Molecular Exam 1

What is the bond type in carbohydrates?

Glycosidic bond

What is the monomer of carbohydrates?

Monosaccharides

What are the polymers of carbohydrates?

Disaccharides and polysaccharides

Where are carbohydrates located in the cell?

Storage/vacuole and decorating lipids/proteins

What is the primary role of carbohydrates?

Molecular identification, protection, and energy production

On which side of membranes are carbohydrates presented?

Only on the surface, not in contact with the cytosol; true for all membrane-bound organelles (e.g., Golgi, ER)

What is the bond type in lipids?

Ester bond

What is the monomer of lipids?

Fatty acid + glycerol/sphingosine

What are the polymers of lipids?

Triacylglycerol/phospholipids

Where are lipids located?

Membranes

What is the primary role of lipids?

Forming semi-permeable membranes

What structural role do lipids play in membranes?

They make up the base of the membrane to which all other molecules attach

What is the bond type in proteins?

Peptide bond

What is the monomer of proteins?

Amino acid

What is the polymer of proteins?

Polypeptide

Where are proteins located?

Everywhere

What is the primary role of proteins?

To perform work

What defines an integral membrane protein?

It spans the entire width of the lipid bilayer

What defines a peripheral membrane protein?

It spans at most only part of the width of the lipid bilayer

What is the bond type in nucleic acids?

Phosphodiester bond

What is the monomer of nucleic acids?

Nucleotides

What is the polymer of nucleic acids?

Oligonucleotides

Where are nucleic acids located?

Nucleus, mitochondria, chloroplasts, cytosol

What are the primary roles of nucleic acids?

Genetic material (making DNA/RNA), energy (ATP and GTP), and regulating cell functions (GTP)

What is the primary structure of a protein?

The chain of amino acids (polypeptide chain)

What is the secondary structure of a protein?

Local folding of the polypeptide chain due to hydrogen bonds (e.g., alpha-helices, beta-strands/sheets, turns)

What is the tertiary structure of a protein?

Folding of secondary structures via disulfide bonds (aka motifs)

What is the quaternary structure of a protein?

Interactions of multiple peptides

What are the two broad strategies for regulating proteins/enzymes?

Availability and Activity

What does availability regulation mean?

Everything is where it needs to be to be used - it is either there or not there

What are the mechanisms of availability regulation?

Gene expression, degradation, compartmentalization, and signaling molecules

What is compartmentalization in enzyme regulation?

When a chemical reaction can only occur in certain areas of the cell

What triggers signaling-molecule-based regulation?

Transmission begins via an external substrate or ligand

What does activity regulation mean?

Adding or subtracting pieces from the enzyme

What are reversible covalent modifications?

Reversibly adding or removing functional groups to activate the enzyme (e.g., lipids, nucleic acids, proteins, carbs, phosphate, sulfate, acetyl, methyl)

How does phosphorylation affect enzymes?

It can be activating or inhibiting, depending on the enzyme

What do kinases do?

Add phosphates

What do phosphatases do?

Remove phosphates

What is proteolytic activation?

Irreversibly cutting enzymes/proteins apart to activate them

What are examples of proteins requiring proteolytic activation?

Digestive enzymes, collagenase, caspases, collagen, blood clotting factors, insulin/hormones

What is allosteric regulation?

Regulation via a different site on the enzyme than where the substrate binds

What is heteroallostery?

When an effector molecule (activator or inhibitor) alters substrate binding

What is homoallostery (cooperativity)?

When each substrate binding alters the efficiency of subsequent substrate binding

What is positive cooperativity?

The next substrate has an easier time binding

What is negative cooperativity?

The next substrate has a more difficult time binding

What are the 3 parts of the Unified Cell Theory?

The cell is the most basic unit of life; all living things are made of at least 1 cell; new cells are made from existing cells

What is the structure of the nucleus?

The nuclear membrane encloses the genome and is contiguous with the ER

What is the function of the nucleus?

DNA and RNA synthesis and ribosomal assembly

What is the structure of the cytoplasm?

Composed of the cytosol and organelles

What is the function of the cytoplasm?

Metabolism occurs here

What is the structure of the plasma/cell membrane?

Outer boundary of the cell; lipid bilayer, proteins, and carbohydrates

What is the function of the plasma/cell membrane?

Protective barrier and first stop in cell signaling

What distinguishes smooth ER from rough ER?

Smooth ER has no ribosomes; rough ER has ribosomes on its membrane

What is the function of the endoplasmic reticulum?

Protein/lipid synthesis, protein folding and quality control, Ca++ storage, and part of cell signaling

What is the structure of the Golgi apparatus?

