Biology Exam 2

Why do cells need to have a selective barrier between themselves and the outside enviornment

to maintain a stable internal environment (homeostasis) and to control what enters and exits the cells.

What is the definition for lipid

An organic substance that does not dissolve in water but dissolves well in nonpolar organic solvents. Lipids include fatty acids, fats, oils, waxes, steroids, and phospholipids.

Carbon and Hydrogen evenly share electrons due to similar EN. Why is this relevant to the behavior of lipids in water?

This is relevant because since C and H atoms share electrons evenly, they are nonpolar. Lipids contain many CH bonds and so they are largely non polar. Water is polar so lipids do not dissolve well in water because polar and non polar substances dont dissolve well.

Describe in words the general structure of fatty acids.

Carboxyl group attached to a hydrocarbon chain

Difference between a saturated and an unsaturated fatty acid, and what effect it has on overall structure

A saturated fatty acid has no double bonds so it is straight and an unsaturated fatty acid has double bonds meaning it has kinks in it. This means that the overall structure for an unsaturated fatty acid is bent

why do fats made from more saturated fatty acids have a different melting temperature than those with more unsaturated fatty acids?

Saturated fatty acids have no C=C double bonds, meaning that the molecule is straight. The straight chains pack more tightly together, which causes stronger London dispersion forces between molecules. Because the attractions are stronger, more heat is needed to separate the molecules. In unsaturated fatty acids, the kinks prevent the molecules from packing tightly together, which leads to weaker intermolecular interactions.

What is the primary biological role of fat?

To store energy

what are the four components fat is built from

The four components are one glycerol molecule and three fatty acid molecules.

What is another word for fat?

Triglyceride. Remember that a fatty acid is the individual component of the triglyceride.

How are fats different from phospholipids (composition and function)?

Fats primarily store energy and consist of glycerol and three fatty acid chains. Phospholipids form the selectively permeable bilayer of cell membranes and consist of glycerol, two fatty acid chains, and a phosphate-containing polar head.

Five components of phospholipid

Polar head group, phosphate group, glycerol, and two fatty acid chains

What does amphipathic mean

A molecule that interacts with water and that does not interact with water. The polar side will interact w water and the non polar side will not (hydrophobic and hydrophillic)

How does the hydrophobic effect explain the spontaneous reorganization of phospholipids in water to form lipid bilayers, and why will they also form a spherical structure?

Phospholipids have hydrophobic and hydrophilic areas. The hydrophobic tails will cluster together to minimize their exposure to water, and so a lipid bilayer will form. The bilayer can enclose into a sphere, which eliminates any exposure to water. The bilayer can form a sphere to eliminate exposed hydrophobic edges, creating a stable structure.

How is the hydrophobic effect driven by entropy?

When nonpolar molecules come together, there's less hydrophobic surface that is exposed to water, so the surrounding water molecules become less ordered.

Which type of molecules have high permeability through cell membranes, and which kind of molecules have low permeability through cell membranes? Why is this true?

Small, nonpolar molecules have high membrane permeability because they can dissolve in and diffuse through the hydrophobic interior of the phospholipid bilayer. Large polar molecules and charged molecules have low permeability because entering the nonpolar interior is energetically unfavorable.

What is the relationship between the length and saturation of the fatty acid tails of a membrane lipid and the permeability and fluidity of the membrane

Longer and more saturated fatty acid tails pack tightly together, so the fluidity and permeability are low. The shorter and more unsaturated tails pack less tightly together, which increases fluidity and permeability.

How does cholesterol reduce permeability?

It fills gaps in membranes that are created by the kinked lipid tails.

What is meant by membrane fluidity?

how easily phospholipids can move laterally within the lipid bilayer

Does increasing temperature increase or decrease the fluidity and permeability of membranes?

Increasing the temperature will increase the fluidity and permeability of membranes because, since the temperature is increased, the phospholipids will move more, increasing the permeability.

What is diffusion, and how is it entropy-driven?

Diffusion is the movement of molecules from a high concentration to a low concentration. It is entropy-driven because spreading the molecules out increases the number of possible arrangements of the molecule.

Assuming a solute can move directly through a membrane, what direction will it move if there is a higher concentration outside the cell than inside the cell?

It'll move inside the cell.

What if there was a higher concentration inside the cell than outside the cell?

