AP Bio Unit 6

a little bit painful..... but I added a bit of color and joy to make it better

Purines

Double-ring nitrogenous bases (adenine, guanine)

Pyrimidines

Single-ring nitrogenous bases (uracil, thymine, cytosine - UTC)

Plasmids

Circular DNA not part on any chromosome, found in proks

Deoxyribose vs Ribose

Deoxyribose - DNA

Ribose - RNA

Ribose has an OH- group at 2’

Think: “(de-oxy)genated” = missing oxygen

Transcription (basic)

Complimentary mRNA produced using the DNA as a template

Think: Printer making a copy to be used

Translation (basic)

mRNA is sent to ribosome so that it can be used to create a polypeptide chain based on its sequence

tRNA

During translation, pairs complimentary bases to mRNA (anticodon) and carries a corresponding amino acid

5-carbon sugars

Part of DNA and RNA. Carbons counted clockwise, 1’ to 5’

Attaches to other sugars on the 3’ carbon!

Phosphodiester bonds

Covalent bonds of the connected sugar and phosphate groups that made the “sides” of the DNA ladder

mRNA processing

ONLY in euks. In nucleus.

GTP cap and poly-A tail are added to the ends, and certain parts are spliced and removed

Introns and Exons

In mRNA splicing, introns are non-coding parts that are REMOVED, while exons are KEPT

DNA replication

1. INITIATION

• Helicasespilts strands apart

• Topoisomerase prevents DNA at replication fork from being too wound up

• Primase adds RNA primers to strands

2. ELONGATION

• DNA polymerase binds to primers and starts DNA replication

3. TERMINATION

• RNA primers eventually replaced w/ DNA by another type of DNA polymerase

• Ligase glues together fragments of the DNA strand

Leading vs Lagging Strands

Leading strand: DNA polymerase follows helicase path during replication so that the strand is unbroken

Lagging strand: DNA polymerase goes the opposite direction and has to keep stopping and starting, creating fragments

Okazaki fragments

Fragments in the lagging strand during DNA replication caused by the DNA polymerase not following the direction the DNA is being opened

Helicase

Enzyme that unzips DNA during DNA replication

Topoisomerase

Enzyme that prevents the DNA ahead of the replication fork from supercoiling - smooths it out

Ligase

Enzyme that joins DNA fragments together at the end of DNA replication

3’ and 5’

Ends of DNA are 3’ and 5’, going in opposite directions

DNA and RNA polymerase go 3’ to 5’ but the strand they make is made from 5’ to 3’ because the new strand is antiparallel to the template strand

Primase

Adds RNA primers during DNA replication to mark where the DNA polymerase will start

Alternative splicing

A way mRNA can be changed without changing the DNA post-transcription. The same pre-mRNA has parts removed and kept differently that result in different proteins

GTP cap

Added to 5’ end of mRNA in euks during mRNA processing. Helps with ribosomal recognition

poly-A tail

Added to 3’ end of mRNA in euks during mRNA processing. Stabilizes mRNA

rRNA

Ribosomal RNA. Makes up ribosomes

Transcription (euks)

1. INITIATION

• Transcription factors bind to TATA box in promoter region (DNA sequence)

• RNA polymerase binds to promoter

2. ELONGATION

• RNA polymerase builds mRNA strand from template DNA

3. TERMINATION

• RNA polymerase transcribes terminator sequence in DNA

• mRNA detaches, now pre-mRNA

4. mRNA PROCESSING and SPLICING

• GTC cap added to 5’ end, poly-A tail added to 3’ end

• Introns removed, exons kept

Transcription (proks)

Same as euks except:

• INITIATION: RNA polymerase binds directly to promoter in DNA

• TERMINATION: mRNA is produced at the end ready to use

• No mRNA processing!

Translation

1. INITIATION

• Initiator tRNA binds to start codon on mRNA (‘Met’ amino acid)

  • On P-site

2. ELONGATION

• tRNA anticodon matches codons on mRNA

  • On A-site

• Amino acids brought by tRNA form peptide bonds

• Repeat! Codons move A → P → E sites

3. TERMINATION

• Stop codon reached, polypeptide released

Point Mutations

Alters 1 base pair of a gene

Missense mutation

Amino acid is replaced by another (type of point mutation)

Nonsense mutation

Stop codon is coded too early, leading to incomplete amino acid sequence (type of point mutation)

Frameshift mutation

Nucleotides added or deleted, shifting all nucleotides downstream of the mutation

Silent mutation

Alteration in nucleotide that doesn’t change amino acid sequence

Large scale mutations

Chromosomal mutations, ex. wrong # of chromosomes

Horizontal gene transfer

Proks get genes from other proks instead of passing them down

Transformation

Proks/bacteria take in plasmid from environment and start expressing that gene

Conjugation

Proks/bacteria DIRECTLY exchange plasmids through a pilus (tube)

Transposition

Movement of segments known as transposons between DNA molecules

Transduction

Virus transfers a gene from an old host to a new host, can cause recombination of genes

Gene expression

Not every gene is expressed all the time - phenotype determined by which genes are turned on

Cell differentiation/specialization

Cells have different gene expression, which leads to them becoming different cells

Transcription factors

Molecules that bind to DNA, controls rate of transcription

Epigenetic regulation

Environmental factors affecting gene expression

THINK: “E” for environmental

Packing of DNA

How tightly DNA is packed (wrapped around histones) changes transcription

Too tight = transcription can’t occur, genes turned OFF

DNA methylation

Blocks transcription factors, genes turned OFF

Histone acetylation

Unwinds DNA, enabling transcription

Genes turned ON

Promoter

Nearby control sequence on DNA

Where RNA polymerase and transcription factors bind

Enhancer

Distant control sequences on DNA where activators can bind and increase rate of transcription

siRNA

= Small interfering RNAs

“Death” tag for mRNA, destroys mRNA and silences gene turning it OFF