In what phase of the cell cycle does protein synthesis take place?	Protein synthesis is the process by which cells create proteins by translating genetic information,which occurs during the G1 and G2 phases of the cell cycle.
DNA to RNA. What do we call this process?	The process of converting DNA into RNA is called transcription.
Where does it occur in eukaryotes? In prokaryotes?	In eukaryotes, transcription occurs within the nucleus, while in prokaryotes, it takes place in the cytoplasm.
What enzyme adds nucleotides to the template strand?	The enzyme that adds nucleotides to the template strand is RNA Polymerase, which occurs during transcription.
DNA and RNA have two structural differences. What is the difference in the sugar? In the nucleotides?	DNA uses deoxyribose sugar and thymine, while RNA uses ribose sugar and uracil instead of thymine.
What is messenger RNA?	Messenger RNA (mRNA) is a type of genetic material that carries instructions from DNA to the ribosomes, where proteins are made.
What is ribosomal RNA?	Ribosomal RNA (rRNA) is a type of RNA that forms the core structure of ribosomes and helps in protein synthesis.
What are transfer RNAs?	Transfer RNAs (tRNAs) are molecules that help translate genetic code into proteins by carrying amino acids to the ribosome during protein synthesis.
How is mRNA edited before it leaves the nucleus? distinguish exon from intron.	Before mRNA leaves the nucleus, it is edited by removing non-coding regions called introns and joining the coding regions called exons together.
What is a ribozyme?	A ribozyme is an RNA molecule that has the ability to catalyze chemical reactions, similar to an enzyme.
What is RNAi? How do scientists use it?	RNA interference (RNAi) is a process where small RNA molecules block gene expression, and scientists use RNAi as a tool to study gene function, develop therapies, and understand disease mechanisms.
RNA to Proteins. What do we call the process?	The process by which RNA is used to synthesize proteins is called translation.
Since there are 20 amino acids and there are only 4 nucleotides. It can not be a 1:1 ratio. What is the ratio of nucleotides : 1 amino acid?	The ratio of nucleotides to amino acids is 3:1. This is because each amino acid is coded for by a sequence of three nucleotides, called a codon, in the mRNA.
What do we call this group of nucleotides on mRNA that codes for a single amino acid?	A group of three consecutive nucleotides on mRNA that codes for a single amino acid is called a codon.
How many different ways can 4 letters be arranged in triplets?	If you have 4 distinct letters and want to arrange them in triplets (groups of 3), there are 64 different ways to do so.
Why is the genetic code described as redundant? Is redundancy a good thing? Why?	The genetic code is described as redundant because multiple codons (sequences of three nucleotides) can specify the same amino acid. This redundancy is beneficial as it provides some protection against mutations and allows for flexibility in protein synthesis.
What is the start codon? How many stop codons are there?	The start codon, which signals the beginning of protein synthesis, is AUG, while there are three stop codons: UAA, UAG, and UGA.

Where are the ribosomal subunits put together in the cell?	In eukaryotic cells, ribosomal subunits are assembled within the nucleolus.
What is associated with the ribosome besides RNA?	Besides RNA, ribosomes are also associated with ribosomal proteins, which are crucial for the ribosome's structure, function, and interactions with other molecules during protein synthesis.
What are the three binding sites on a ribosome? In order - first, second and third.	The three tRNA binding sites on a ribosome, in order, are the A site (aminoacyl), P site (peptidyl), and E site (exit).
What type of RNA binds to those binding sites on the ribosome?	On the ribosome, messenger RNA (mRNA) binds to one site, while transfer RNA (tRNA) binds to three specific sites (A, P, and E sites), facilitating protein synthesis by carrying amino acids to the ribosome.
What is the role of tRNA?	tRNA's primary role is to act as an adaptor molecule during protein synthesis, specifically translating mRNA codons into amino acids, ensuring the correct amino acid is added to the growing polypeptide chain.
What do we call the 3 nucleotides at the bottom of the tRNA that bind with the mRNA?	The three nucleotides at the bottom of the tRNA that bind with the mRNA are called the anticodon.
What are the three stages of translation?	The three stages of translation are initiation, where the ribosome and mRNA bind, elongation, where the polypeptide chain grows, and termination, where the process ends.