It'll move outside the cell.

Will there be any net movement when the concentrations are equal on both sides?

No, there will be no net movement.

Why is it important to distinguish net movement and movement when referring to a solute moving through a membrane?

Because there is movement, but there is no change in concentration. Solutes are still moving in and out of the cell, but it's in equilibrium.

What is osmosis?

It's a movement of water across a membrane from an area of low solute concentration to high solute concentration.

What does it mean for a cell to be in a hypertonic, hypotonic, or isotonic solution?

If it's hypertonic, then the concentration of solute outside the cell is high. For a cell to be hypotonic, the concentration of solute inside the cell is high, and isotonic is equal inside and outside.

What is an integral membrane protein, and what are the properties the amino acids will have for the parts of the protein that are facing the inside of the membrane?

An integral membrane protein is a protein embedded in the phospholipid bilayer, and the parts of the protein that are facing inside the membrane will be nonpolar.

what are periperal membrane proteins

Proteins that attach to the surface of the phospholipid bilayer but do not penetrate into the hydrophobic layer

Can carbohydrates be attached to the proteins and lipids that reside on the exterior of the membrane?

Yes.

Explain the fluid mosaic model.

It describes the cell membrane as a fluid phospholipid bilayer, which contains proteins and many other molecules. Fluid means the lateral movement of phospholipids and some proteins, and mosaic means that there are many different components embedded in or attached to the membrane.

What are detergents and what do they do

Detergents are amphipathic molecules with hydrophilic heads and hydrophobic tails. Their hydrophobic regions interact with the fatty acid tails of phospholipids, disrupting and breaking apart membranes. Detergents can also surround the hydrophobic regions of transmembrane proteins, allowing these proteins to become soluble in water.

How do solutes with certain properties cross the membrane?

Channel or carrier proteins. Transport proteins are used for ions which requires active transport

How is diffusion of a solute directly through a membrane different from facilitated diffusion across a membrane?

Facilitated diffusion requires channel or carrier proteins that help the solute get through the membrane. There are only certain places in the membrane where that solute can pass through because it needs the protein to help it pass through

Describe the structure of a channel protein.

A channel protein is an integral membrane protein. The membrane-facing side contains nonpolar, hydrophobic amino acids, and the channel-facing side contains polar, charged amino acids that will interact with substances in water.

What two features of a channel can make it selective for specific solutes?

Size and shape
Polarity and Charge

what is channel gating and what is an example of something that can control this

It's the opening and closing of ion channel proteins to regulate movement of solutes across the membrane, and it can be controlled by changes in voltage, the binding of specific molecules, or mechanical forces.

What does protein conformational change mean, and how are these involved in the transport process of a carrier protein like GLUT1?

A protein conformational change is a change in a protein's shape. In Glut1, glucose binds to the carrier protein, which causes it to change its shape and exposes the glucose to the inside of the cell, and then releases the glucose.

The sodium-potassium pump is an example of a primary active transporter. This means that it directly uses energy (usually from ATP) to power the transport of a solute against its electrochemical gradient. Describe the steps in this process. Pay particular attention to how ATP is used to force the conformational changes in this case

The sodium-potassium pump binds 3 Na⁺ ions inside the cell. ATP phosphorylates the pump, causing a conformational change that releases Na⁺ outside. Then 2 K⁺ ions bind, triggering dephosphorylation and another conformational change that releases K⁺ inside. One ATP is used per cycle.

Secondary active transporters still pump solutes against their concentration gradient and still require energy. What is the source of that energy?

The sodium-glucose symporter uses energy stored in the sodium electrochemical gradient to transport glucose against its concentration gradient. Na⁺ moves down its electrochemical gradient into the cell, providing the energy to bring glucose into the cell. The sodium gradient is maintained by the ATP-powered sodium-potassium pump.

Be aware of the fact that the cell can use active transport to establish very different concentrations of ions inside and outside of the cell (table slide 21). This will set up a system where an event (signal) can open a channel that allows ions to quickly flow down their electrochemical gradient and affect the behavior of the cell. This is an important part of how neurons work, for instance

Active transport creates ion gradients using energy. When a signal opens an ion channel, ions flow down their electrochemical gradient, changing the cell's electrical state and potentially triggering a response.

