Final Exam Flashcards
What are the three tenets of cell theory?
- All cells come from pre-existing cells.
- The cell is the basic unit structure of life.
- All living organisms are composed of one or more cells.
Describe the primary role for each of the different cellular organelles. (7)
Plasma Membrane: contains organelles and controls what enters and exists the cell.
Nucleus: stores DNA.
Mitochondria: produces energy in the form of ATP.
Endoplasmic Reticulum: transports molecules around the cell and synthesizes proteins and lipids.
Golgi Apparatus: packages proteins and sorts them to their final destination.
Cytoskeleton: stabilizes the membrane and generates motion.
Endosomes/Lysosomes/Peroxisomes: break down molecules into their building blocks.
Describe the differences between prokaryotes and eukaryotes.
Prokaryotes have no nucleus or organelles, are smaller, unicellular, replicate through binary fission, and are asexual.
Eukaryotes contain an nucleus and organelles, are larger, multicellular, replicate through mitosis or meiosis, and can be sexual or asexual.
Describe the various types of cells and their function. (8)
Epithelial: form barriers and absorb or secrete substances
Muscle: generate skeletal and organ movement
Nerve: conduct electrical signals
Connective Tissue: hold cells together
Bone: Give strength and support to the body (osteoclasts degrade cells while osteoblasts build new cells)
Secretory: secrete substances
Adipose: store fat
Red Blood Cells: move and deliver oxygen around the body (have no nucleus or organelles but are eukaryotic)
Why is water necessary for supporting life?
Water is polar, liquid at room temperature, most dense as a liquid, and has a high specific heat capacity. The polarity of water makes it an excellent solvent that aids in nutrients delivery, removal of wastes, and providing an environment for cells with the movement of chemical messengers. Water’s high specific heat capacity allows thermoregulation that allows the body to regulate its temperature by maintaining or releasing heat.
Why is carbon necessary for supporting life? What are the 4 major classes of carbon based molecules?
Carbon is necessary for supporting life because it is a small molecule that can form 4 different bonds. The major classes are:
Lipids- amphipathic building blocks for fats and oils
-Cholesterol regulates fluidity and is a precursor for hormones and acids
-Phospholipids that form cell membranes
-Triglycerides that are body fat used to store energy
Carbohydrates- monosaccharides (1), disaccharides (2), oligosaccharides (3-10), or polysaccharides (chains)
Nucleotides - building blocks for DNA, RNA, and ATP
Amino Acids- building blocks for peptides and proteins with a carboxylic acid, amino, and R-group
-can be hydrophobic (interacting with hydrophobic molecules), charged hydrophilic (interact with water), polar (form H-bonds to stabilize proteins), and aromatic molecules (assist in protein structure)
- when 20+ amino acids are linked by peptide bonds, they form proteins that fold into a 3D shape
Explain what constitutes nucleotides and how they form DNA.
Nucleotides consist of a 5-carbon sugar that is a cyclic monosaccharide numbered from 1-5, phosphate which is part of a sugar-phosphate backbone linked at the 5’ and 3’ carbons, and a nitrogenous base that is attached to the 1’ carbon.
Nitrogenous bases consist of purines (A/G) and pyrimidines (C/T/U) that are bonded with H-bonds in an anti parallel order. These bases are hydrophobic while the sugar phosphate backbone is hydrophilic so DNA twists into a double helix to keep the backbone outside, toward the aqueous environment.
What types of RNA is there? What is the difference between RNA and DNA?
RNA can be mRNA (carries instructions), tRNA (brings amino acids for protein synthesis), rRNA (makes ribosomes to translate RNA into proteins), and siRNA (turns genes off).
RNA is different from DNA because it is single stranded, contains Uracil instead of Thymine, and has ribose (oxygen) at the 2’ carbon.
Explain DNA replication.
DNA replication is a semi-conservative process, meaning that only one strand is replicated. It is split into three steps, initiation, elongation, and termination. In initiation, DNA helicase binds the the origin of replication and begins to unwind the DNA forming a replication fork, with the use of energy. RNA primase then adds RNA primer nucleotides so that DNA polymerase can copy the DNA. During elongation, DNA polymerase elongates RNA primers in a 3’ to 5’ direction, catalyzing phosphodiester bonds between the nucleotides. On the leading strand, polymerase elongates nucleotides in a continuous 3’ to 5’ direction, creating a continuous 5’ to 3’ orientation. On the lagging strand, Okazaki fragments are made where RNA primase continually adds primers while SSBPs bind to open nucleotides to mitigate damage. An enzyme then replaces the primers with DNA and ligase catalyses the phosphodiester bonds between nucleotides, creating a continuous strand. During termination, there is an overhand on the lagging strand that does not allow enough space for RNA primers to be added. If this overhang is left, the DNA strand will degrade and important genetic information will be lost. To fix this telomerase adds telomeres that act as an RNA template that connect to the overhang, providing room for primers to be added and polymerase to continue elongating the strand.
