CSB349H1 Study Guide - Spring 2018, Comprehensive Midterm Notes - Gene, Dna, Messenger Rna
12 Oct 2018
School
Department
Course
Professor
CSB349H1
MIDTERM EXAM
STUDY GUIDE
Fall 2018
Lecture 1(a): Genome Repeats
What is in the (human) genome?
• Build 35: 2.85 Gigabases, 10-5 error rate (1 in 100,000 is incorrect)
o “Build 35” = 35th time people tried to put the pieces of the human genome together
o Gigabase = 1,000,000,000 bases
ð Entire genome is ~3.08 Gigabases
o 200Mbases short; cannot be (not) sequenced
§ Most of this consists of heterochromatin
(telomeres, centromeres) and other
repetitive DNA
ð Most of our genome is not even human genes
o Repetitive elements make up 45% of the genome
o Only ~20,000 protein coding genes making up 1.5% of the genome
Types of Repetitive DNA Sequences:
1. Tandemly Repeated Sequences
a) Satellite DNA
b) Minisatellite DNA
c) Microsatellite DNA
§ Repeat that occur adjacently to each other
2. Interspersed Repeated Sequences
a) Transposons (~1-2kb)
b) Miniature Inverted Repeat Transposable Elements (MITES) (<0.5kb)
c) SINES (<0.5kb)
d) LINES (>5kb)
§ Repeats that occur randomly in the genome
find more resources at oneclass.com
find more resources at oneclass.com
Tandem Repeats:
a) Satellite DNA:
o Repeat units can range between 10’s to 100’s of base-pairs found in large clusters
(millions) making up a large percentage of our genome
§ Rich A+T sequences more common than C+G rich sequences
§ Centromeres; structure part that holds together chromosomes
• Heterochromatic
b) Minisatellite DNA:
o Repeat units are usually up to 25 base-pairs found in clusters up to 20kb in length
§ Telomeres; tips of the chromosomes (100’s of copies of 5’-TTAGGG-3’)
• Heterochromatic
c) Microsatellite DNA:
o Repeat units are usually 2-6 base-pairs found in clusters <150 base-pairs
§ “CA” is the most common repeat
§ Located in euchromatin
§ Highly variable between individuals (# of repeats)
• Sequencing length polymorphisms are used in genetic profiling
Interspersed Repeats:
a) Transposons (~1-2 kb):
o Transpose directly via a DNA intermediate
o A single gene encodes for a transposase flanked by inverted terminal repeats (ITR)
§ Transposase catalyzes the excision of the transposon from its original location
and promotes its position somewhere else in the genome
o Transposition is non-replicative; functionally disrupt a gene if they “jump” into it
b) Miniature Inverted Repeat Transposable Elements, MITES (<0.5 kb)
o High copy # in the genome and their transposition is non-autonomously regulated
§ Palindromic repetitive elements containing ITR throughout the genome
§ Found in proximity to genes and can regulate their expression by acting as
cis-regulatory motifs
c) Short Interspersed Nuclear Elements, SINES (<0.5 kb)
o Transpose through an RNA intermediate
o Related to retroviruses, but do not contain long terminal repeats
§ High abundance and mobility within the genome
d) Long Interspersed Nuclear Elements, LINES (>5 kB)
o Remnants of retroviruses
o Contain 2 open reading frames (ORF)
§ One ORF encodes for a reverse transcriptase
o Often have a degenerate 5’ end, representing an incomplete reverse transcription
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
What is in the (human) genome: build 35: 2. 85 gigabases, 10-5 error rate (1 in 100,000 is incorrect, build 35 = 35th time people tried to put the pieces of the human genome together, gigabase = 1,000,000,000 bases. Entire genome is ~3. 08 gigabases: 200mbases short; cannot be (not) sequenced. Most of this consists of heterochromatin (telomeres, centromeres) and other repetitive dna. Most of our genome is not even human genes: repetitive elements make up 45% of the genome, only ~20,000 protein coding genes making up 1. 5% of the genome. Types of repetitive dna sequences: tandemly repeated sequences, satellite dna, minisatellite dna, microsatellite dna. Repeat that occur adjacently to each other: interspersed repeated sequences, transposons (~1-2kb, miniature inverted repeat transposable elements (mites) (<0. 5kb, sines (<0. 5kb, lines (>5kb) Repeats that occur randomly in the genome. Tandem repeats: satellite dna, repeat units can range between 10"s to 100"s of base-pairs found in large clusters (millions) making up a large percentage of our genome.