Cell theory

All organisms are made of cells. Cells are the basic units of structure and function in life, and all cells come from pre-existing cells through cell divison

How do prokaryotes replicate cells

binary fisson

What are microtubules and actin filaments

Both are cytoskeletal structures. Microtubules are hollow tubes made of tubulin that help with intracellular transport, cell structure, and chromosome separation. Actin filaments are thin protein fibers that help with cell shape, movement, and contraction.

How do motor proteins, microtubules, and actin filaments function in cargo transport and cell division?

Motor proteins use ATP to walk along microtubules and carry cargo. Microtubules help move chromosomes during cell division. Actin filaments and motor proteins form a contractile ring that splits the cell during cytokinesis.

What is the polarity of microtubules, and what happens at the minus and plus ends?

The minus end originates from the MTOC (microtubule organizing center), while the plus end grows as tubulin proteins are added.

What is the MTOC in animal cells, and what is it composed of?

The MTOC is the centrosome, which contains two centrioles made largely of tubulin proteins, along with other components.

What are the phases of the eukaryotic cell cycle?

Interphase consists of G1, S, and G2. M-phase consists of mitosis and cytokinesis.

What happens during G1, S, and G2 phases of interphase?

G1: Cell grows and performs normal functions, deciding whether to divide. S: DNA is replicated. G2: Cell continues growing, replicates organelles, and prepares for mitosis.

What are cell cycle checkpoints, and why are they important?

Checkpoints ensure that conditions are appropriate before the cell progresses to the next phase. They regulate progression through changes in gene expression and protein activation or inactivation.

What are the phases of mitosis and the major events of each phase?

Prophase: Chromosomes condense and the spindle begins forming. Prometaphase: Nuclear envelope breaks down and spindle microtubules attach to kinetochores. Metaphase: Chromosomes align in the middle. Anaphase: Sister chromatids separate. Telophase: Nuclear envelopes reform and chromosomes decondense.

What happens to DNA amount and chromosome number during S phase?

The total DNA amount doubles, but chromosome number stays the same because each chromosome now consists of two sister chromatids. They are counted separately only after separating during anaphase.

What are sister chromatids and what proteins connect them to each other?

Sister chromatids are identical copies of a replicated chromosome. Cohesin proteins hold them together until separation.

What does cytokinesis accomplish? What is the role of the contractile ring and what is it made of?

Cytokinesis divides the cytoplasm into two daughter cells. A contractile ring made of actin filaments and myosin motor proteins contracts to pinch the animal cell in two.

How many chromosomes do human body cells have before and after DNA replication and mitosis?

Human body cells have 46 chromosomes. After S phase, they have 46 replicated chromosomes (92 chromatids). After mitosis and cytokinesis, each daughter cell has 46 unreplicated chromosomes with genetic content identical to the original cell before S phase.

What are the centromeres of chromosomes? What is the kinetochore complex?

The centromere is the chromosome region where sister chromatids are joined. The kinetochore is a protein complex assembled at the centromere that attaches chromosomes to spindle microtubules.

What is the spindle apparatus and how does it connect to chromosomes?

The spindle apparatus consists of microtubules originating from MTOCs (centrosomes in animals). Spindle microtubules attach at their plus ends to chromosome kinetochores.

How does shortening of microtubules at their plus ends pull sister chromatids to opposite poles?

Tubulin subunits are removed from the plus ends of kinetochore microtubules, shortening them and helping pull the attached sister chromatids toward opposite spindle poles.

How does binary fission in prokaryotes compare to mitosis in eukaryotes?

Prokaryotes replicate their chromosome and separate the copies using protein machinery, followed by division of the cell membrane and wall. Both processes separate genetic material before cell division, but prokaryotes do not undergo mitosis.

How did the experiment involving M-phase promoting factor (MPF) demonstrate regulation of the G2-to-M transition?

Transfer of cytoplasm from an M-phase cell into a cell in G2 can trigger entry into mitosis. This demonstrates that a cytosolic factor, MPF, promotes the transition from G2 to M-phase.

What is the relationship between a cyclin and a cyclin-dependent kinase (Cdk)?

Cyclins are regulatory proteins that bind specific Cdks to regulate their activity. Cdks are kinases that phosphorylate target proteins. Different cyclins pair with particular Cdks to regulate cell cycle transitions.