Explain RNA transcription.
RNA transcription occurs in three steps; initiation, elongation, and termination. During initiation, transcription factors bind the the regulatory region, upstream of the gene that will be encoded. This allows for RNA polymerase II to attach to the promoter region known as the TATA box. The transcription factor then guides RNA pol II to the gene that will be transcribed, unwinds the DNA to provide access, and phosphorylates RnA pol II twice to activate its function. During elongation, RNA pol II moves down the strand of DNA, synthesizing mRNA by adding nucleotides to the 3’ end of the template strand in a transcription bubble formed by RNA pol II for protection of single-stranded DNA. In termination, RNA is cleaved from RNA pol II by an enzyme, the bubble collapses, RNA dissociates, and the RNA pol II detaches from the DNA. With no proofreading function, transcription occurs multiple times until the correct copy, that can form complimentary hydrogen bonds to match the DNA template, is created
Describe the post-translational modifications of mRNA.
5’ methylguanosine cap: GTP is added to the 5’ end of mRNA by a triphosphate linkage, then a methyl is added to the 7’ of guanosine.
3’ polyadenylation: poly(A) adds over 200 adenosines making a poly(A) tail that is added to the mRNA.
Splicing: introns are removed from the RNA while exons are kept. Alternative splicing can occur where multiple molecules of mRNA are made with the use of different exons.
What are the different characteristics of each amino acid?
Non polar: glycine, alanine, valine, isoleucine, leucine, proline
Polar: serine, asparagine, threonine, cysteine
Negative: glutamic acid, aspartic acid
Positive: arginine, lysine, Argentine, histidine
Aromatic: trp, tyrosine, phenylalanine
Explain the process of translation.
There are three steps to translation: initiation, elongation, and termination. In initiation, initiation factors, including the 5’ cap binding factors, PABP, and other initiation factors, bind to the mRNA molecule. The small ribosomal subunit then attaches to the mRNA molecule at the 5’ end, near the methylguanosine cap guided by initiation factors. The small ribosomal subunit attaches to the initiator tRNA, which carries the amino acid methionine. The small ribosomal subunit and initiator tRNA then crawl forward until the start codon is found. The initiator tRNA then bind to the start codon, allowing the large ribosomal subunit to enclose the mRNA, with the initiator tRNA in the P site. PABP falls of and translation begins. In elongation, aminoacyl tRNAs attach to the ribosome in the A site where the tRNA is charged with GTP and has an anticodon complimentary to the A site. The GTP is converted to GDP and peptidyl transferase moves the peptide in the P site to the tRNA amino acid in the A site. The ribosome next translocates down one codon on the mRNA, moving the mRNAs and tRNAs from the A and P sites to the P and E sites. The E site is where spent tRNA is ejected from the ribosome. In termination, the stop codon is reached, attracting complimentary release factors that fit into the A site of the ribosome and substitute water for an amino acid to attach to the peptide in the P site, producing carboxylic acid and releasing the peptide. After the peptide is released, a ribosome release factor occupies the A site, releasing the large and small ribosomal subunits from the mRNA.
How does the cell repair DNA?
DNA polymerase can proofread and correct errors during DNA replication, while DNA repair proteins continually scan for error during the cell cycle.
What are the different types of mutations? Which is the most detrimental?
Point mutations: a single nucleotide is changed, resulting in one of three outcomes: silent mutation, the amino acid does not change; missense mutation, the mutation causes the amino acid to change; or a nonsense mutation, where the mutation replace the amino acid codon with a stop codon, ending translation and preventing the production of the rest of the amino acid. This is very detrimental.
Insertion: an extra base pair is added to DNA shifting the reading frame and altering every amino acid produced (frameshift mutation)
Deletion: a base pair or more is removed from the DNA sequence. This alters the reading frame if not in multiples of three (frameshift mutation)
Large scale deletion, insertion, and recombination: involve entire chromosomes or parts of chromosomes. These mutations are often lethal.
Which is NOT an essential characteristic of water?
a. It is liquid at room temperature
b. It is polar and forms covalent bonds
c. It is densest as a liquid
d. It has a high heat of vaporization
B- water is polar but it forms hydrogen bonds, not covalent bonds.
