Eukaryotic Cell Unit 1

What are the 5 universal features of cells?

DNA storage, passing genetic information to offspring, processing genetic information, plasma membrane, and energy requirement.

What is the central dogma?

DNA → RNA → protein

What is transcription vs. translation?

Transcription: DNA → RNA.

Translation: RNA → Protein

What is ATP and why is it important?

ATP is the cell's universal energy currency. Cells use energy for growth, reproduction, responding to the environment, and copying/transcribing/translating genetic information.

What is the main difference between DNA and RNA?

DNA has deoxyribose, T, and is double-stranded; RNA has ribose, U, and is generally single-stranded.

What are the three major types of RNA and their functions?

mRNA: carries genetic information.
rRNA: makes up ribosomes.
tRNA: carries amino acids and contains an anticodon for translation.

What is the difference between prokaryotic and eukaryotic cells?

Prokaryotes lack a nucleus and membrane-bound organelles; eukaryotes have a nucleus and membrane-bound organelles.

How can you identify a eukaryotic cell in a picture?

Look for a nucleus and membrane-bound organelles.

Which organisms are prokaryotes and which are eukaryotes?

Prokaryotes: Bacteria and Archaea.
Eukaryotes: Plants, protists, fungi, and animals.

What does the nucleus do?

Contains DNA and is the site of transcription.

What does the rough ER do?

Makes proteins destined for membranes, secretion, or lysosomes.

What does the smooth ER do?

Lipid synthesis and calcium storage.

What does the Golgi do?

Sorts proteins.

What do lysosomes do?

Degrade and recycle cellular materials.

What do peroxisomes do?

Detoxification

What do mitochondria do?

Produce ATP.

What do chloroplasts do?

Use CO₂ and sunlight to make complex carbohydrates.

What is the function of the nucleolus?

Ribosome production.

What is a ribosome's function?

Translates mRNA into a peptide/protein.

What evidence supports the idea that mitochondria and chloroplasts originated from bacteria?

They have double membranes, their own DNA, and reproduce by dividing.

What is the basic idea of eukaryogenesis/endosymbiosis?

An archaeal host cell engulfed bacteria that became symbiotic and eventually evolved into organelles such as mitochondria and chloroplasts.

What must you include when drawing eukaryogenesis?

Archaea, bacteria, mitochondria, chloroplast, nuclear DNA, mitochondrial DNA, chloroplast DNA, nuclear envelope, and membrane.

What are the three components of the cytoskeleton?

Microfilaments, intermediate filaments, and microtubules.

What are microfilaments made of and what do they do?

Actin; involved in cell movement and cytokinesis.

What do intermediate filaments do?

Provide stability; examples include keratin and lamins.

What do microtubules do?

Move vesicles, position organelles, and pull chromosomes during cell division.

How do you distinguish the three cytoskeletal components?

Microfilaments = actin/movement
Intermediate filaments = stability
Microtubules = transport/chromosomes

What is the difference between cytosol and cytoplasm?

Cytosol = fluid portion.
Cytoplasm = entire cell contents excluding the nucleus.

What are proteins made of?

Amino acids connected by peptide bonds.

What is primary protein structure?

The unique sequence of amino acids; amino acids are connected by peptide bonds.

What is secondary protein structure?

α-helices and β-pleated sheets, held together by hydrogen bonds between the protein backbone.

What is tertiary protein structure?

The overall 3D folding of a protein, stabilized by hydrogen bonds, electrostatic attractions, hydrophobic interactions, and disulfide bonds.

What is quaternary protein structure?

Multiple protein subunits functioning together.

How do you identify an α-helix vs. β-sheet?

α-helix = spiral/coil.
β-sheet = folded sheet/strand structure.

What is a disulfide bond?

A covalent bond between two cysteine side chains; formed in the rough ER.

What is a protein domain?

A structural unit of a protein that folds independently.

What do chaperone proteins do?

Help proteins fold correctly by interacting with hydrophobic regions and making proper folding more reliable.

Why does protein structure matter for protein function?

A protein's amino acid sequence determines its folding and 3D shape, and its shape allows it to perform its specific function.

What is an enzyme?

A catalyst that speeds up a reaction without being consumed.

How do enzymes speed up reactions?

They lower activation energy and stabilize the transition state.

What can an enzyme NOT do?

It cannot make a reaction spontaneous; it lowers activation energy.

What is the difference between competitive and allosteric regulation?

Competitive: molecule competes for the active site.
Allosteric: molecule binds somewhere other than the active site and can activate or inhibit the protein.

What is phosphorylation, and which amino acids can be phosphorylated?

Phosphorylation adds a phosphate group using ATP. The amino acids are serine, threonine, and tyrosine (STY). Kinases add phosphate; phosphatases remove it.

How does a GTPase work, and what is an example?

The whole GTP molecule binds and changes the protein's conformation; GTP hydrolysis to GDP causes another conformational change. Ras is an example.

What is an RNA nucleotide made of?

Ribose sugar + phosphate + nitrogenous base (A, U, G, or C).

How is RNA structurally different from DNA?

RNA is generally single-stranded, contains ribose and U instead of T, and can fold into complex 3D shapes.

What determines the shape of an RNA molecule?