How are cyclin concentrations regulated during the cell cycle?

Cyclins are synthesized and degraded at particular cell cycle phases. Their changing concentrations help control when specific Cdks can become active.

How is M-phase promoting factor (MPF) activated?

MPF consists of a cyclin and a Cdk. Cyclin accumulates through interphase and binds the Cdk. The Cdk receives activating and inhibitory phosphates. In late G2, a phosphatase removes the inhibitory phosphate, activating MPF.

What does activated MPF do, and how do Cdks phosphorylate proteins?

Activated MPF phosphorylates target proteins to promote entry into M-phase. Cdks use ATP to transfer phosphate groups to amino acids in target proteins, producing ADP and often changing protein shape and activity.

What happens to the cyclin of MPF during M-phase?

The cyclin is rapidly degraded during M-phase, causing MPF activity to decrease.

How do growth factors, cyclin-Cdk complexes, Rb, and E2F regulate the G1-to-S transition?

Growth factors stimulate cyclin and E2F expression. Rb initially binds and inhibits E2F. In late G1, the cyclin-Cdk complex becomes active and phosphorylates Rb, releasing E2F. E2F activates genes required for DNA replication in S phase.

Why is Rb considered a tumor-suppressor gene?

Rb acts as a brake on cell cycle progression by binding and inhibiting E2F. Loss of functional Rb can allow inappropriate progression into S phase and contribute to cancer.

What is the difference between benign, malignant, and metastatic tumors?

Benign tumors grow abnormally but do not invade neighboring tissues. Malignant cancers invade surrounding tissues. Metastatic cancer cells can detach, travel through blood or lymph, and establish tumors in distant tissues.

What are tumor-suppressor genes and proto-oncogenes?

Tumor-suppressor genes normally restrain cell division or protect against abnormal growth. Proto-oncogenes normally promote cell growth and division when appropriate. Mutated proto-oncogenes can become oncogenes that promote excessive growth.

What types of mutations in tumor-suppressor genes and proto-oncogenes promote cancer?

Loss-of-function mutations in tumor-suppressor genes remove cell cycle brakes. Gain-of-function mutations in proto-oncogenes create overactive oncogenes. Cancer generally requires multiple mutations affecting growth control.

What are the learning objectives for meiosis in Chapter 13?

The uploaded study guide refers to separate Chapter 13 learning objectives but does not include them. Review the Chapter 13 objectives supplied in class.

What are the differences between mitosis and meiosis?

Mitosis involves one division, producing two genetically identical daughter cells with the same chromosome number. Meiosis involves two divisions, producing four genetically different haploid cells with half the original chromosome number.

How does meiosis lead to heterogeneity in gametes?

Crossing over during prophase I exchanges DNA between homologous chromosomes. Independent assortment randomly distributes maternal and paternal homologs into gametes. Both produce genetic variation.

What enzyme catalyzes RNA synthesis, and in what direction is RNA synthesized?

RNA polymerase catalyzes RNA synthesis in the 5′ to 3′ direction by adding nucleotides to the RNA's 3′ end.

Does RNA synthesis require a primer?

No. RNA polymerase can initiate RNA synthesis without a primer, unlike DNA polymerase.

How is transcription different from DNA replication in terms of direction and product?

Transcription proceeds in one direction along a gene and produces single-stranded RNA. DNA replication proceeds bidirectionally from origins and produces double-stranded DNA.

How does the mechanism of RNA synthesis compare to DNA synthesis?

The growing RNA's 3′ OH attacks the alpha phosphate of an incoming ribonucleotide triphosphate, forming a phosphodiester bond and releasing pyrophosphate. Unlike DNA synthesis, RNA synthesis uses ribonucleotide triphosphates.

What is the role of sigma factor in prokaryotic transcription?

Sigma factor associates with bacterial RNA polymerase to form the holoenzyme and helps it recognize and bind promoters.

What is the function of a promoter?

A promoter is a DNA region recognized by transcription machinery that directs where transcription begins and which direction RNA polymerase transcribes.

What part of the DNA does sigma factor bind (the name of the regions, not the sequences)?

Sigma factor recognizes the -35 and -10 promoter regions upstream of the transcription start site.

What happens at the +1 site?

The +1 site is the transcription start site, where RNA polymerase begins synthesizing RNA using the DNA template.

