Ch2 LOs Flashcards
2.1: Explain the relationship between atoms and molecules.
Atoms are the fundamental unit of an element, made of protons, neutrons, and electrons. Molecules are structures made of two or more atoms held together by covalent bonds.
2.2: Explain what electronegativity means.
Electronegativity is the tendency of an atom’s nucleus to attract the shared electrons in a covalent bond.
2.2: Explain how electronegativity influences the electron positions in a covalent bond.
The electrons are closer to whichever atom has the most electronegativity.
2.2: Explain how electronegativity influences the partial charges on atoms in a covalent bond.
The more electronegative atom has a partial negative and the other atom would have a partial positive charge.
2.3: Compare hydrogen bonds and covalent bonds in terms of the mechanisms and strength of attraction between the atoms involved.
A hydrogen bond is an attraction between a partial positive charge on a hydrogen atom and a partial negative on another atom. A covalent bond is an attraction between two atoms based on shared electrons.
Hydrogen bonds are not as nearly strong as covalent bonds.
2.6: what is an acid?
An ion or molecule that releases a proton.
2.6: What is a base?
An ion or molecule that acquires a proton.
2.6: What is PH? The scale?
Quantifies the concentration or protons in a solution.
14- Basic
7- Neutral
0- Acidic
3.1: Compare the structure of DNA and RNA.
DNA Primary: sequence of nucleotides
RNA Primary: nucleotides
DNA Secondary: Double helix (H bonding)
RNA Secondary: stem and loop (not all RNA has a secondary structure)
RNA tertiary: several stem-and-loop sections twist and fold across each other to form a new 3-dimensional shape.
3.1: Compare the chemical composition of DNA and RNA.
Ribonucleotides contain ribose while deoxyribonucleotides contain deoxyribose. The two molecules are identical except for what might seem like a tiny difference—an OH on the 2′ carbon of ribose versus an H bonded to the 2′ carbon of deoxyribose.
3.1: Compare the location and function of DNA and RNA.
- DNA holds in coded form and create an mRNA copy. In contrast, RNAs can adopt a wide variety of shapes and have groups of atoms that can participate in an important array of chemical reactions.
-The C-OH group on the 2′ carbon of a ribonucleotide can participate in a lot more chemical reactions than the C-H group on the 2′ carbon of a deoxyribonucleotide.
3.2: Define complementary base pairing, and explain its connection to the observation that DNA strands are antiparallel.
4.1: Explain how the genetic code relates transcription to translation.
During translation, the translation machinery “reads” the nucleotides in an mRNA in groups of 3 (codon).
4.1 Why is the genetic code redundant?
The code is redundant, meaning that many amino acids are coded for by more than one codon.
4.1: Why is the genetic code conservative?
The code is conservative, meaning that changes in the third position of a codon are less likely to change which amino acid is added to a protein than changes in the first or second positions.
4.1: Why os the code unambiguous?
Meaning that each codon specifies exactly one amino acid or punctuation mark
4.2: On diagrams of translation initiation, translation elongation, and translation termination, label the small and large ribosomal subunits, mRNA, tRNA, rRNA, reading frame, start codon, stop codon, release factor, and tRNA binding sites (E, A, and P). Circle and label the locations where codon- anticodon recognition and peptide bond formation occur.
4.2: What is tRNA and which parts are labeled?
-Key to bridging the RNA protein language barrier
-The attachment site, which always has the nucleotide sequence CCA, is where amino acids bind so they can be carried by the tRNA.
-The anticodon is a sequence of three bases at the other end of the tRNA. The specific sequence labeled UAC in this figure, shown here in the 3′ to 5′ direction, is complementary to an AUG codon in an mRNA.
4.2: How many tRNAs are there?
So for each of the 20 amino acids, there is a different tRNA with a different anticodon.
4.2: Ribosomes
Protein-making machines.
4.2: RNA subunits
A large subunit and a small subunit. The boundary between the two subunits is defined by where the pink mRNA strand is shown on the cartoon model. When translation is not occurring, the subunits are separate. However, when translation is occurring, the subunits are bound together to form a single structure.
4.2: A site
where amino acid-charged tRNAs enter the ribosome. If the anticodon of a tRNA binds to the exposed codon in the mRNA, the tRNA and mRNA bind together.