Its nucleotide sequence.

What are the three major types of RNA?

mRNA, rRNA, and tRNA.

What does RNA polymerase do?

Synthesizes RNA by adding ribonucleotides to the 3′ end.

Does RNA polymerase need a primer?

No. It can start transcription from scratch.

What is a promoter?

A DNA region where transcription machinery assembles to begin transcription.

What does TBP do?

The TBP subunit of TFIID recognizes and binds the TATA promoter.

What are general transcription factors?

Proteins that help RNA polymerase assemble and initiate transcription at the promoter.

What does TFIIH do?

Uses ATP to separate DNA strands and phosphorylates the C-terminal tail of RNA polymerase.

Why is phosphorylation of RNA polymerase's C-terminal tail important?

It allows RNA polymerase to be released from the general transcription factors and begin transcription.

What are transcriptional activators?

Regulatory proteins that bind enhancer regions of DNA and promote transcription.

What does Mediator do?

Connects and communicates between activators, general transcription factors, and RNA polymerase.

What role does chromatin remodeling play in transcription?

It changes chromatin structure to make DNA more accessible to transcription machinery.

What three major processing events occur to eukaryotic pre-mRNA?

5′ cap, 3′ poly-A tail, and RNA splicing.

What is the 5′ cap?

A modified guanine added to the 5′ end of mRNA.

What is the poly-A tail?

A stretch of about 150–250 adenines added to the 3′ end of mRNA.

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

Increase RNA stability and help with nuclear export/translation recognition.

Is the poly-A tail encoded directly in DNA?

No. It is added to the RNA after transcription.

What are exons and introns?

Exons: expressed sequences retained in mature mRNA.
Introns: sequences removed during splicing.

What is the spliceosome?

A complex of small nuclear RNAs and proteins that removes introns and joins exons.

What is a ribozyme?

Catalytic RNA.

What happens at the branch point during splicing?

An adenine at the branch point helps create a loop in the intron during its removal.

What is alternative splicing?

Different combinations of exons can be joined to produce different proteins from the same gene.

Why is alternative splicing important?

It increases the coding potential of genes and allows production of different proteins.

How does mature mRNA leave the nucleus?

It passes through the nuclear pore complex.

What proteins help recognize/export mature mRNA?

Poly-A binding proteins, cap-binding proteins, and exon junction complexes.

What are the three main components required for translation?

mRNA = message; ribosome = machine; tRNA = adaptor.

What does tRNA carry?

An amino acid and an anticodon that recognizes an mRNA codon.

What is the structure of a tRNA?

It has a characteristic folded/cloverleaf structure, with the amino acid attached to its 3′ ACC end.

What is the wobble position?

The third position of the codon/anticodon interaction where non-standard base pairing can occur for some tRNAs.

What does aminoacyl-tRNA synthetase do?

Covalently attaches the correct amino acid to its corresponding tRNA.

How many aminoacyl-tRNA synthetases are there?

20, one for each amino acid.

Why is tRNA charging important?

It ensures the correct amino acid is attached to the correct tRNA before translation.

What are the A, P, and E sites of the ribosome?

A = accepts aminoacyl-tRNA
P = peptide bond/peptidyl site
E = exit

What does the small ribosomal subunit do?

Correctly matches mRNA codons with tRNA anticodons.

What does the large ribosomal subunit do?

Catalyzes peptide bond formation.

Why is the ribosome considered a ribozyme?

RNA in the ribosome catalyzes peptide bond formation.

What codon starts translation and which amino acid does it specify?

AUG → methionine.

Where does the initiator tRNA bind?

The P site of the small ribosomal subunit.

What happens during translation elongation?

tRNA binding → peptide bond formation → large-subunit translocation → small-subunit translocation.

What do EF-Tu/EF1 and EF-G/EF2 do?

They are elongation factors that use GTP hydrolysis to improve translation efficiency/accuracy and help move the ribosome.

What are the three stop codons?

UAA, UAG, UGA.

What happens when a stop codon reaches the ribosome?

A release factor binds, water cleaves the bond, the peptide is released, and the ribosomal subunits dissociate.

What are major ways gene expression can be regulated?

Transcription factors, chromatin changes, RNA splicing, RNA degradation, RNA lifespan, protein folding/modification, protein lifespan, and protein degradation.

What holds nucleotides together in a DNA strand?

Phosphodiester bonds.

What holds the two DNA strands together?

Hydrogen bonds between complementary bases.

What does antiparallel mean?

The two DNA strands run in opposite directions: one 5′→3′ and the other 3′→5′.

What are purines vs. pyrimidines?

Purines: A and G (two rings).
Pyrimidines: C and T (one ring).

What is a gene?

A functional unit of DNA that can encode a protein or RNA.

What are the three important chromosome regions discussed in lecture?

Origin of replication, telomeres, and centromere.

What is the origin of replication?

The location where DNA replication begins.

What are telomeres?

Repetitive DNA sequences at the ends of chromosomes.

What is the centromere?

Specialized chromosome DNA where the kinetochore attaches and helps organize chromosome movement during mitosis.

What is chromatin?

DNA organized with histone and non-histone proteins.

What is a nucleosome?

DNA wrapped around a histone protein complex.