Lecture 3 genetics

Starts in Lecture 2 slides

x-ray

_-_ was commonly used in old-fashioned Sanger sequencing to visualize the radioactive DNA fragments

5,3

When you read a Sanger sequencing gel from bottom to top, you are reading it in the 3/5 to 3/5 direction

electric

In modern Sanger: An _ field pulls the negatively charged DNA through a capillary electrophoresis, and smaller DNA pieces, of their own fluorescent color, reach the detector first

transcription machinery

a general term used to describe the proteins/molecules that work together to carry out transcription, including RNA polymerase, a sigma factor (prokaryotes), general transcription factors (eukaryotes), activators/repressors, etc.

expression

the accuracy of the consensus matches and the appropriate spacing ultimately influence the level of gene _

old, modern

Old/Modern Sanger identifies bases using radioactivity + separate A/T/G/C lanes; Old/ modern Sanger identifies them using different fluorescent labels.

basal promoter

The _ promoter is the short region of DNA upstream of the +1 start site where basic transcription machinery assembles (like proteins, but are not technically apart of the basal promoter region)

TATA-binding protein, general

this is apart of one of the_ transcription factors, TFIID, which assembles first onto the TATA box. then, other _transcription factors assemble, then recruiting RNA polymerase II, completing the initiation complex and beginning the transcription process at +1

regulatory

a type of transcription factor that is responsible for affecting how much/when/where transcription occurs, and includes activators and repressors

general

a type of transcription factor that help RNA polymerase II initiate transcription

Yes

Can enhancers/silencers be located in introns?

intron

Enhancers located in an _ of a gene being transcribed means that the enhancer DNA sequence will be copied into the pre-mRNA along with the rest of the intron, but be spliced out with the mature mRNA

Coactivator

a type of protein associated with helping enhancer proteins (activators) to interact with the basal promoter machinery

transcription, translation

_ occurs in the nucleus, whereas _ occurs in the cytoplasm

nucleus

in prokaryotic cells, there is no physical separation of the processes due to a lack of a _

5

To which end (5 or 3 prime) of RNA is the 7-methylguanosine nucleotide added to?

poly-A tail

What is the name of the end where a bunch of adenines are added?

Poly(a) polymerase

Which enzyme adds the adenines in the poly-A tail?

gene

Introns are transcribed from DNA to pre-mRNA because like the exons, they are apart of the _ in DNA

domains

what are the names of sections of a protein that have different roles, contributing to what the protein overall can do?

exons

_ roughly correspond to protein regions that have different roles

ex: one may encode a protein region that binds to another molecule

alternative splicing

this process allows different versions/isoforms (different structure/location/interaction/function) of a protein to be produced from the same gene

Domain

An independent folding unit of a protein

intronic

You don’t have to make precise joins between DNA segments as rearrangements of exons occurs due to large stretches of _ sequences

5, 3

Alternative splicing occurs in the _ to _ prime directions, which means that exons cannot be randomly rearranged in order (downstream exon cannot end up before more upstream exons)

stress

In a particular _-response gene, the intron remains in the processed RNA (not necessarily mature mRNA yet), and is not immediately spliced out. The functional protein is not produced until this occurs in the cell

termination, 5, poly-a, splicing

After RNA polymerase ends at the _ signal, it undergoes RNA processing, including adding the _’ cap, _-_ tail, and _, to get you to mature mRNA

promoter, start codon

In DNA, the _ tells transcription machinery where transcription beings, and in mRNA, the _ _ tells translation machinery where protein coding begins

AUG, methionine

the codon, _ ,encodes _, which is often the first amino acid in a newly synthesized protein. However, this can be removed from the finished/mature protein

codon

this is a set of 3 RNA nucleotides that specifies an amino acid or a stop signal during translation

transcription

RNA polymerase is mainly for transcription/translation

amino acid

A codon encodes a _ _

universal

the genetic code is nearly _, meaning that the same mRNA codons correspond to the same amino acids in different organisms. However, there are some exceptions in mitochondria and certain microbes like archae bacteria

common ancestry

the concept that organisms evolved from shared ancestors

genetic code

this likely developed in life’s history and was inherited by descendant organisms, explaining why many organisms use these rules

