Biology Exam 2: Proteins, Nucleic Acids, Cell Structure & Membranes

What determines a protein's primary structure?

The linear sequence of amino acids in the polypeptide chain.

What is protein secondary structure?

Local folding patterns of the polypeptide backbone, stabilized mainly by hydrogen bonds involving the backbone.

What mainly stabilizes protein secondary structure?

Hydrogen bonds involving the peptide backbone.

What largely drives protein tertiary structure in water?

Interactions among R groups, especially hydrophobic effects, along with other R-group interactions.

What is protein tertiary structure?

The overall three-dimensional shape produced by interactions among amino-acid R groups.

What is protein quaternary structure?

The arrangement and interactions of multiple polypeptide subunits in one functional protein.

Why can a single amino-acid substitution change protein function?

Changing an amino acid changes its R-group properties, which can alter interactions, folding, shape, and therefore function.

What amino-acid substitution is used in the lecture's sickle-cell example?

Glutamate (Glu) is replaced by valine (Val).

Why does the Glu→Val substitution in sickle-cell hemoglobin matter?

Valine creates a hydrophobic patch that promotes abnormal hemoglobin interactions and polymerization under low oxygen.

What happens to hemoglobin during sickle-cell polymerization?

Hemoglobin molecules interact and form polymers under low oxygen, contributing to red blood cell shape changes.

What is denaturation?

Loss or disruption of a protein's normal three-dimensional shape.

What conditions can cause protein denaturation?

High temperature, extreme pH, and certain chemicals.

Does denaturation necessarily break the amino-acid sequence?

No. The primary sequence can remain intact even when higher-level structure is disrupted.

What do molecular chaperones do?

They assist proteins in folding properly.

What determines how amino acids interact within a protein?

The chemical properties of their R groups.

What does sequence → folding → shape → function mean?

A protein's amino-acid sequence influences folding, folding produces a particular shape, and shape enables the protein's function.

What are the three components of a nucleotide?

A 5-carbon sugar, a phosphate group, and a nitrogenous base.

What sugar is found in DNA?

Deoxyribose.

What sugar is found in RNA?

Ribose.

Which base does RNA use instead of thymine?

Uracil.

What bond forms the sugar-phosphate backbone of nucleic acids?

Phosphodiester bonds.

What does antiparallel mean for DNA?

The two DNA strands run in opposite directions.

Why does DNA pair one purine with one pyrimidine?

To maintain a consistent width of the DNA double helix.

What are the purines?

Adenine and guanine.

What are the pyrimidines used in DNA?

Cytosine and thymine.

What are the pyrimidines used in RNA?

Cytosine and uracil.

If a DNA strand is given 5'→3', what must you remember when finding its complementary strand in 5'→3'?

The complementary strand is antiparallel, so the complementary sequence must be written as the reverse complement.

What is a major role of DNA?

Long-term storage of genetic information.

What is a major role of RNA?

Transferring genetic information and carrying out functional roles in the cell.

What does mRNA do?

Carries a copied genetic message used to direct protein synthesis.

What does tRNA do?

Carries amino acids during protein synthesis.

What does rRNA do?

Forms structural and catalytic components of ribosomes.

What is the information flow emphasized in the lecture?

DNA sequence → RNA sequence → amino-acid sequence → protein folding/interactions → cellular behavior.

What are the three statements of cell theory presented in the lecture?

Living organisms are composed of cells; the cell is the fundamental unit of life; cells arise from preexisting cells.

What structures are found in all cells according to the lecture?

A plasma membrane, cytoplasm, genetic information, and ribosomes.

What is the surface-area formula for a cube?

Surface area = 6L².

What is the volume formula for a cube?

Volume = L³.

As a cell grows, which increases faster: surface area or volume?

Volume increases faster than surface area.

Why does a growing cell face an exchange problem?

Metabolic demand rises while surface area available for exchange does not increase as quickly as volume.

What cellular processes depend on exchange across the cell boundary?

Nutrient entry, waste removal, gas exchange, and signaling.

What does a low surface-area-to-volume ratio mean for a cell?

There is relatively less surface area available for exchange compared with the amount of cellular volume needing support.

What does a light microscope use to form images?

Visible light.

What is the approximate resolution of a light microscope in the lecture?

About 200 nm.

Can living specimens be viewed with a light microscope?

Yes.

What is TEM especially useful for?

Viewing internal cellular ultrastructure.

What is SEM especially useful for?

Viewing detailed external surfaces.

What is the cytoskeleton?

An internal network of protein filaments that supports cell shape, movement, organization, transport, and chromosome movement.

What are the three major cytoskeletal filament types?

Microtubules, actin filaments, and intermediate filaments.

What are major microtubule functions?

Chromosome movement, cilia and flagella, cell organization, and intracellular transport tracks.

What is a major function of actin filaments?

Cell movement and organization.

