell's organic material in a process known as autophagy. Lysosomes break down cellular waste products, fats, carbohydrates, proteins, and other macromolecules into simple compounds, which are then transferred back into the cytoplasm as new cell-building materials.
How does the lysosome aid in apoptosis (programmed cell death)?
This pathway of apoptosis can be activated by death receptors, lipid mediators, and photo-damage. Lysosomal proteases can be released from the lysosomes into the cytosol, where they contribute to the apoptotic cascade upstream of mitochondria.
How does the vacuole assist in storage of macromolecules?
Vacuoles are membrane-bound sacs that function in storage and transport. They assist in the storage of macromolecules by containing enzymes that can break down these large molecules. In plant cells, vacuoles also help break down macromolecules by hydrolyzing fatty acids, amino acids, and toxins.
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