How does sigma factor binding determine the orientation of RNA polymerase?

Sigma factor recognizes two promoter regions in a particular orientation. This positions RNA polymerase to transcribe the correct DNA strand in the correct direction.

What happens to the RNA-DNA hybrid as RNA polymerase moves along the DNA?

About 8 base pairs of newly synthesized RNA remain paired with the DNA template inside RNA polymerase. Older RNA separates from the template and exits as a single strand.

How does a hairpin loop followed by uracil bases terminate transcription in prokaryotes?

The hairpin causes RNA polymerase to pause. The following U-rich RNA forms weak A-U base pairs with DNA, allowing the RNA transcript to detach and transcription to terminate.

How does transcription initiation differ between prokaryotes and eukaryotes?

Prokaryotes use RNA polymerase with a sigma factor to recognize promoters. Eukaryotes use numerous general transcription factors to recognize promoters and recruit RNA polymerase.

How many major RNA polymerases are found in eukaryotes?

Three major nuclear RNA polymerases (I, II, and III), each recognizing different promoter types and transcribing different categories of RNA.

How is eukaryotic mRNA processed compared with prokaryotic mRNA?

Eukaryotic pre-mRNA undergoes 5′ capping, splicing, and 3′ polyadenylation. Prokaryotic mRNA generally does not undergo these processing steps.

What are introns?

Introns are sequences transcribed into pre-mRNA that are removed during RNA splicing. The remaining exons are joined together.

What is the spliceosome, and how does it recognize and remove introns?

The spliceosome is a complex containing snRNPs, which include proteins and small nuclear RNAs. Its RNA components base-pair with splice-site and branch-site sequences, allowing precise intron removal and exon joining.

What are the steps of the RNA splicing mechanism?

1. The 2′ OH of a branch-point adenosine attacks the 5′ splice site, forming a lariat. 2. The upstream exon's 3′ OH attacks the 3′ splice site, joining the exons. 3. The intron lariat is released and typically degraded.

What molecule is added to the 5′ end of eukaryotic mRNA during capping?

A modified guanine nucleotide called 7-methylguanosine is added as the 5′ cap.

How is the poly-A tail added to eukaryotic mRNA?

The 3′ end of the pre-mRNA is cleaved, and a series of adenine nucleotides is added to create the poly-A tail.

What are the functions of the 5′ cap and poly-A tail?

Both protect mRNA from exonuclease degradation and improve translation efficiency by helping recruit the mRNA to translation machinery.

What is an aminoacyl-tRNA, and why is it necessary for translation?

An aminoacyl-tRNA is a tRNA covalently attached to its amino acid. It acts as an adaptor that delivers the appropriate amino acid to the ribosome.

What is the structure of tRNA, and how does its anticodon function?

tRNA is approximately 75-95 nucleotides long, with a cloverleaf secondary structure and twisted L-shaped tertiary structure. Its anticodon base-pairs with the complementary mRNA codon.

What enzymes charge tRNAs, and how do they recognize the correct tRNA?

Aminoacyl-tRNA synthetases attach the correct amino acid to tRNAs. Each amino acid has a corresponding synthetase, which recognizes its appropriate tRNAs using identity features, including anticodon-loop contacts.

Why is aminoacyl-tRNA synthetase specificity important for translation?

These enzymes must match the correct amino acid with the correct tRNA. This is the step that connects nucleotide coding information to amino acid identity; later, the ribosome mainly matches codons with anticodons.

How does ATP participate in charging a tRNA, and where is the amino acid attached?

Aminoacyl-tRNA synthetase uses ATP to activate an amino acid, then attaches it to the 3′ OH of the terminal adenosine on the tRNA's CCA arm.

How does wobble allow one tRNA anticodon to bind more than one mRNA codon?

The third codon position pairs less strictly with the first anticodon position. This flexibility permits some nonstandard base pairs, such as anticodon G pairing with codon U or C.

How does inosine at the wobble position affect codon recognition?

Inosine in the first position of a tRNA anticodon can pair with U, C, or A at the third codon position, allowing one tRNA to recognize three different codons.

What is the composition of a ribosome, and why is it considered a ribozyme?

Ribosomes contain small and large subunits made of rRNA and proteins. The large subunit's rRNA catalyzes peptide bond formation, making the ribosome a ribozyme.