Unit 2 - Genes to Functional Proteins

What molecule is this?

Uracil

What molecule is this?

Ribose sugar

Where do phosphates usually attach to?

C5

Compounds with adenosine

CoA, NAD, FAD

DNA is read

5’ → 3’

Why is RNA unstable?

Multiple OH present causes phosphate to swap between the C2 and C3

DNA Full Turn Length

36A

How wide is DNA

20A

A-DNA

Shorter, wider, and more compact right-handed helix than B DNA that forms in minimal water

X Ray Crystallography

x-rays scatter as they pass crystallized proteins causing interferences to create diffraction patterns which atoms are deduced

Cryo Electron Microscopy

Electrons are fired at frozen proteins that scatter and pass through a magnifier

What is the determinant of DNA stability

Stacking interactions (hydrophobic effect, LD forces)

DNA Reannealment

Only happens properly when cooling happens slowly

Reverse Transcription

Converting RNA to DNA

Species translate certain codons

More than others

Glu → Val

Sickle Cell

Gene size or noncoding DNA is proportional to

Organismal complexity

Sequencing Polymers

Break strands into pieces, sequence them and put them back together using the overlapping fragmenets

Bacteriophages have

Unmethylated DNA

Palindromic DNA

A 5’-3’ sequence matches the sequence on the other srand when read 5’-3’ too

EcoRI

Recognizes GAATTC and cuts after G base to create a sticky end

EcoRV

Recognizes GATATC and cuts after T base to create a blunt end

Agarose

Used for larger molecules in gel electrophoresis to help distinguish between sequences

Polyacrylamine

Gel for electrophoresis with small molecules to give better resolution and tell between single base pairs

Electrophoretogram

Restriction digests of a plasmid with several different enzymes (can verify with electrophoresis)

PCR itself doesn’t

Sequence, PCR (multiple) does not equal polymerase reaction (singular)

ddNTP

Lacks 3’ OH for sanger sequencing

Next Generation Sequencing

Reads many fragments at the same time quickly

Cappilary Electrophoresis

Separates molecules via silica and read bases as it passes through a laser to create a chromatogram

Illumina Sequencing

Uses fluorescence bases to track the nucleotides being added invidiually, then washed off and repeated

PacBio

Creates accurate long reads that fluorescense during synthesis

Nanpore Sequencing

Identifies DNA and RNA sequences by measuring changes in electrical current as single molecules pass through nanopore

Cloning vectors given

Antiobiotic resistant genes to select for only bacteria with plasmids

LacZ

Makes B-galactosidase

B-galactosidase

Cleaves bond between galactose and sugar

CRISPR

Cas9 with gRNA binds to cDNA to cleave DNA or insert replacement DNA

DNA Fingerprintings uses

PCR for short tandem repeats that its size vary among individuals

qPCR

PCR continually makes new DNA sequences that bind to fluorescent probes, so that the amount of the DNA sequence can be monitored over time

What molecule is this?

Adenine

What molecule is this?

Guanine

What is purine numbering?

What molecule is this?

Cytosine

What molecule is this?

Thymine

What is pyrimidine numbering?

What molecule is this?

Deoxyribose sugar

B DNA

Classic right-handed helical dsDNA found in nature under normal physiological conditions

B DNA Full Turn

3.4nm (34A)

What is the sugar numbering?

Why is G-C harder to break?

A-T minor grooves are tighter and increase entropy when broken, and less stacking energy

DNA Barcoding

technique for identifying the species pres ent in a sample of environmental DNA