Lecture 2 genetics

Huntington’s

What is the name of the progressive disease, caused by neuronal damage, that causes movement, thinking/cognition, and mood and behavior?

HTT

Which gene includes CAG repeats within the DNA sequence associated with Huntington’s disease?

polyglutamine

What is the name of the CAG repeat stretch within the Huntingtin protein?

misfolding/aggregation

What does having too many glutamines in the polyglutamine region lead to for the protein?

CAG

Does the coding strand contain CAG or GTC repeats for Huntingtin proteins?

3, 5

RNA polymerase reads the template strand in the _ to _ direction, encoding a single stranded mRNA, which is built in the opposite direction

autosomal dominant

What is Huntington’s considered that only one disease-causing HTT allele is sufficient?

• ex: one allele has 45 CAG repeats and another has 20 CAG repeats

heterozygous

the name of when a person has two different versions/alleles of a gene

• 1 allele from mom and one from dad

allele

the name for a version of a gene

• ex: one allele has 20 CAG repeats, the other has 45 repeats

autosomal

term for gene is not on a sex chromosome

chromosome

DNA + associated proteins to help packing (histones)

pcr

_ is a method that can be used to determine the number of CAG repeats and whether an expanded HTT allele is present

diploid

What are you considered since you receive one allele from mom and one from dad?

phosphate

The _ groups give DNA an overall negative charge

neg, pos

What direction does DNA migrate in the agarose gel? pos/neg electrode to pos/neg?

DNA ladder

what is the term for the “ruler” that has known sizes/lengths of DNA fragments that can be used to estimate sizes based on the migration of DNA in agarose gel?

salts, voltage

Buffers, which are added to agarose powder, contain _ that allow the buffer to conduct an electric current with the application of a _

heat, mold

_ is applied to the agarose and buffer mixture so that the agarose dissolves, and is poured into a _ where it cools and solidifies as a gel

1

If alleles are the same size, they will create 1 or 2 bands in the agarose gel?

2

If someone is heterozygous, they may produce 1 or 2 product(s)

DNA replication, transcription

_ _ is the process in which both DNA strands act as templates to copy DNA before cell division, producing 2 complete ds DNA molecules, while _ is the process in which DNA is used to make RNA< which can then be used to make proteins

PCR, gel electrophoresis, sanger sequencing

_ amplifies DNA, _ _ separates DNA sizes, and _ _ determines the order of DNA

DNA sequencing

_ _ is typically used to be able to detect the change of a single mutant base

ddNTPs, H, OH

_ are nucleotides that have an _ instead of a _ attached to the 3’ carbon

small

There is a _ percentage of ddNTPs added compared to regular dNTPs, in order to stop at different positions and get different sized DNA fragments, telling you where a certain base occurs in the sequence

Sanger

In original _ method, you can separate all of the fragments based on size via gel electrophoresis in different lanes

fluorescent labels

In current Sanger sequencing, _ _ are used to determine the lengths of DNA fragments without the need for lanes

original sanger sequencing

process by which separate reactions containing different ddNTPs create different-length DNA fragments → products are put into separate A, T, G, C lanes of a sequencing gel → electrophoresis separates fragments by size → radioactive labeling allows the DNA fragments to be seen/detected

Modern Sanger sequencing

process by which each ddNTP has a different fluorescent label, and you can put 4 types into the same reaction. It uses electrophoresis but not with agarose gel + buffer

capillary

the type of electrophoresis used in current Sanger sequencing that separates DNA fragments based on sizes and uses a laser/ detector to detect their fluorescent labels

chromatogram

Modern Sanger sequencing utilizes a _, which is generated by a computer and demonstrates different peaks, allowing you to determine the DNA sequence

nucleotides

The special additions to the _ added in Illumina sequencing have 1. fluorescent labels and 2. reversible blocking abilities

Sanger, Illumina

The primary difference between Illumina and Sanger sequencing is that _ has permanent chain-terminating nucleotides, whereas _ has temporary blocking groups to prevent nucleotide additions

adapters

_ are short, known DNA sequences added to the ends of the DNA fragments, which are randomly cut from the long DNA in Illumina sequencing. This allows the DNA fragments to attach to the glass flow cell, allowing it to be amplified into clusters of identical copies

nucleotides

In Illumina sequencing, after a color tells what base was added at each cluster, excess or unincorporated _ are washed away. Then, the fluorescent labels and blocking groups are removed

3

Removing temporary blocking groups and the fluorescent dyes allows the _’ OH to be free for another nucleotide addition

nucleotide

Illumina: Know the first base of many sequences after a complementary _ is added to the template, then remove the special additions → add another _→ know the next base in the sequence for all those clusters/DNA fragments.

mature mRNA, pre mRNA

_ _ consists of the exons only and no more introns, but the _ _ still has introns following transcription

hybridize

mature mRNA can only _ with certain parts of the DNA due to its lack of introns

Nanopore

type of sequencing where DNA passes through a _ in a membrane, which affects an electric current. The bases lead to different electric current signals, which allows for computation of a long DNA sequence molecule continuously

portability

Besides nanopore sequencing being continuous reads of long strand DNA molecules, what is another benefit?