CRISPR

a genome editing process where a particular DNA sequence can be targeted and cut (leading to deletion/modification/insertion of genetic material), which was initially discovered in bacterial defense mechanisms against foreign DNA, but is now used in human genomes

false

True or false: AUG codons only ever encode the first amino acid of a protein sequence

Kozak

For the ribosome to know which AUG to start at, there are _ consensus sequences around the AUG codon that help begin translation

Yes

If a start codon AUG is mutated, could the ribosome start translation at a more downstream AUG if it has a Kozak consensus sequence?

No

Does the ribosome directly bind to AUG when doing translation?

proteins

_ can interact with untranslated regions (UTRs) of mRNA to regulate translation (promote or inhibit it), sequester mRNA to temporarily prevent translation, or control mRNA degradation.

polycistronic

For _ mRNA, the ribosomes can either independently initiate translation at different protein-coding regions. Or some parts of the ribosome may remain associated with the mRNA, and it can continue at another downstream start codon

operon

the term for a group of genes that are regulated and transcribed together to make polycistronic mRNA

monocistronic, polycistronic

polycistronic/monocistronic mRNA is found in eukaryotes, and polycistronic/monocistronic mRNA is found in prokaryotes

eukaryotes, prokaryotes

monocistronic is beneficial for _ in order to better regulate each mRNA (amounts/efficiency), but polycistronic is beneficial for prokaryotes in order to generate multiple proteins quickly

redundancy

term that means: More than one codon can specify the same amino acid.

unambiguous

term that means: Each individual codon specifies only one amino acid (or a stop signal) in the standard genetic code.

No

Do STOP codons encode an amino acid?

No

Are all amino acids encoded by multiple codons?

release factor, polypeptide

When a ribosome encounters a stop codon, a _ _ binds, triggering the release of the completed _ . Translation then terminates, and the ribosomal components are recycled.

nonsense mutation

the mutation where a codon that normally encodes an amino acid instead encodes a premature stop codon, causing the ribosome to terminate translation early and potentially produce a shortened

polypeptide

a chain of amino acids connected by peptide bonds

DNA

Nonsense mutations are often a result of DNA/RNA polymerase errors

silent mutation

the mutation that occurs when the codon is changed, but the amino acid encoded remains the same

missense mutation

the mutation that occurs when the codon changes and produces a different amino acid, which may or may not have a major effect on the protein and its interactions

peptide

proteins are made up of chain(s) of amino acids, which are joined by _ bonds

charged

At physiological pH, are the groups attached to the alpha carbon (COOH and NH2) typically charged or uncharged?

R

Different _ groups are associated with different chemical properties, making amino acids interact differently with each other or the environment, thus affecting polypeptide folding, finally giving proteins different structures and functions

Negatively, positively

Acidic R groups are typically positively/negatively charged at physiological pH, whereas basic R groups are typically positively/negatively charged

cysteine, disulfide

Sulfhydryl groups on the _ amino acid, when interacting, form covalent _ bonds

phosphorylation

Hydroxyl groups on amino acids can undergo _, which can change the protein interactions and functions

Negative

A phosphate group has a positive/negative charge, which when added to an OH group, can change its chemical properties and protein interactions

dehydration

Amino acids undergo a _ reaction, which links the amino and carboxy groups through peptide bonds

dipeptide

What is the term for two amino acids joined by one peptide bond?

N, C

Polypeptides are synthesized from the C/N terminus towards the C/N terminus end

tRNA

What is the name of the small RNA molecule that delivers amino acids to the ribosome during translation?

A-site

What is the name of the location on the ribosome where the aminoacyl-tRNA is accepted?

covalently

An amino acid is _ attached to the 3’ CCA terminus