Virginia Tech Biology 1105 Unit 4 Review

genomics

branch of biology dealing with mapping, sequencing, annotating & analyzing whole genomes

integrates classical & molecular genetics to better understand genomes

genome

entire set of DNA instructions found within a cell, contains all information needed for an individual to develop and function

genetic map

this type of genome map is derived from recombination frequency & linkage analysis

provides relative locations of genes or genetic markers

abstract (don't know where the start and end points are)

physical map

this type of genome map provides precise location in genome and often has a resolution at the nucleotide level

kilobases

Physical Maps

- use landmarks within the DNA sequence

- common landmarks = enzyme cutting sites, small segments of actual nucleotide sequence

- ultimate form of a physical map = placement of many genetic markers on a complete genetic sequence

- units for physical maps: ______________

restriction map

Physical Maps - 2 types

this type of physical map was created by digesting DNA w/ more than 1 restriction enzymes & mapping the location of the enzyme cut sites

provides location of cut sites

chromosome maps

Physical Maps - 2 types

this type of physical map is used to study whole chromosomes or genes which can translocate/move to other chromosomes

uses staining techniques to identify regions of interest & can be viewed using a microscope

lower resolution → allows researchers to view entire chromosomes or genomes at once

Sequence-Tagged Site (STS) Map

this type of map combines high resolution and ability to view large pieces of DNA at a glance

STS = a small stretch of unique DNA, found at only 1 location in the genome that can be amplified using PCR

used to identify location of DNA fragment in genome or piece together fragments by analyzing overlapping STS sites

contig

Sequence-Tagged Site (STS) Map

the presence or absence of an STS site on a fragment helps researchers to organize fragments into a continuous sequence called a ___________

chain-terminating nucleotides

all sequencing methods rely on PCR, electrophoresis, and use of _____________________ ________________

ddNTPs

chain-terminating nucleotides

- the earliest form of CT nucleotides is ____________, which lack a hydroxyl group to which nucleotides are usually added → they act as chain-terminators when incorporated into DNA molecules during PCR

4

ddNTPs

- they can have any of the ____ DNA bases attached

- if the researchers knows which of the 4 ddNTPs is terminating the sequence, they can known the base at that location in the genome sequence

fluorescent

Dideoxy (automated) Sequencing

1. start with a template strand of unknown sequence

2. amplify using PCR

3. incorporate ddNTPs labeled with a _______________ marker for A,T,G,C

4. DNA fragments created by PCR are separated using electrophoresis

5. as fragments pass through tubes during electrophoresis, a laser & photo-detector work in tandem to identify fluorescent ddNTPs

reversed

Next Generation Sequencing

- this method is faster, cheaper, and can sequence larger fragments of DNA in a single reaction compared to automated sequencing

- multiple copies of fragments ensures accuracy

- difference: the CT nucleotides can be __________/changed back into normal nucleotides, which enables each fragment to be sequenced multiple times with new reversible CT nucleotides added each time

contig

most genomes are too large to be sequenced in a single step, so most approaches require breaking genomes into fragments, sequencing those fragments, & then assembling a ___________ by matching overlapping sequences

physical

the clone-contig method of fragmenting a genome to be sequenced is when the genome is fragmented into large pieces of DNA called clones

the clones can be arranged in order based on STS sites, which are __________ mapping landmarks

shotgun

the ______________ method of fragmenting a genome does not rely on any genetic or physical maps

instead, the whole genome is fragmented into pieces for sequencing and computer software assembles all the pieces based on overlapping nucleotide regions

isn't

organismal complexity (is/is not) a function of genome or gene #

genome annotation

through __________ _______________, ever changing DNA sequences are typically recorded in searchable online databases, which researchers use to look for DNA sequences of a known "signature"

open reading frame

genome annotation

the _________ ___________ __________ is the coding region of a gene in between the start and stop codons that can be translated into protein

BLAST

___________ (basic local alignment search tool) compares sequence of an unknown gene of interest to the database

introns

____________ are non-coding regions of DNA that constitute the great majority of each human gene

simple sequence repeats

this type of non-coding DNA is stuttering repeats of a few nucleotides such as CGG, repeated thousands of times

transposable elements

this type of non-coding DNA is DNA sequences that can move within a genome, "jumping genes"

protein

non-coding RNA

- can move from 1 chromosome to another

- are often duplicating as they move

- don't encode for a __________ but have regulatory functions

biological activity

ENCODE (encyclopedia of DNA elements) claimed that 80% of DNA in the human genome is functional, but they claimed functional meant reproductible "______________ ____________"

by this logic, all DNA that is replicated by the enzyme DNA polymerase could be considered functional

however, sites of enzymatic activity are not necessarily functional

evolutionary biologists focus on parts of DNA that have been "selected" through time

genome analysis

____________ _____________ works to identify the role of DNA elements in the genome

3 approaches: comparative, functional, and proteomics

synteny

Genome analysis: comparative genomics

uses information from 1 genome to learn about a 2nd genome

based on ____________ = conserved arrangement of DNA in related genomes, can be derived from comparing physical maps

transcriptome

Genome analysis: functional genomics

uses biotechnology to show connection b/w genotype & phenotype

can be broken into 3 separate categories

- _________________ = study of all RNA molecules produce by genome

- proteome = study of the protein produced by the genome

- study of interaction b/w proteins

DNA microarrays

Genome analysis: functional genomics - transcriptome

_________ _______________ are a tool to determine which genes are being turned on /expressed at a particular location or time, provides insight into function of genes

