DNA and the Organization of the Genome Flashcards
DNA Structure
- Double Helix
- Made of nucleotides with sugar-phosphate backbone
- Two strands held together via hydrogen bonds
- Each strand has a 5’ and 3’ end
- Each strand runs in opposite direction (Anti-Parallel)
DNA Replication
- ) Enzyme Helicase unzips the DNA strands forming a replication fork
- ) Enzyme Primase makes piece of RNA called a Primer on the template which marks the starting point of the new strand of DNA
- ) Enzyme DNA Polymerase binds to the primer and makes the NEW strand of DNA from 5’ to 3’
- ) Enzyme Exonuclease removes the primers and DNA Polymerase fills the gaps with DNA
- ) Enzyme DNA Ligase seals up the fragments of DNA in both strands to form continuous double strand
Leading strand
- New strand of DNA during DNA replication
- Made continuously from 5’ to 3’
Lagging strand
- New strand of DNA during DNA replication
- NOT made continuously as it runs in the opposite direction of the leading strand
- Still made in the 5’ to 3’ direction
- Made in small chunks called Okazaki Fragments, each of which is started with an RNA primer
Exonuclease
- Enzyme that removes the RNA primers from both the leading and lagging strand after the new strand of DNA is completed
- Another DNA Polymerase then fills in the gaps with DNA
DNA Ligase
Enzyme that seals up the fragments of DNA in both strands to form continuous double strand
Semi-Conservative DNA Replication
Each new DNA molecule has one old (conserved) strand and one new strand
Number of chromosomes in human somatic (non-germline) cells
- 46 Chromosomes
- Arranged in 23 pairs: 22 pairs of autosomes (non-sex chromosomes) and 1 pair of sex cells
Autosome
Any chromosome that is not a sex chromosome
Sex cells
Male and Female
Male: XY
Female: XX
Chromatin
The complex of DNA and proteins of which chromosomes are composed
Nucleosome
- Primary structural unit of chromatin, consisting of DNA wrapped twice around a core of 8 histone molecules
- Histones have (+) charge
- Phosphate groups on DNA have (-) charge
Histones
Proteins associated with DNA in chromatin. Two copies each of histones H2A, H2B, H3, and H4 make an octamer that is the core of a nucleosome
When is chromatin condensed into compact chromosomes?
- During cell division the chromatin is condensed into compact chromosomes that can easily be separated into two daughter cells
- When not in cell division the chromatin is in its decondensed state in the nucleus to allow access to the DNA for gene expression
Gene
- Functional hereditary unit of the genome
- Sequence of chromosomal DNA that is required for the production of a functional product
Protein-coding gene
Segment of DNA containing the code for the amino acid sequence of a polypeptide chain and the regulatory sequences necessary for its expression
What is the product of noncoding genes?
RNA products
What direction does transcription occur along DNA?
5’ to 3’
- What direction of DNA is considered upstream?
- What direction is downstream?
- The 5’ end is upstream
- The 3’ end is downstream
- This is because transcription is read from 5’ to 3’ along the DNA
Promotor sequences
- At the 5’ end of each gene
- Includes sequences responsible for the proper initiation of transcription
- Common sequence that determines the start site in many genes is the TATA box
- Promoter sequences are binding sites for the proteins called transcription factors
Exons
- Segments of genes that ultimately determine the amino acid sequence of the protein
- Kept in the mature mRNA during splicing
Introns
- Intervening sequences present in the genomic DNA but removed from the mRNA during splicing
- Not represented in the final protein product
Cis Regulatory Elements
Sequences on the same molecule of DNA as the gene they regulate
Trans Regulatory Elements
Sequences that regulate genes distant from the gene from which they were transcribed
Enhancer
- Regulatory element
- DNA sequence that acts in cis to increase transcription of a gene
Locus Control Region (LCR)
A DNA domain, situation outside a cluster of structural genes, responsible for appropriate expression of the genes within the cluster
Silencer
A DNA sequence that acts in cis to decrease transcription of a nearby gene
Transcription Factor
- Large class of proteins
- Regulates transcription by forming complexes that bind to regulatory regions of genes to either promote or inhibit transcription
Nucleotide general structure
- Phosphate Group
- 5-Carbon Sugar
- Nitrogenous Base
4 Nucleotide Bases in DNA
- Adenine (A)
- Thymine (T)
- Cytosine (C)
- Guanine (G)
Purines
- Adenine (A)
- Guanine (G)
- Made of 2 rings
Pyrimidines
- Cytosine (C)
- Uracil (U) - (RNA only)
- Thymine (T)
- Made of 1 ring
Nucleotide Complementary Base Pairing
(A) binds to (T) via 2 Hydrogen Bonds
(C) Binds with (G) via 3 Hydrogen Bonds
Interphase Subphases
- G1 Phase:
- S Phase: DNA Replication
- G2 Phase:
DNA Replication 3 Main Steps
- ) Initiation
- ) Elongation
- ) Termination
Initiation Main Steps
- ) Group of protein form the pre-replication complex
- ) Looks for specific nucleotide sequences (Origins of Replication) along the DNA strand (lots of A and T bases)
- ) DNA Helicase can easily separate strands here (A = T only has 2 hydrogen bonds)
- ) Creates replication fork
Single Stranded DNA Binding Proteins
Stabilize the unstable single DNA stands during DNA replication
DNA Topoisomerase
- DNA that is double stranded becomes more tight when nearby DNA is unzipped into single strands
- DNA Topoisomerase loosens up this tight DNA coil
Elongation Main Steps
- ) RNA Primase randomly synthesizes small lengths of RNA called RNA Primers
- ) RNA Primers bind to complementary strands of DNA
- ) DNA Polymerase attaches to this segment of DNA + RNA Primer
- ) DNA Polymerase adds complementary nucleotides to the signle stranded DNA (Moves 3’ to 5’ and synthesizes 5’ to 3’)
What is the structural difference between DNA and RNA?
- DNA uses Thymine (T) and RNA uses Uracil (U)
- DNA uses Deoxyribose sugars and RNA uses Ribose sugars
Termination mains steps
- ) Telomere (repeating sequences of TTAGGG) at the end of the chromosome signals DNA Polymerase to hop off the strand
- ) The two new (semi-conserved) DNA strands separate, finalizing DNA replication