Which of the statements concerning liquids is incorrect?
a.lipids are oils and fats
b.they are generally hydrophobic
c.they readily dissolve in water
d.they are made of hydrocarbons
C- lipids do not readily dissolve in water
Oligosaccharides are composed of how many carbons?
a.1
b.2
c.3-10
d.11 or more
C- oligosaccharides are made of 3-10 carbons
What do all amino acids have in common?
a.long chains of saturated carbons
b.a carboxylate group
c.long chains of unsaturated carbons
d.a sulfhydryl group
B- all amino acids have a carboxylate group
What is not a component of a nucleotide?
a.a base
b.a pentose sugar
c.at least one phosphate group
d.a hexose sugar
D- nucleotides have a pentose sugar,not a hexose sugar
Which of the following is a characteristic of a prokaryotic cell?
a.has nucleus and membrane bound organelles
b.small relative to eukaryotic cells
c.undergoes mitosis for cell division
d.usually multicellular
B- prokaryotes are small relative to eukaryotes
Which of the following describes a connective tissue cell?
a.creates material that holds cells together
b.gives strength and support to the body
c.form protective barriers
d.formed into the bone marrow and move throughout the body
A- connective tissue cells create material that hold cells together
Where in the cell is most of the energy produced?
a.endoplasmic reticulum
b.peroxisome
c.nucleus
d.mitochondria
D- mitochondria produces the most energy in the cell
Which of the following cell types would you predict to have the most mitochondria?
a.blood cell
b.connective tissue cell
c.muscle cell
d.nerve cell
C- muscle cells have the most mitochondria
DNA nucleotides:
a.use ionic bonds to hold base pairs together
b.form the base pairs with adenine and cytosine and thymine and guanine
c.have purines forming base pairs with pyrimidines
d.form strands that run parallel to each other
C- DNA nucleotides have purines form base pairs with pyramides (AT CG)
RNA is different from DNA because it:
a.uses uracil rather than thymine
b.is more stable in the cell
c.contains deoxyribose
d.does not require energy for synthesis
A
Okazaki fragments:
a.are the lagging strand synthesis of DNA
b.pack DNA 7-fold
c.occur due to DNA damage from UV radiation
d.allow for continuous replication of DNA
A
DNA mutations are:
a.a permanent change to the DNA sequence
b.always lethal for the cell
c.prevented by helicase proofreading in the cell
d.only solved during DNA replication
A
The creation of messenger RNA is known as:
a.translation
b.replication
c.transcription
d.translocation
C
Ribosomes are:
a.made of ribosomal rRNA
b.found in the nucleus
c.transcribe RNA
d.not enzymes
A
Describe the structure and function of the nucleus’ various components. (7)
The nucleus’ primary function is to protect DNA and allow genes to function. It does this by allowing DNA to replicate, regulating access to DNA, and organizing DNA.
Nuclear envelope: double membrane structure that attaches to the ER cisternae to control what enters and exits the nucleus and separate the DNA from the other cellular structures.
Nuclear pores: pores in the nuclear envelope regulate traffic. Large molecules like proteins cannot freely fats while small molecules like ions and water can.
Chromatin: DNA organized into fibres
Chromosomes: highly condensed chromatin
Nucleolus: creates RNA and stores the DNA that encodes those genes
Nucleoplasm: provides fluid around the envelope for suspension
Nuclear Matrix: organizes chromosomes and provides a scaffold to maintain shape
Describe the different levels of DNA packaging.
1) Double helix: antiparallel strands of DNA coiled into a double helix to protect DNA and regulate transcription.
2) Nucleosomes: DNA wraps around histones creating “beads” that are separated by linker-DNA. (7-fold)
3) Chromatin fibre: Nucleosomes coil into chromatin fibre. (42-fold)
4) Chromatin looped domain: chromatin fibre is looped into a chromatin looped domain. (750-fold)
5) Heterochromatin: hyper condensed chromatin looped domain that is inactive and found in
Interphase. This can further condense into chromosomes for mitosis.
During euchromatin, the DNA is still active, but during heterochromatin, the DNA in so condensed that it is inactive.
Describe the structure and function of the endomembrane system’s components. (8)
The endomembrane system is a process that is used to transport cargo through exocytosis or endocytosis.
Nucleus: nuclear envelope and pores connect to the ER cisternae for cargo to travel out of the nucleus
Endoplasmic Reticulum: organized flattened disks called cisternae that connect to the nucleus
- RER - has ribosomes for protein translation and modification
- SER - does not have ribosomes, so it synthesizes lipids, converts carbohydrates to glucose, and regulates calcium ion levels
Transport Vesicles: shuttles cargo between organelles by budding off lipid membranes, transporting across the cell, and fusing with acceptor membranes to release cargo
Golgi Apparatus: labels proteins with signals to direct cargo to its final destination
- Cis - receives proteins from the ER
- Medial - sugar groups, called oligosaccharides, are added to proteins and lipids or are modified
- Trans - performs final packaging and sorts cargo to its final destination
Endosomes: gather content coming into the cell through endocytosis and sorts it to its final destination
Lysosomes: break down proteins, lipids, and sugars
Peroxisomes: break down molecules the produce hydrogen peroxide in order to neutralize the cell and mitigate damage
Explain how proteins transport into the endomembrane system.
