Week 3 Readings

Question 1

homologous genes

Answer 1

when genes from different organisms have very similar nucleotide sequences, it is highly probable that they descended from a common ancestral gene

Question 2

the vast majority of our DNA does not code for proteins or functional RNA molecules; instead, it includes

Answer 2

a mixture of sequences that help regulate gene activity, plus sequences that seem to be dispensable

Question 3

how is genome size measured?

Answer 3

in nucleotide pairs of DNA per haploid genome

Question 4

list the 6 basic types of genetic change that are crucial in evolution

Answer 4

1. mutation within a gene
2. mutation within regulatory DNA sequences
3. gene duplication and divergence
4. exon shuffling
5. transposition of mobile genetic elements
6. Horizontal gene transfer

Question 5

mutation within a gene

Answer 5

• may change, delete, or duplicate one or more nucleotides
• thus alter the splicing of a gene’s RNA transcript or change the stability, activity, location or interactions of its encoded protein

Question 6

mutation within regulatory DNA sequences

Answer 6

gene expression may be affected by a mutation in the DNA sequence that controls transcription of the gene

Question 7

gene duplication and divergence

Answer 7

• a cell can make an extra copy of a gene/genome
• as the cell continues to divide, the original DNA sequence and duplicate sequence can acquire different mutations and assume new functions and patterns of expression

Question 8

exon shuffling

Answer 8

two or more existing genes can be broken and rejoined to make a hybrid gene containing DNA segments that originally belonged to separate genes

Question 9

transposition of mobile genetic elements

Answer 9

can move from one chromosomal location to another, thus altering activity or regulation of a gene

Question 10

horizontal gene transfer

Answer 10

a piece of DNA can be passed from the genome of one cell to that of another, even to that of another species

Question 11

how have biologists constructed a phylogenetic tree that goes all the way back to the origins of life?

Answer 11

• focused on the gene that codes for the ribosomal RNA (rRNA) of the small ribosomal subunit
• because the process of translation is fundamental to all living cells, this component of the ribosome has been highly conserved in all living species

Question 12

human genome sequence

Answer 12

the complete list of nucleotides contained in our 23 chromosomes

Question 13

other than its primary aim, how has the Human Genome project helped us?

Answer 13

• improvements in sequencing technologies
• new tools for handling large amounts of data
• cost of DNA sequencing has dropped

Question 14

significance of transposons in our DNA

Answer 14

almost half of our DNA is made up of transposons that have colonised our genome over evolutionary time. most can no longer move

Question 15

the number of protein-coding genes in the human genome may be unexpectedly small, but their relative size is unusually large. what does this mean?

Answer 15

• only about 1300 nucleotide pairs are needed to encode an average-sized human protein of about 430 amino acids; yet the average length of a human gene is 26,000 nucleotide pairs.
• most of this DNA is non-coding introns or regulatory DNA sequences

Question 16

what does in-situ hybridisation allow us to do?

Answer 16

allows a specific nucleic acid sequence - either DNA or RNA - to be visualised in its normal location

Question 17

how does in-situ hybridisation work?

Answer 17

makes use of single-strand DNA or RNA probes labeled with either fluorescent dyes or radioactive isotopes to detect complementary nucleic acid sequences within a cell, tissue, or organism

Question 18

state 2 main applications of in-situ hybridisation

Answer 18

• explore how transcription regulators guide the development of multicellular organisms, providing important info ab when and where these genes carry out their function
• detect particular DNA sequences in an individual chromosomes (eg diagnose genetic abnormalities)

Question 19

why do females and males have different numbers of types of chromosomes?

Answer 19

males, with their Y chromosomes, have an extra type of chromosome

Question 20

homologous chromosomes

Answer 20

maternal and paternal versions of each chromosome

Question 21

karyotype

Answer 21

an ordered display of the full set of an organism’s chromosomes

Question 22

define a gene

Answer 22

a segment of DNA that contains the instructions for making a protein or RNA molecule

Question 23

different possible functions of an RNA molecule

Answer 23

• used to produce a protein or may be final product
• eg may have structural or catalytic roles
• may play a part in regulating gene expression

Question 24

how do we know junk dna is important?