What codon shows up on the A site of the ribosome during initiation?	The codon that shows up on the A site of the ribosome during initiation is the start codon, which is typically AUG.
What is the longest of the three stages? Why?	The longest stage of translation is elongation because it involves the repeated process of codon recognition, amino acid addition, and translocation of the ribosome along the mRNA.
How much energy is used per peptide bond to make a protein?	The formation of each peptide bond during protein synthesis requires the equivalent of 4 ATP molecules.
At what stage does the protein release factor bind to the mRNA codon? (Note: there are three different protein released factors)	Protein release factors bind to mRNA codons during the termination stage of translation.
What is the difference between the protein release factor and the other tRNAs?	The protein release factor is involved in ending translation by triggering the release of the newly made protein, while other tRNAs bring amino acids to the ribosome during protein synthesis.
Where in the cell does translation take place?	Translation, the process of converting mRNA into a protein, takes place on ribosomes located in the cytoplasm of the cell.
What is a polyribosome?	A polyribosome is a group of ribosomes attached to a single mRNA molecule, working together to synthesize multiple copies of a protein simultaneously.
The endoplasmic reticulum is a membrane continuous with what other membrane?	The endoplasmic reticulum (ER) membrane is continuous with the nuclear membrane.
What do we call the endoplasmic reticulum that has ribosomes attached to it? Note: There are also free (unattached) ribosomes in the cytoplasm.	The endoplasmic reticulum with ribosomes attached to it is called the rough endoplasmic reticulum (RER).
Where do proteins go to get a small sugar attached to them after they are made?	After proteins are made, they travel to the Golgi apparatus to receive small sugar attachments (glycosylation).
In what structure do proteins travel from the ER to the Golgi body?	Proteins travel from the endoplasmic reticulum (ER) to the Golgi body within COPII-coated transport vesicles.
These structures move along microtubule tracks from the ER to the Golgi. What moves them along the tract?	COPII-coated transport vesicles move along microtubule tracks from the ER to the Golgi via motor proteins, specifically dynein and kinesin.
What is the evidence that the “RNA World “came before the DNA World we live in now? (What two functions does RNA have that we currently see in DNA and proteins)	The "RNA World" hypothesis suggests life began with RNA, not DNA, because RNA can store genetic information like DNA and also catalyze chemical reactions like proteins.
What is a mutation? What can cause a mutation?	A mutation is a change in the DNA sequence of an organism, and can be caused by errors during DNA replication, exposure to mutagens (like radiation or chemicals), or even by spontaneous DNA breakdown.
Define point mutation.	A point mutation is a genetic alteration where a single nucleotide base is changed, inserted, or deleted within a DNA or RNA sequence, potentially leading to changes in gene expression or the encoded protein.
Why is an insertion/deletion mutation way worse than a substitution mutation? Use the word “frame-shift” in your explanation.	Insertion/deletion mutations are generally more damaging than substitution mutations because they cause a frame-shift, altering the reading frame of the subsequent codons, leading to a completely different, and likely non-functional, protein sequence.
What is the mutation rate in humans?	The mutation rate in humans is approximately 1 in 10 billion nucleotides per generation.
Why are most point mutations considered neutral? (what percent of the human genome actually codes for proteins, and what often happens when a point mutation occurs on the third nucleotide of a codon).	Most point mutations are neutral because they happen in non-coding regions or don't change the protein. Only about 1-2% of the human genome codes for proteins, and a mutation on the third nucleotide of a codon often doesn’t change the protein.
What is the role of mutations and evolution?	Mutations create genetic variation, which is essential for evolution, as they provide the raw material for natural selection to act upon.
What did Linus Pauling use the amino acid sequence of hemoglobin of three different animals to figure out? (what does mutation rate tell us)?	Linus Pauling used the amino acid sequence of hemoglobin from three different animals to show Mutation rates are proportional to evolutionary distance.
Why are mitochondrial mutation rates used as evidence for human evolution?	Mitochondrial mutation rates are used as evidence for human evolution because they provide a genetic timeline, showing how humans and other species have diverged over time through inherited mitochondrial DNA.

Does every cell in a multicellular organism transcribe the same genes? Why?	No, cells in a multicellular organism typically do not transcribe the same genes, even though they contain the same DNA. This is because different cell types express different sets of genes, leading to specialized functions.