4.2: Charged vs uncharged tRNA
A “charged tRNA” is a transfer RNA molecule that has an amino acid attached to it, making it ready to deliver that specific amino acid to the ribosome during protein synthesis, while an “uncharged tRNA” is a tRNA molecule that does not have an amino acid attached and therefore cannot participate in protein translation.
4.2: P site
Where peptide bond formation takes place.
4.2: E site
Exit site.
4.3: Use a copy of the genetic code to predict the sequence of the amino acids produced from a given mRNA or double-stranded DNA fragment. Identify the template and non-template (coding) strand. Identify the start and stop codon.
Where tRNAs sit once the amino acid they were carrying has been added to the growing protein. The now-uncharged tRNA exits the ribosome from this site.
4.2: Translation Elongation process
Each tRNA involved in building a protein moves through the ribosome by first entering the A site, moving to the P site, and exiting from the E site. A charged tRNA enters a ribosome and leaves uncharged.
4.2: Translation termination
- once stop codon is reached, translation is stopped because there is no tRNA that binds to it.
-Instead, a protein that has essentially the same shape as a tRNA interacts with the stop codon and binds to it. This protein is called the release factor.
4.2: How is it possible for the release factor to be a protein but still bind to the 3 ribonucleotides in a stop codon?
The R-groups at the base of the tRNA-shaped release factor form hydrogen bonds and other interactions with the ribonucleotides of the stop codon.
4.2: Ribozyme
An RNA molecule that catalyzes a chemical reaction, analogous to enzymes, which are protein catalysts.
4.4: Discuss the structure and functions of the main players in translation (tRNAs and ribosomes)
4.5: On diagrams of transcription initiation and transcription elongation, label the template and coding strands, initiation complex, promoter site, RNA polymerase, ribonucleotides, the direction of RNA polymerase movement, and direction of RNA synthesis.
4.5: Template strand
The strand in a DNA double helix that is “read” by RNA polymerase during transcription.
4.5: coding strand
The strand in a DNA double helix that matches the sequence of bases in the RNA product of transcription, except that the DNA contains thymine (T) and the RNA contains uracil (U).
4.5: Promoter
The regulatory sequence in a gene where RNA polymerase initiates transcription.
4.5: RNA polymerase
An enzyme that catalyzes the formation of phosophodiester linkages between ribonucleotides, forming an RNA product that is complementary to the sequences of bases in a DNA template.
5.1: Describe at least three functions that proteins serve in cells.
catalysis, transporting materials, movement, cell structure, defense, signaling and communication
5.2: Label the four components of an amino acid and explain the role of each in terms of how the molecule functions in a protein.
5.2: Amino groups
act as bases and tend to pick up a proton when they are in water
5.2: carboxyl group
tend to act as acids and drop a proton
5.2: R group
Bonded to the central carbon. What makes each amino acid unique is the structure of its R-group.
5.3: Predict whether the R-group on an amino acid that you haven’t seen before will 1) interact with water, and 2) act as an acid (proton donor) or base (proton acceptor).
5.4: Describe each of the four levels of protein structure and explain how each influences the protein’s final size, shape, and chemical properties.
Protein Primary
the sequence of amino acids, linked via peptide bonds
Protein Secondary
formation of ⍺-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone atoms
Protein tertiary
folding into a 3-D shape stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions
Protein quaternary
assembly of multipart proteins from folded subunits, stabilized by hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions
5.5: Compare which bonds are responsible for producing a protein’s 1) primary structure, 2) secondary structure (alpha-helices and beta-pleated sheets), and 3) tertiary structure.
Primary- peptide bonds
Secondary- hydrogen bonds between backbone atoms
Tertiary- H-bonds, ionic bonds, S-S bridges, hydrophobic interactions
Quaternary- hydrogen bonds, ionic bonds, S-S bridges, and hydrophobic interactions
6.1: Draw the general structure of a monosaccharide, disaccharide, and polysaccharide. Give an example of each.
6.1: Glycosidic linkage
A covalent bond that links monosaccharides together to form polymers.
6.1: Glycan
A polymer made up of monosaccharides joined by glycosidic linkages. (Synonymous with ‘polysaccharide.’)
6.1: Carbohydrates
A family of molecules that includes both monosaccharides and glycans.
6.1: alpha linkage
same side
6.1: beta linkage
opposite side
6.3: Explain how the structures of cellulose, chitin, glycogen, and starch support their functions.
Cellulose gives plants structural strength, because the combination of β-glycosidic linkages and hydrogen-bonded strands creates a tough, mesh-like material that is difficult for molecular machines to break down.