• next gen sequencing doesn’t have this!

proteins

Nucleic acids can be coated with _ to visualize them under electron microscopes

expressed, effects

Just because a cell contains a gene that encodes a protein does not mean that the gene is _. The _ of a gene can depend on where, when, and how much is expressed

DNA, protein

A _ mutation does not necessarily contribute to effects, which may be adverse, but rather abnormal/altered _ directly contributes

Yes

Do most cell types (muscle, neuronal, liver, etc.) have the same genome?

mature red blood cells

What is an exception to most cell types having the same genome?

genes

Since many cells have the same genome, they are different because different _ are expressed or turned on/off

nucleus

Red blood cells lose their _ during development, so there is no genome in it, but its precursor cell that developed into a red blood cell did

gene regulation

Different sets of genes being expressed in certain cell types at different amounts, times, and locations, are all results of mechanisms of _ _

transcription

Some genes are non-protein-coding, meaning that it stops after the _ step to make functional RNA

rRNA

what is the functional RNA associated with the ribosome structures, combined with proteins too, that perform translation with mRNA to make proteins?

tRNA

What is the functional RNA that brings the appropriate amino acid to the ribosome according to their mRNA sequence?

RNA polymerase

What is the enzyme that makes RNA from DNA?

rNTPS

What are the building blocks for RNA?

DNA, RNA

RNA/DNA polymerase requires a primer to begin synthesis, but RNA/DNA polymerase does not

deoxyribose, ribose

_ is the sugar for dNTPS and _ is the sugar for rNTPS

2, rNTP, dNTP

The _’ carbon has an OH group when it is a _, and this carbon has an H group when it is a _

rNTPs

ATP, UTP, GTP, and CTP are examples of _

phosphodiester bonds

the type of covalent bonds used to connect nucleotides in DNA or RNA, forming the sugar-phosphate backbone

deamination

the process by which cytosine loses an amino group and becomes uracil, which would be a change identifiable in DNA, as DNA has “t” bases rather than “u,” so “u” would be an evident as abnormal and a target for repair

one

For a given gene, one/two DNA strand(s) is/are the template strand(s) used to make RNA

template, coding

Notice the RNA is complementary to the coding/template strand and therefore looks like the coding/template strand, except RNA has U instead of T.

thymine, uracil

Thymine/uracil has a methyl group, and thymine/uracil has a hydrogen in that place

noncoding, coding

The template aka noncoding/coding strand is complementary to RNA, and the non-template strand aka noncoding/coding is the same sequence as RNA, except the DNA has a T instead of U

3 5, 5 3

RNA polymerase reads 3/5 to 3/5, and makes RNA 3/5 to 3/5

antiparallel

The template DNA strand runs in the same/opposite direction as the RNA, meaning that they are _ to each other

3 5, 5 3

RNA polymerase reads _ to _ along the template strand, and synthesizes RNA from _ to _

T, coding

The bases are the same, but U replaces _ in RNA relative to the coding/template strand

A

_ becomes U when transcribing the DNA template to RNA

consensus sequence

the name of common DNA sequence patterns found when comparing many promoter sequences

+1

The -35 and -10 regions are promoter sequences/elements located upstream of the _ _ transcription start site

-35, -10 +1

RNA polymerase binds at the _ _ and _ _ regions, but starts transcription at the _ _

TATAAT

the sequence for the -10 region, aka Pribnow box, is typically similar to that of: _ _ _ _ _ _

consensus sequence

how similar the -10 and -35 sequences are to the _ _ can determine the level of gene expression

TTGACA

the typical sequence for the -35 region is: _ _ _ _ _ _

Yes

Are the -10 and -35 regions exclusive to bacterial DNA?

promoter

The _ determines where transcription starts and the direction in which it proceeds

coding

the RNA _ region begins at +1 and continues downstream

nucleotide

+1 is the position on DNA where RNA polymerase copies the first _ into RNA

TATA, CAAT, GC

the _ box is typically closer to the +1 transcription site than the _ or the _-rich sequences in eukaryotes

Genes

_ are present on both strands of the DNA, and the direction of the promoter tells polymerase which way to go (must read 3’ to 5’)

eukaryotic promoters

_ _ have different elements and are more flexibly arranged, leading to more complex gene expression

basal transcription

the basic/minimal machinery/process needed to initiate transcription, without additional machinery to affect levels of transcription

• in bacteria, this consists of the promoter, RNA polymerase + sigma, RNA pol binds, DNA opens, transcription begins

• in eukaryotes: promoter elements, like TATA, general transcription factors assemble, help recruit RNA pol, transcription beings

bacteria

Bacteria/eukaryote regulation is generally located at or near the promoter/+1 region, where regulatory proteins influence

eukaryotes

Bacteria/eukaryotes have regulation happen at the promoter and at regulatory sequences located far upstream or downstream of the genef

activator

The protein that binds to enhancers, allowing the DNA to bend, which then interacts with the transcription machinery at the promoter and influences how effectively RNA polymerase initiates transcription