What is a major function of intermediate filaments?

Mechanical resistance and structural support.

What do microtubules provide for intracellular transport?

Tracks along which motor proteins can move cargo.

What would happen if kinesin could no longer move along microtubules?

Directed vesicle movement would decline.

Why is compartmentalization important in cells?

It creates distinct spaces where specialized reactions can occur.

What is the general relationship among organelles, trafficking, and cell organization?

Specialized organelles perform particular tasks, while trafficking moves materials to their correct destinations.

What is the main information-processing role of the nucleus?

It contains the cell's genetic information and coordinates access to that information.

What do nuclear pores control?

Selective traffic into and out of the nucleus.

What is the nucleolus responsible for?

rRNA production and ribosomal subunit assembly.

What do ribosomes do?

Synthesize proteins.

Are ribosomes membrane-bound organelles?

No.

What is the difference between free and ER-bound ribosomes?

They are structurally the same; their location is associated with the destination of the proteins they synthesize.

What is rough ER associated with?

Protein production for proteins entering the secretory pathway.

What are major smooth ER functions?

Phospholipid/lipid synthesis, detoxification, Ca²⁺ storage, and some carbohydrate metabolism.

What is the basic job of the Golgi apparatus?

Receive, modify, sort, and ship cellular products.

What does a transport vesicle do?

Moves material between compartments while maintaining separation between those compartments.

What is the secretory pathway for a protein destined for secretion?

Ribosome → rough ER → transport vesicle → Golgi → secretory vesicle → plasma membrane.

What happens to a protein in the Golgi?

It can be modified, sorted, and directed toward its destination.

What is the basic function of lysosomes?

They provide an acidic compartment for macromolecule breakdown and recycling.

What can lysosomes digest?

Macromolecules and material brought into the cell by endocytosis.

What is a central plant vacuole used for?

Storage and maintenance of turgor pressure.

What happens to plant-cell turgor when the central vacuole loses water?

Turgor pressure decreases and the cell becomes less rigid.

What is a food vacuole used for in protists?

Digestion.

What is a contractile vacuole used for in freshwater protists?

Removing excess water.

What features do mitochondria and chloroplasts share?

Multiple membranes, their own DNA, their own ribosomes, and the ability to divide.

What is the main function of mitochondria?

Specialized energy metabolism.

What is the main function of chloroplasts?

Photosynthesis.

What are chromoplasts associated with?

Pigment.

What are amyloplasts/leucoplasts associated with?

Storage.

What are peroxisomes specialized for?

Oxidative reactions and detoxification.

What is the main structural material of the plant cell wall?

Cellulose.

How does the plant cell wall help control expansion?

It provides structural support and limits excessive expansion caused by water uptake.

What is the extracellular matrix (ECM)?

A network outside cells containing proteins and carbohydrates that provides support, attachment, organization, and signaling context.

What is a protein-sorting signal?

Information in or associated with a protein that helps direct it to the correct cellular destination.

How can an amino-acid sequence function as an address?

A particular sequence can be recognized by the cell's targeting machinery and direct the protein to a specific location.

What is co-translational protein targeting?

Targeting and movement into a destination occur while the protein is still being synthesized.

What organelle is the lecture's main example of co-translational targeting?

The endoplasmic reticulum.

What is post-translational protein targeting?

A completed protein is targeted to its destination after translation.

Which organelles are examples of post-translational targeting in the lecture?

Mitochondria, nucleus, chloroplasts, and peroxisomes.

Why does the secretory pathway use vesicles?

Vesicles transfer material between compartments without simply mixing the contents of those compartments.

What is the basic structure of a phospholipid bilayer?

Hydrophilic surfaces face the aqueous environments while hydrophobic regions face inward toward each other.

Why does a phospholipid bilayer form in water?

Hydrophilic portions interact with water while hydrophobic portions avoid water, producing the bilayer arrangement.

In an artificial membrane containing only phospholipids, which listed type of substance crosses most readily?

Small nonpolar molecules such as O₂.

Why do ions generally need membrane transport proteins?

The hydrophobic interior of the bilayer is unfavorable for charged ions.

Why does glucose generally require a transport protein to cross the bilayer?

Its chemical properties make crossing the hydrophobic membrane interior unfavorable.

What are major functions of membrane proteins?

Transport, signaling, enzymatic activity, adhesion, anchoring, and cell identification.

What does the fluid mosaic model describe?

A membrane whose components can move laterally and that contains many different molecular components.

What does 'fluid' mean in the fluid mosaic model?

Membrane components can move within the plane of the membrane.

What does 'mosaic' mean in the fluid mosaic model?

The membrane contains many different types of molecular components.

What is a peripheral membrane protein?

A protein associated with the membrane surface, commonly through noncovalent interactions with lipids or other proteins.

What type of membrane movement is common for membrane components?

Lateral diffusion within the same leaflet.