The first step of getting a protein into the endomembrane system is allowing the protein to get inside the lumen of the ER. The location of protein synthesis on the ribosomes of the RER is important because it allows proteins to be transported directly into the endomembrane system, following translation. Translocation is the process of moving proteins into the ER and it occurs in 4 steps. First, the presence of an ER signal sequence is translated as part of the protein. Next , as the signal sequence emerges from the ribosome, it interacts with a signal recognition particle receptor that binds to the ribosome and pauses protein translation. During the pause in translation, the SRP docks onto the ER membrane by interacting with a SRP receptor called the translocon, which allows and facilitates the translocation of the protein into the ER. Translation restarts and once the protein has translated into the ER, the signal peptide sequence is cleaved, translation finishes, and the protein fold inside the lumen.
If the protein is destined to embed in the lipid membrane, the transmembrane signal sequence anchor with be recognized initiating the process of embedding into the lipid bilayer. The transmembrane signal sequence embeds into the lipid bilayer and become the transmembrane domain of the protein once it is mature and functional.
Explain how proteins are folded and modified in the cell.
Once in the lumen, proteins can fold with the help of PDI and BiP. PDI forms disulfide bonds between the thrill groups in the side chain of cysteines to help the protein fold properly and stabilize it. BiP, termed chaperonins help fold polypeptides by binding hydrophobic patches, bringing them together to help them fold into the hydrophobic interior of mature proteins. It does this until it can no longer access hydrophobic patches. Once folded, proteins, lipids, sugars, and functional groups are added to the protein, peptide bonds are cleaved, and the signal sequence at the N-terminus is removed.
Explain the protein structures and provide an example of each.
Primary: linear peptide sequence from N->C terminus (polypeptide chain)
Secondary: either alpha helixes that are coiled with H-bonds between every 4th amino acid, or beta pleated sheets that form rows of amino acids in a parallel or antiparallel manner
Tertiary: 3D structure of a complete protein that was folded by chaperones and disulfide bonds (myoglobin)
Quaternary: multiple tertiary proteins assembled into a complex with subunits (hemoglobin or histones)
Explain the steps to vesicles trafficking.
1a) Cargo selection: signal sequences and receptors on the membrane gather cargo to the area of the membrane that will be turned into a vesicle.
1b) Coat proteins: coat proteins from the cytosol bind to the area on the membrane that will become the vesicle and cause receptors and other proteins with signal sequences to cluster on the surface of the membrane.
2) Budding: coat proteins interact with cytosolic adaptor proteins to form a mesh-like basket that pulls the membrane into a bulging shape that will become the vesicle.
3) Scission: Dynamin cuts the membrane to pinch off the budding vesicle and release is into the cytoplasm.
4) Uncoating: coat and adaptor proteins are disassembled and recycled.
5) Transport: vesicles attach to motor proteins, like kinesin, in the cytosol to move along the microtubules of the cytoskeleton for control of direction and destination.
6) Tethering: at its destination, tether proteins attach to a receptor on the acceptor membrane to find the correct acceptor target proteins
7) Docking: when acceptor target proteins are found, the vesicle docks on the surface.
8) Fusion: the lipid membrane become continuous with the acceptor membrane with the interaction of v-SNAREs and t-SNAREs (v-SNARE = vesicle)
9) Disassembly: remaining tether, fusion, and receptor proteins are disassembled and recycled back to the initial organelle. The cargo is released into the accepting organelle.
Explain the stages of endocytosis.
Endocytosis is the import of cargo from out of the cell into the cell. Initially, Clathrin forms a vesicle initiating invagination of the plasma membrane to form a vesicle that can take cargo from outside of the cell to the early endosome. During uncoating, Clathrin disassembles with the help of cytosolic proteins Auxillin and Hsc 70. The early endosome is made up of vesicles from the plasma membrane and trans golgi network that contain cargo and cargo receptors. Vesicles with M6P and their cargo (proton pumps, LIMPs, and hydrolases) fuse with the endocytic vesicle forming the early endosome. Proton pumps begin to acidify the lumen decreasing the pH to 6.4-6.8 so that the cargo receptors and M6P receptors change shape and release their cargo. Depending on their signal sequences, some cargo and receptors can be sent to storage granules, across the cell, or into the cell. The early endosome then matures into the late endosome where the pH is 5.0-6.0 and receptors and cargo is still recycled and degraded into essential building blocks like sugar and amino acids. When the pH reaches levels lower than 5.0, proteases are activated to convert the late endosome into a lysosome that has a protective glycocalyx layer of LIMPs and glycosylated proteins that protect the lysosome from self degrading of proteases.
Where do each of the coat proteins take cargo? (4)
COP II - shuttles from the ER to the golgi
COP I - shuttles from the golgi back to the ER
Clathrin - used for endocytosis and exocytosis
M6P - transports cargo to the lysosome
