BIO 1A03 MIDTERM - Module 1 and 2: Cell Structure, Metabolism, and Gene Expression

Vocabulary practice flashcards generated from lecture notes

The population of microorganisms or microbes residing in a specific environment, visible only under a microscope.

Microbiome

Streptococcus salivarius

A normal inhabitant of the upper respiratory tract and oral cavity that contributes to the formation of dental plaque.

Staphylococcus haemolyticus

A bacterial species residing on skin that can be pathogenic if it enters the body.

Bacteroides thetaiotaomicron

An intestinal bacterium that aids in the breakdown of plant material in the digestive tract.

Endomembrane System

A group of membrane-bound organelles in eukaryotic cells—including the endoplasmic reticulum, Golgi apparatus, and lysosomes—that perform lipid and protein synthesis.

Endosymbiotic Theory of Organelle Evolution

The theory that key eukaryotic organelles, specifically mitochondria and chloroplasts, originally evolved from independent prokaryotic bacteria that were engulfed by ancestral eukaryotic cells.

Photosynthesis

The process by which plant cells convert light energy into chemical energy, described by the equation $6\text{CO}_2 + 12\text{H}_2\text{O} + \text{light energy} \rightarrow \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{H}_2\text{O} + 6\text{O}_2$.

Cellular Respiration

The process of releasing chemical energy stored in the bonds of carbohydrates in plant and animal cells in the form of ATP.

Glycolysis

An aerobic metabolic process occurring in the cytoplasm that splits glucose into two pyruvate molecules, yielding a net gain of $2\text{ ATP}$ and $2\text{ NADH}$.

Krebs Cycle

The stage of cellular respiration in the mitochondrial matrix that processes acetyl CoA and yields $6\text{ NADH}$, $2\text{ ATP}$, $2\text{ FADH}_2$, and $4\text{ CO}_2$ per glucose molecule.

Proton-motive force

An electrochemical gradient established during electron transport by pumping protons ($\text{H}^+$) into the intermembrane space.

Monosaccharides

Simple sugars—such as glucose, fructose, and galactose—that polymerize via glycosidic linkages to form disaccharides and polysaccharides.

Polysaccharide

A complex carbohydrate polymer used for energy storage, such as starch in plant cells and glycogen in animal cells.

Fluid Mosaic Model

A structural model of the cell membrane describing phospholipids and embedded proteins as capable of moving laterally within the lipid bilayer.

Aquaporins

Channel proteins exclusively permeable to water that facilitate the rapid passage of large volumes of water across the cell membrane.

Osmosis

The movement of water across a membrane from a solution of lower solute concentration (hypotonic) to a solution of higher solute concentration (hypertonic).

Tonicity

The ability of an extracellular solution to make water move into or out of a cell by osmosis, classified into hypertonic, isotonic, and hypotonic states.

Active Transport

The transport of solutes across a membrane against their concentration gradient (from low to high concentration), fueled by energy from ATP hydrolysis.

Primary Active Transport

A mode of active transport that directly uses energy derived from the hydrolysis of ATP to transport molecules against a concentration gradient.

Secondary Active Transport

A mode of active transport that indirectly uses ATP by leveraging an established electrochemical gradient to move solutes.

Porin Proteins

Amphipathic barrel-shaped membrane proteins with a hydrophilic core that facilitate water transport across the cell membrane.

Nucleolus

A specialized structure within the eukaryotic nucleus where ribosomal RNA (rRNA) is transcribed.

Condensation Reaction

A chemical reaction that polymerizes monomers (such as amino acids) by removing a water molecule.

Hydrolysis

A chemical reaction that breaks polymers apart into individual monomers by the addition of water molecules.

Primary Structure

The unique sequence of amino acids in a polypeptide strand translated from mRNA and held together by covalent peptide bonds.

Secondary Structure

Localized folding patterns in a polypeptide chain, such as alpha helices and beta pleated sheets, stabilized by backbone hydrogen bonding.

Tertiary Structure

The overall three-dimensional shape of a polypeptide resulting from interactions between R-groups (side chains), which determines protein function.

Quaternary Structure

The overall protein structure that results from the combination and interaction of multiple polypeptide tertiary subunits.

Molecular Chaperones

Proteins that bind to hydrophobic regions of nascent polypeptide chains to ensure correct protein folding.

Signal Recognition Particle (SRP)

A protein-RNA complex that binds to a signal sequence at the amino-terminal end of a growing polypeptide chain and halts translation until bound to the SRP receptor on the ER membrane.

Trans Face

The exit face of the Golgi apparatus that forms new transport vesicles and releases modified proteins outside the cell or to other organelles.

Plasmids

Small, circular DNA molecules in prokaryotes carrying 1-2 non-essential genes (such as antibiotic resistance) that replicate independently and can be transferred between cells.

Transformation

A change in cellular behavior or phenotype resulting from the uptake and incorporation of exogenous genetic material from outside the cell.

Chromosome

A double-stranded DNA molecule associated with proteins and RNAs; eukaryotic chromosomes are large and linear, while prokaryotic chromosomes are small and circular.

Phosphodiester Linkage

The covalent bond formed through a condensation reaction that links the sugar and phosphate groups of adjacent nucleotides in a nucleic acid chain.