7.1: Compare the monomer subunit, bond responsible for polymerization, and important biological function(s) observed in proteins, nucleic acids, and carbohydrates.
7.1: Proteins
-monomer subunit
-bond responsible for polymerization
-important biological functions
-amino acids
-peptide bond (formed via dehydration synthesis between the carboxyl group of one amino acid and the amino group of another)
-Enzymes catalyze biochemical reactions
-structural support
-transport
-cell signaling
-immune response
7.1: Nucleic Acids
-monomer subunit
-bond responsible for polymerization
-important biological functions
- nucleotides
-phosphodiester bond (links the phosphate group of one nucleotide to the hydroxyl group on the sugar of another)
-store genetic info
-transmit genetic info
-energy transfer
7.1: Carbohydrates
-monomer subunit
-bond responsible for polymerization
-important biological functions
-monosaccharides
-glycosidic bond (formed between hydroxyl groups of two monosaccharides)
-energy storage
-structural support
-cell recognition and signaling
7.2: Compare the primary, secondary, and tertiary structures of proteins, RNA, and DNA.
7.2: structures of protein
1) peptide bonds
2) a-helices and/or pleated sheets stabilized by hydrogen bonds
3) Folding into specific shapes stabilized by ionic bonds, hydrogen bonds, S-S bonds, and/or hydrophobic interactions
7.2: structures of RNA
1) Phosphodiester linkages
2) loop and stem
3) specific shapes stabilized by hydrogen bonds
7.2: structures of DNA
1) phosphodiester linkages
2) double helix formed from antiparallel strands stabilized by hydrogen bonds
3) supercoiling (twisting on itself)
Defend the following three statements: 1) amino acids are much more diverse in structure and chemical properties than nucleotides, 2) in terms of diversity in shape and chemical properties, proteins > RNA > DNA, and 3) in terms of diversity in function, proteins > RNA > DNA.
8.1: Use drawings, models, or other representations to compare the structures of fats, phospholipids, and steroids.
8.1: Fats
are made up of three hydrocarbon-rich molecules called fatty acids, each of which is attached to a 3-carbon molecule called glycerol.
8.1: steroids
have a bulky structure containing carbon atoms arranged in four “fused rings.” Steroids vary in the R-groups attached to this core structure, with the example shown here featuring an -OH group on one end and a hydrocarbon tail with 8 carbons on the other.
8.1: Phospholipids
are a family of molecules that have two long hydrocarbon “tails” and a “head” that includes a phosphate group and a polar group. The polar groups in phospholipids got their name because they each contain one or more charges or partial charges. When you start analyzing different phospholipids, you’ll find that each type has 1) a different polar group, and 2) hydrocarbon tails that vary in length and/or degree of saturation.
8.1: Amphipathic Lipids
Polar and nonpolar
- ex: cholesterol
9.4: Given several models of membranes, predict how differences in phospholipid composition and cholesterol content will affect their relative fluidity and permeability, and explain your reasoning.
9.1: Draw a cell membrane and label integral and peripheral proteins, carbohydrate components, and lipid components.
9.1: Peripheral membrane protein
A protein found on the inner or outer surface of a cell membrane.
9.1: Transmembrane protein
A protein that spans the lipid bilayer of a cell membrane.
9.2: Compare the processes of diffusion, osmosis, and facilitated diffusion, and provide biological examples that illustrate each process.
9.2: Diffusion
the spontaneous movement of atoms, ions, and molecules from areas of higher concentration to areas of lower concentration.
9.2: osmosis
- an example of diffusion
-refers specifically to the diffusion of water across membranes - from an area of higher concentration (low solute concentration) to an area of lower concentration (higher solute concentration)
9.5: Given several ions and molecules, predict the relative rates at which they will cross a plasma membrane in the absence of membrane proteins. Explain your reasoning.
9.5: Selective permeability
Means that some substances can cross membranes much more readily than others.
9.5: The ability of a substance- an atom, an ion, or a molecule- to pass through a lipid bilayer depends on two things:
size and charge
9.5: which molecules can move across a cell membrane?
Small, nonpolar molecules like oxygen (O2) and carbon dioxide (CO2), as well as small polar molecules like water (H2O)
9.5: which molecules can’t move across a cell membrane without assistance?
larger molecules, charged ions, and most polar molecules
9.2: Concentration gradient
a difference in a substance’s concentration in space—usually across a cell membrane
9.2: Facilitated diffusion
(passive) diffusion of substances across cell membranes through integral membrane proteins
10.1: Define passive and active transport and explain the role of channels, carriers, and pumps in transport.