Give an example of a protein that is produced in the cells of the pancreas cells that is not produced in a skin cell.	An example of a protein produced by pancreatic cells but not skin cells is insulin.
What is a transcription factor?	A transcription factor is a protein that helps regulate the transcription of specific genes by binding to nearby DNA.
What is an operon?	An operon is a group of genes in bacteria that are controlled together by a single promoter and regulated as a unit.
What is the promoter site in an operon?	In an operon, the promoter site is a specific DNA sequence where RNA polymerase binds to initiate transcription of the genes within that operon.
What attaches to the promoter site that will transcribe the genes?	The enzyme RNA polymerase and associated transcription factors bind to the promoter site to initiate gene transcription.
What will block the promoter site?	A promoter site can be blocked by repressor proteins binding to specific DNA sequences, such as the operator, which overlaps with the promoter, preventing RNA polymerase from binding and initiating transcription.
What will release it from blocking the promoter site?	Inducers can bind to the repressor, causing it to release from the promoter site and allowing transcription to occur.
What is the “on” switch for the lac operon?	The "on" switch for the lac operon is the presence of lactose.
How many genes (that code for enzymes) are in the lac operon?	The lac operon contains three genes (lacZ, lacY, and lacA) that code for enzymes involved in lactose metabolism.
Regulation of DNA in eukaryotes can be done by histones. What molecule attaches to a histone tail that will prevent the gene from being transcribed (an off switch)?	Methyl groups attach to a histone tail, which can prevent the gene from being transcribed by turning it off.

What tool do scientists use to transfer small amounts of liquids?	Scientists commonly use pipettes to transfer small amounts of liquids, typically less than 10 mL.
What instrument would you use to transfer 5 microliters of a liquid? 120 microliters? 450 microliters?	To transfer 5 microliters, 120 microliters, or 450 microliters of a liquid, you would use a micropipette. 5μl - P20 120μl - P200 450μl - P1000
What tool do scientists use to separate/identify DNA fragments by size?	Scientists use gel electrophoresis, a technique that separates DNA fragments based on size using an electric field, to separate and identify DNA fragments by size.
What is the gel made of?	The gel used in gel electrophoresis is typically made from either agarose or polyacrylamide.
What is the overall charge on a molecule of DNA?	The overall charge on a DNA molecule is negative, due to the presence of negatively charged phosphate groups in its sugar-phosphate backbone.
What pulls the DNA? What goes faster, a small or large fragment of DNA? Why?	An electric field pulls the DNA, with smaller fragments moving faster because they face less resistance in the gel.
Why do you include a DNA marker (ladder)?	A DNA marker (ladder) is included to provide a reference for estimating the size of unknown DNA fragments based on their migration distance in the gel.
What is a plasmid?	A plasmid is a small, circular, double-stranded DNA molecule that is distinct from a cell's chromosomal DNA, naturally found in bacteria and some other organisms, and can replicate independently.
Humans use plasmids as a tool for what?	Humans use plasmids as versatile tools primarily for cloning, transferring, and manipulating genes, as well as for producing proteins and developing gene therapies.
What tool (enzyme from bacteria) do scientists use to cut DNA at specific sites to create sticky ends?	Scientists use restriction enzymes to cut DNA at specific sites, creating "sticky ends" for DNA manipulation and cloning.
What is the first enzyme that cuts DNA discovered in E. coli called?	The first enzyme discovered in E. coli that cuts DNA, also known as a restriction endonuclease, is EcoRI.
What gene do scientists include on a plasmid so you can isolate bacteria on a Petri dish of ampicillin?	Scientists include an ampicillin resistance gene on a plasmid to allow for the isolation of bacteria on a Petri dish containing ampicillin.
What gene (for a protein) do scientists attach to make a molecule glow red?	To make a molecule glow red, scientists often attach the gene for a red fluorescent protein (RFP).
What do we call the process of putting foreign DNA into a bacterial cell?	The process of putting foreign DNA into a bacterial cell is called transformation.
How do we control the expression of rfp in our transgenic bacteria? What “turns on” the arabinose operon in pARA-R plasmid?	You control rfp expression in your transgenic bacteria by adding arabinose to the growth medium.

Protein Synthesis and Genetic Engineering Study Guide