Transcription

The synthesis of an RNA molecule from a DNA template strand catalyzed by RNA polymerase.

Promoter

A specific regulatory DNA sequence where RNA polymerase and transcription factors attach to initiate RNA synthesis.

5' Cap

A modified 7-methylguanosine nucleotide added to the 5' end of primary mRNA transcripts in eukaryotes to protect against degradation and aid in ribosome attachment.

Poly(A) Tail

A string of 150-200 adenine nucleotides added to the 3' end of eukaryotic primary mRNA following recognition of the polyadenylation signal sequence ($\text{AATAAA}$).

Spliceosome

A molecular machine composed of five small ribonucleoproteins (snRNPs) that recognizes splice sites to excise introns and splice exons together.

Introns

Non-coding regions of a primary RNA transcript that are excised during pre-mRNA processing.

Exons

Coding regions of a primary RNA transcript that remain after splicing and are translated into the amino acid sequence of a protein.

Sigma Factors

Prokaryotic initiation factors that facilitate the binding of RNA polymerase to specific promoter sequences, such as the -10 and -35 regions.

Rho-independent Terminator

A prokaryotic termination signal containing inverted repeats that fold into a GC-rich hairpin loop, pausing RNA polymerase and releasing the RNA transcript.

Rho-dependent Termination

A prokaryotic termination process where Rho protein binds a rut site on the transcript and uses ATP energy to track along mRNA and disassemble the transcription complex.

Codon

A sequence of three nucleotides in mRNA that specifies a particular amino acid or translation stop signal.

Open Reading Frame

The protein-coding region of an mRNA sequence that is read in triplets from start codon to stop codon.

Translation

The process by which ribosomes decode mature mRNA triplets to assemble a specific sequence of amino acids into a polypeptide chain.

Four Main Cellular Macromolecules

1. Nucleic acids: store and transmit genetic information.

2. Proteins: carry out structural and catalytic cellular tasks.

3. Carbohydrates/Polysaccharides: serve as structural components and energy stores.

4. Phospholipids: form the cell membrane boundary.

Factors Influencing Membrane Fluidity

1. Fatty acid saturation: double bonds of unsaturated fatty acid create kinks that increase fluidity.

2. Chain length: shorter carbon chains pack less tightly, increasing fluidity.

3. Temperature: higher temperatures increase fluidity.

4. Cholesterol: buffers fluidity, keeping membranes fluid at low temperatures and stabilized at high temperatures.

How can we determine R-group polarity in terms of structure?

nonpolar/hydrophobic R-groups often feature aromatic benzene rings or nonpolar hydrocarbon chains that aggregate away from water, whereas polar/charged hydrophilic R-groups form hydrogen or ionic bonds in aqueous environments.

Free Ribosomes

Ribosomes suspended in the cytosol that translate proteins destined to function within the cytosol or be targeted to non-endomembrane organelles like the nucleus, mitochondria, or chloroplasts.

Chaperonins

Complex protein structures that sequester nascent polypeptide chains inside an isolated cavity, providing a protected environment for proper folding without improper aggregation or external interference.

Function of RNA Polymerase I

Transcribes genes for rRNA (Ribosome, site of protein synthesis)

What is the coding strand and what are the other terms for it?

The non-template strand is identical in sequence to the mRNA (except U for T) and is called the coding strand, sense strand, or plus (+) strand.

What is Rho-dependent termination

Rho-dependent termination uses the Rho protein binding to a rut site, moving along mRNA using ATP hydrolysis to unwind the RNA-DNA complex.

Properties of the Genetic Code

The genetic code is redundant (multiple distinct codons specify the same amino acid) and unambiguous (a specific codon specifies only one amino acid).

Frameshift Mutation

An insertion or deletion of a number of nucleotides not divisible by 3, altering the open reading frame and shifting how subsequent nucleotide triplets are translated into amino acids.

What is Rho-independent termination?

Rho-independent termination uses inverted repeats that form a GC-rich hairpin loop to pause RNA polymerase and release the RNA.

Non-coding strand

The strand read by RNA polymerase is called the template strand, non-coding strand, antisense strand, or minus (-) strand.

What molecules can and can’t pass through the cell membrane?

CAN: small non-polar molecules and gases

CAN’T: large molecules, charged ion, large amounts of water

What does it mean when a phospholipid bilayer has low permeability?

Less saturated fatty acids and more cholesterol

What does it mean when a phospholipid bilayer has high permeability?

More unsaturated fatty acid and less cholesterol

What happens in the RER during protein synthesis?

Undergoes final adjustments. Creates transport vessicle that delivers the protein to the golgi apparatus

What occurs in the golgi apparatus during protein synthesis

Carbohydrate chains added or modified, which act like shipping labels for where the protein needs to go. Final modifications are done here.

Protein is released outside the cell through trans-face through a vessicle

Free ribosomes produce…

proteins that are meant to function inside the cell

Bound ribosomes produce…

proteins that are able to enter into the RER

what happens in the sodium potassium pump

Na and K move from areas of low concentration to high concentration (against the gradient). Na moves out of cell and K moves in the cell.
For every 3 Na, 2 K is pumped out

How do deoxyribose and ribose sugar differ

on the 2’ carbon of deoxyribose sugar, there is an H vs. on a ribose sugar, there is an OH