10.1: Passive transport
any movement of ions or molecules that does not require an input of energy
10.1: Active Transport
any movement of ions or molecules that requires an input of energy.
10.1: Membrane channels have three key points:
- Have a distinctive structure
-Channels are extremely specific
-regulation: few, if any, channels, are open at all times
-They have open and closed configurations that are highly regulated
10.1: Membrane carriers
Are similar to membrane channels but do not open a channel. They change its shape.
10.1: Pumps
The unique aspect of pumps is that they transport substances against—or up—a concentration gradient (and/or electrical gradient—but more on that later).
10.2: Describe the role of electrochemical gradients in primary and secondary active transport.
10.3: Describe the processes of endocytosis and exocytosis.
10.4: Predict what will happen to a cell when it is placed in a hypertonic, hypotonic, or isotonic solution.
11.3: Explain how and why ions and molecules move in response to concentration gradients.
When a concentration gradient exists, ions and molecules will move from regions of high concentration to regions of low concentration by diffusion.
11.2: Explain how ions move in response to electrical potential gradients, and why.
11.2: Membrane voltage
In cells, an electrical potential created by a separation of charge across a membrane. Also called a transmembrane potential or a membrane potential.
11.2: electrical current
In cells, a flow of charge in the form of ions.
11.1: Based on the information you are given about a specific cell, predict how it will be affected by ion movements that occur in response to a change in electrical potential gradients.
11.1: Electrochemical gradient
The overall gradient across a cell membrane or organelle membrane, produced by differences in concentration of substances combined with differences in the distribution of charge.
12.1: Explain why viruses are considered obligate intracellular parasites, and why viral diseases are difficult to treat with drugs.
Viruses can only reproduce by entering a host cell and using the host cell’s molecular machinery, ATP, and other resources to make copies of themselves.
Because there are so few virus-specific proteins, it is difficult for researchers to design drugs that damage a virus without damaging the host.
12.3: State the arguments for why viruses could be considered alive or not alive, then state and defend your opinion on this question.
Alive:
-they evolve
-they replicate
Dead:
-they can’t perform metabolism
-they don’t have cell membranes
12.2: Using a diagram, explain how the following events in a virus’ life cycle occur: enter a host cell, produce viral proteins, replicate viral genome, assemble new virions, exit host cell, transmission to a new host.
A virus begins its life cycle by entering a host cell, typically binding to specific receptors on the cell surface and gaining entry through membrane fusion, endocytosis, or direct injection of its genetic material. Once inside, the virus produces viral proteins by using the host’s machinery to transcribe and translate its genome. Simultaneously, it replicates its genome using either host or viral enzymes, depending on whether it is a DNA or RNA virus. Newly synthesized viral components then assemble into new virions, often through self-assembly. The virus exits the host cell either by lysis, which destroys the cell, or by budding, which allows the virus to acquire a membrane envelope. Finally, transmission to a new host occurs through various means, such as direct contact, airborne droplets, or vectors, ensuring the continuation of the viral infection cycle.
12.2: Enveloped vs non enveloped viruses exit of cell
Enveloped viruses insert their surface proteins into a lipid bilayer present in the host. Non-enveloped viruses have a mechanism for disrupting the host cell’s membrane as well as its cell wall, if one is present.
12.2: Protease
An enzyme that catalyzes breaking peptide bonds in a long string of amino acids. Some proteases function as digestive enzymes; other break long amino-acid chains at specific points to create several to many independent proteins.
13.1: Compare key elements of prokaryotic versus eukaryotic cell structure.
13.1: What are the common elements found in every cell?
cell membrane, genetic material, ribosomes, cytoskeletal elements, organelles, cell wall, flagella
13.1: Archaean Cells
-live in extreme habitats
-not known to cause disease or are important to humans
-have unique hydrocarbon chains in their membrane lipids
-unique types of carbohydrates in their cell walls
13.1: Bacterial Cells
Although a few species have linear chromosomes, most bacteria have a single, circular chromosome — a circular double helix that associates with DNA-binding proteins and coils and folds on itself into a compact structure.
13.1: Eukaryotic Cells
- have a double membrane nucleus (nuclear envelope) studded with pores
13.2: Compare key elements of plant versus animal cell structure.
