Chapter 4 Flashcards
DNA, Chromosomes and Genomes
Define chromosomes
Structure composed of a DNA molecule (in eukaryotes linear, in prokaryotes circular) and associated proteins, and which carries part of or all of the hereditary information of an organism.
Define chromatin
Complex of DNA, histones and non-histone proteins found in the nucleus of a eukaryotic cell.
Define nucleosomes
Bead-like structure in eukaryotic chromatin composed a short length (147bp) of DNA wrapped around a core of 8 histones (normally H2A, H2B, H3 and H4), as well as linker DNA (the DNA between the histone complexes).
Define Karyotype
The full set of chromosomes of a cell arranged by size, shape and number
Defines genes
Region of DNA that is transcribed as a single unit and carries information for a discrete hereditary characteristic, either a protein or an RNA molecule.
How many genes does yeast have?
~6600 genes
How many genes do humans have?
~30.000 genes (21.000 coding genes)
Why can the different between genome size and amount of genes vary so much between two organisms?
A lot of intergenic DNA in the human genome. Intergenic DNA has many functions such as regulating gene expression and large-scale organization of chromatin. Also, repetitive sequences scattered throughout the genome, as wells as, transposable elements.
What is transposable elements/jumping genes/transposons?
Sequences of DNA that “jumps” from one location in the genome to another., with the risk of destroying or altering the genes activity.
How many chromosomes does humans have?
22 autosome chromosomes (not sex chromosomes)
What is the differences between male and female chromosomes?
Females have 23 pairs of X chromosomes and males have 24 different X and Y chromosomes
4) List three specialized DNA sequences and their function that act to ensure that the number and morphology of chromosomes are constant from one generation to the next.
Telomers – repetitive nucleotide sequences at the end of eukaryotic DNA which in most cells are shortened during replication. Shortening of the telomers act as buffer preserving important genetic information during cell division. Furthermore, telomers protect DNA ends from repair mechanisms which would otherwise falsely recognize these as double stranded breaks.
Centromers – Sequences where kinetochore complexes assemble during cell division, and pull apart sister chromatids.
Origin of replication – Sequences from where replication is initiated.
Describe level of DNA condensation and interaction
- 10 nm fiber (bead-on-a-string)
Hydrogen bonds, salt bridges and hydrophobic interactions maintain DNA to histone interaction.
Describe level of DNA condensation and interaction
- 30 nm fiber
Interaction between histone tails (which can be modified by post translational modification of histone tails), as well as, the linker histone H1 maintains the zig-zag organization of the 30nm fiber.
Describe level of DNA condensation and interaction
- Chromatin looping (“700nm fiber”)
Highly condensed chromatin (M phase). Held together by Cohesin (holds sister chromatids together) and Condensin (structural proteins).
Define epigenetic inheritance
Inheritance of any feature from one generation to another that does not result from changes in the sequence of DNA
Define heterochromatin
Region of an interphase chromosome that is highly condensed
Define Euchromatin
Region of an interphase chromosome that is less condensed
In what type of chromatin are actively expressed genes most often found?
Euchromatin, as this is less condensed compared to heterochromatin.
What is the histone code?
Post-translational modification (PTM) can occur at numerous amino acid residues of histone in a nucleosome. The histone code is the specific set of PTM on a nucleosome. Each combination of modifications is thought to lead to a specific biological outcome.
Why does the cell have histone variants?
The presence of different histone variants in nucleosomes leads to different biological outcome. Histone variants can therefore used by the cell to specify the function of the nucleosome.
Protein groups and their control of nucleosomal modification
Define transcription factors
Interacts sequence-specifically with DNA and can recruit writers or erasers
Protein groups and their control of nucleosomal modification
Define readers
Reads histone and DNA modifications and can recruit writers or erasers
Protein groups and their control of nucleosomal modification
Define writers
Adds histone or DNA modifications
Protein groups and their control of nucleosomal modification
Define Erasers
Removes histone or DNA modifications
Protein groups and their control of nucleosomal modification
Define Barrier
Shields or counteracts the spreading of histone or DNA modifications
Protein groups and their control of nucleosomal modification
Define Chromatin remodeling complexes
Moves histones relative to DNA at the cost of ATP
Protein groups and their control of nucleosomal modification
Define Histone chaperones
Replaces histones within the histone core of nucleosomes, thereby binding and regulation nucleosome assembly
Defines a promoter
Region of DNA that initiates transcription of a particular gene.
Defines an enhancer
Small region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur.
Define transcription factor
Protein that controls the rate of transcription of genetic information by binding to a specific DNA sequence. Regulates genes expression.
Help recruit cofactors and other proteins
Define motif
A protein sequence motif, or pattern, can be broadly defined as a set of conserved amino acid residues that are important for protein function and are located within a certain distance from each other
Define histone methylation
Associated with inactive chromatin
Define histone acetylation
Associated with active cromatin
Provide evidence that transcription factor/DNA interactions are dynamic
- GFP tagged Glucorticoid Receptoer (GR) and mCherry tagges Estrogen Recepter (ER) are two receptors which recognize the same DNA motif.
- The receptors only transiently occupied DNA
- When both were activated and present, both receptors were able to bind to the same motif.
- One receptor did not block for the other to bind, showing that the process is dynamic.
Provide evidence that transcription factor/DNA interactions are dynamic
- GFP tagged Glucorticoid Receptoer (GR) and mCherry tagges Estrogen Recepter (ER) are two receptors which recognize the same DNA motif.
- The receptors only transiently occupied DNA
- When both were activated and present, both receptors were able to bind to the same motif.
- One receptor did not block for the other to bind, (they seemed to enhance each other) showing that the process is dynamic.
Shows TFs are not competitive
14) How do inactive and active chromatin regions differ in condensation and localization within in the nucleus?
Active
- less condensed (euchromatin), histone marks indicating active chromatin (acetylation), chromatin is further away from nuclear envelope compared to inactive chromatin.
Inactive
- condensed (heterchromatin), histone modifications indicative of inactive chromatin (methylation), chromatin is closer to nuclear envelope compared to active chromatin.
14) How do inactive and active chromatin regions differ in condensation and localization within in the nucleus?
Active
- less condensed (euchromatin), histone marks indicating active chromatin (acetylation), chromatin is further away from nuclear envelope compared to inactive chromatin.
Inactive
- condensed (heterchromatin), histone modifications indicative of inactive chromatin (methylation), chromatin is closer to nuclear envelope compared to active chromatin.
How is cellular identity pass on from parent cell to daughter cell?
Chromatin structures can be epigenetically inherited in the daughter cells by different mechanisms
Histone marks are maintained by reuse of histones after the replication fork by spreading of existing marks.
Histones already have modifications specific from the parent cell, and these histones are inherited by the daughter cells to form new chromatin structures.
All the existing proteins from the cytoplasm and nucleus is divided into two, wherein TF’s specific to the cell identity are already present, and will therefore influence the chromatin structure in the daughter cell.
Methylation of the DNA is catalyzed post cell division by DNA maintenance methylases.