Stacks/discs of membrane called cisternae

What is the function of the Golgi apparatus?

Protein/lipid modification and trafficking center

What is the structure of lysosomes?

Contain digestive enzymes that function at low pH

What is the function of lysosomes?

Degrade organelles and biomolecules

What is the structure of mitochondria?

Made of 2 membranes, a matrix, and its own genome

What is the function of mitochondria?

Energy metabolism, cell signaling, cell differentiation, cell death

What is the structure of chloroplasts?

2 outer membranes, stroma, and its own genome

What is the function of chloroplasts?

Photosynthesis

What is the structure of peroxisomes?

1 membrane and contains oxidative enzymes

What is the function of peroxisomes?

Oxidation reactions leading to lipid metabolism

What is the structure of the nucleolus?

rRNA and ribosomal proteins, plus regulatory and modifying proteins/RNA

What is the function of the nucleolus?

Making ribosomal subunits

What is the function of Cajal bodies?

Help with splicing transcripts

What is the function of nuclear speckles?

Storage sites for regulatory and repair factors

What is the function of paraspeckles?

Sequester mRNA and proteins on long noncoding RNA

What is the function of Polycomb bodies?

Help silence gene expression

What is the function of PML nuclear bodies?

Regulate cell life and death

When are clastosomes present?

Only when proteasomes are activated

What is the function of Histone Locus bodies?

Assemble histones

What are the components of the cytoskeleton?

Actin/microfilaments, tubulin/microtubules, and intermediate filaments

What is the function of the cytoskeleton?

Cellular shape, mitotic spindle formation, and motion

What are the components of ribosomes?

rRNA and ribosomal proteins, composed of 2 subunits

What is the function of ribosomes?

Protein synthesis/translation

What are the components of the extracellular matrix?

Secreted proteins and sugars

What is the function of the extracellular matrix?

Cell shape and signal transmission

According to endosymbiosis theory, how did the nucleus form?

Loss of the rigid cell wall in an ancient anaerobic archaeon allowed horizontal gene transfer, and the cell membrane folded inward to make a primitive nuclear membrane

According to endosymbiosis theory, what is the mitochondrion?

An engulfed, intact aerobic bacterium

What is the mitochondria-late hypothesis of endosymbiosis?

Mitochondria arose due to eating prey

What is the hydrogen hypothesis of mitochondrial endosymbiosis?

Mitochondria arose from merging symbionts

What is the regulatory nucleotide in G protein signaling?

GTP

What do GTPases do?

Hydrolyze GTP

What do GEFs (Guanine nucleotide Exchange Factors) do?

Regenerate G proteins by replacing spent GDP with fresh GTP

What do GAPs (GTPase Activating Proteins) do?

Stimulate G proteins to hydrolyze GTP, inactivating them

What ultimately regulates when cellular work is done in G protein signaling?

GEF and GAP

What does necessary but not sufficient mean?

A needed part of the whole but not enough by itself (e.g., proteins in cell replication)

What does sufficient but not necessary mean?

Can function on its own but is redundant or unsustainable (e.g., proteins as genetic material)

What does necessary and sufficient mean?

Everything that is needed (e.g., DNA as genetic material)

What are the 4 key characteristics of genetic material?

Replication of self, stable storage of information, expression of information, and variation through mutation

What did Frederick Griffith's experiment show?

Injecting mice with dead virulent smooth strain plus avirulent rough strain killed the mice, and living smooth strain bacteria were found, indicating transfer of genetic info (the transforming principle)

What did the Avery, MacLeod, and McCarty experiment show?

Treating dead smooth strain bacteria with protease, ribonuclease, or deoxyribonuclease and testing for transformation showed only DNase treatment blocked transformation, indicating DNA was the active transforming factor

What was the purpose of the Hershey and Chase experiment?

To determine whether the genetic material was DNA or protein

How did Hershey and Chase label bacteriophages?

With radioactive sulfur (for proteins) and radioactive phosphorus (for DNA)

What did the Hershey and Chase experiment conclude?

DNA is the genetic material, since high radioactivity was found in bacteria infected with phosphorus-tagged phages

What is the Central Dogma of Molecular Biology?

DNA to RNA to Protein (replication, then transcription, then translation)

What are the exceptions to the Central Dogma?

Reverse transcription (RNA to DNA), RNA-directed DNA repair (RNA to DNA), and RNA virus replication (RNA to RNA)

What is a gene?

A region of DNA coding either for the mRNA encoding an amino acid sequence in a polypeptide, or for a functional RNA molecule