Answer 24

comparisons of the genome sequences from many different species reveal that small portions of junk DNA are highly conserved among relative species

Question 25

give an example of how there is no simple relationship between gene number, chromosome number, and total genome size

Answer 25

- human genome is 30 times smaller than some plants and 10 times smaller than some species of amoeba - humans have a total of 46 chromosome, but some species of deer have 7 and some carp have more than 100

Question 26

interphase chromosomes

Answer 26

exist as long, thin threads of DNA in the nucleus and cannot be easily distinguished in the light microscope

Question 27

replication origin

Answer 27

site where DNA replication begins

Question 28

telomeres

Answer 28

mark the ends of each chromosomes and serve as a protective cap that keeps the chromosome tips from being mistaken by the cell as broken DNA in need of repair

Question 29

centromere

Answer 29

allows duplicated chromosomes to be separated during M phase

Question 30

how are interphase chromosomes specially organised?

Answer 30

- each tends to occupy a particular region of the nucleus to prevent entanglement - some chromosomal regions are physically attached to sites on the nuclear envelope or lamina which help chromosomes remain within their distinct territories

Question 31

proteins that bind to DNA to form eukaryotic chromosomes are traditionally divided into

Answer 31

histones and non-histone chromosomal proteins

Question 32

function of histones

Answer 32

responsible for the first and most fundamental level of chromatin packing - the nucleosome

Question 33

how did investigators determine the structure of the nucleosome core particle?

Answer 33

treated chromatin in its unfolded form with enzymes called nucleases, which cut the DNA by breaking phosphodiester bonds. when nuclease digestion is carried out for a short time, only the exposed DNA between the core particles (linker DNA) will be cleaved, allowing the core particles to be isolated

Question 34

SMC

Answer 34

structural maintenance of chromosomes proteins

Question 35

functions of SMCs

Answer 35

associate with additional proteins to form an SMC ring complex that uses the energy of ATP hydrolysis to motor along the DNA, pushing out a loop of DNA in its wake

Question 36

cohesion

Answer 36

SMC ring complex that organises the structure of interphase chromosomes - cohesion rings will travel along the DNA, extruding loops until they run up against a sequence-specific clamp protein - these proteins stall the cohesions and bind to one another, which draws together the DNA at the base of each loop - it is the spacing and location of the clamp proteins that dictates the size and contents of each chromosomal loop

Question 37

condensins

Answer 37

SMC ring proteins containing difference SMCs and accessory proteins than cohesins

Question 38

function of condensing

Answer 38

- as cells prepare to divide, condensing replace most of the cohesins that formed the loops in the interphase chromosome - then use the energy of ATP hydrolysis to form loops of their own, which wind the chromatin into a tighter mass of coils

Question 39

two ways to adjust local structure of chromatin

Answer 39

- ATP-dependent chromatin-remodelling complexes - histone-modifying enzymes

Question 40

ATP-dependent chromatin-remodelling complexes

Answer 40

large protein machines, present at about one copy for every 5 nucleosomes, which can use the energy of ATP hydrolysis to change the position of nucleosomes on the DNA. they can render DNA more or less accessible

Question 41

histone-modifying enzymes

Answer 41

- generate reversible chemical modification of histones - tails of all four of the core histones are particularly subject to these covalent modifications, which include the addition and removal of acetyl, phosphate, methyl groups

Question 42

acetylation of lysines

Answer 42

can reduce the affinity of the tails for adjacent nucleosomes, thereby loosening chromatin structure and allowing access to particular nuclear proteins

Question 43

how do modifications serve as docking sites on histone tails for a variety of regulatory proteins?

Answer 43

different patterns of modifications attract specific sets of non-histone chromosomal proteins to a particular stretch of chromatin. some of these proteins promote chromatin condensation whereas others promote chromatin expansion and facilitate DNA access

Question 44

heterochromatin

Answer 44

- most highly condensed form of interphase chromatin - makes up around 40% of typical interphase chromosome - half remains permanently condensed (eg centromeres) - the remaining contains genes whose activity has been silenced (ie embryogenesis genes)

Question 45

euchromatin

Answer 45

- 60% of interphase chromatin - a lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription.

Question 46

why is DNA replication called semiconservative?

Answer 46

each parent strand serves as the template for one new strand, so each of the daughter DNA double helices ends up with one of the original strands plus one completely new strand

Question 47

what types of proteins begin DNA synthesis?

Answer 47

initiator proteins at replication origins

Question 48

why is DNA rich in A-T base pairs typically found at replication origins

Answer 48

A-T base pair is held together by fewer hydrogen bonds than a G-C base pair. therefore, it is easier to pull apart

Question 49

why is beginning DNA replication at many places at once helpful?

Answer 49

it greatly shortens the time a cell needs to copy its entire genome

Question 50

why is it critical that DNA synthesis be initiated only once at every replication origin?

Answer 50

failure to regulate this process could cause genes to be copied too many times or even lost