the scientists must create the microarray chip with "known" genes

next-generation

Genome analysis: functional genomics - transcriptome

RNA sequencing (RNA-seq) uses _______-_____________ sequencing to capture ALL the mRNA transcripts being created at a particular time, which helps to collect information on ALL gene expression rather than just suspected genes

alternative

Genome analysis: functional genomics - proteomics

______________ splicing & post-transcriptional regulation make it tough to predict a protein's structure from DNA sequences alone, making the proteome more difficult to analyze than the transcriptome

mass-spectrometry

Genome analysis: functional genomics - proteomics

_______-_________________ uses charge:mass ratio to identify protein or component amino acids

calculates charge:mass ratio of each peptide & compares those values with database to identify proteins

protein microarrays

Genome analysis: functional genomics - proteomics

___________ _______________ further fragment proteins to determine its component amino acids

- work similar to DNA microarrays

- instead of DNA sequences applied to a chip, antibodies are applied & used to identify the protein in a sample

harmful genes

genomics can be used in medicine to identify ___________ ________ and in forensics to identify bodily remans & weaponized pathogens

development

4 major _________________ processes

1. cell division

2. differentiation

3. pattern formation

4. morphogenesis

model

___________ organisms

1. easier to study since less complex

2. avoid ethical concerns

cell division, differentiation

C. elegans

model organism for what 2 development processes

1st model organisms for which a complete cell lineage was mapped

pattern formation

Drosophila melanogaster

model organisms for what development process in embryos

shown that development is driven by changes in gene expression

cell division, morphogenesis

Xenopus laevis (African clawed frogs)

model for what 2 development processes

large, translucent eggs are ideal for studying cell divisions of embryos

frogs undergo body form change from tadpole to adult stage

G1, G2

Cell Division

- transforms single-celled zygote into a multicellular organism

- during early embryonic development, cell divisions occur rapidly, with which 2 cell cycle phases absent

cell cleavage

Cell Division

primary purpose of rapid divisions = split zygote cytoplasm into smaller volume (________ ______________)

cell cleavages

Cell Division

-once a certain number of _______ ____________ have occurred and development has progressed, G1 & G2 return to the cell cycle, increasing cell cycle length

zygote

a ___________ will divide to become every cell in your body

stem cell

this type of cell is any cell that has not adopted a particular cell fate, and therefore has the potential to become 1 of many cell types

self-renewal

Differentiation

- produces specialized/differentiated cells, which arise from division of stem cells

- ______-___________: when a stem cell divides, 1 daughter cell will give rise to cell that differentiate, while the other daughter cell replaces the original stem cell & retains properties of that stem cell

lineage

Differentiation

- depends on changes in gene expression

- DNA sequence in every cell of a given organism is the same, but different cell types will express different genes

- differentiated progressively restricts the number of fates a cell that descends from a stem cell can adopt

- descendent cells are in the same cell ___________ if they all can be traced back to the same stem cell

potency

stem cell __________ = range of possible cell fates the descendent cells may adopt

totipotent

this type of stem cell has the highest potency level

- able to form all tissues, including all extraembryonic tissues that are required to support embryonic development

- examples: zygote, blastomeres

pluripotent

this type of stem cell has the second highest potency level

- able to form all organism tissues, but not the extraembryonic tissues

- examples: embryonic stem cells

multipotent

this type of stem cell has the third highest potency level

- can only form certain types of cells

- cannot divide to form a complete organism

- examples: adult stem cells, which can differentiate into muscle cells, fat cells, neurons

unipotent

this type of stem cell has the lowest potency level

- only able to differentiate into 1 type of cell

- example: spermatogonia stem cells can only differentiate into sperm

axes

Pattern formation

- creates the body plan of an organism

- similar to blueprints for a building

- depends on differential gene expression based on location

- establishes 3 main body _______: anterior & posterior, dorsal & ventral, left and right

Hox genes

Pattern formation

each body segment is formed at correct locations through expression of _______ ________

conserved

Pattern formation

hox genes are highly ____________

hox mutations result in replacement of correct body part with those associated w/ another segment, not malformation

Morphogenesis

_________________________

- generation of an organism's body form

- similar to actual construction of building according to blueprints (pattern formation)

- depends on: cell growth, cell division, cell migration, changes in cell shape, apoptosis

cell growth and division are primarily responsible for increasing size and number of cells within an organism as it develops

extracellular matrix

Morphogenesis: Cell Migration

some cells must be able to migrate to different locations for the body form of an organism to develop properly

cells migrate through the ________________ __________, a mixture of carbohydrates & proteins secreted by cells to provide them with support and protection

function

Morphogenesis: changes in cell shape

- failure to adopt correct cell shape leads to inability of cell to ____________

- example: an adult stem cell can change shape into a muscle cell, a nerve cell, or a fat cell

necrosis

Morphogenesis: apoptosis

- programmed cell death

- highly controlled pathway that is activated by expression of genes in a cell death pathway

- different from ___________ = cell death caused by injury

appendages

Morphogenesis: apoptosis

during development, apoptosis is often used to "sculpt" _______________ or reduce cell numbers

example: webbed fingers → human fingers, tadpole with tail → tailless adult frog

undifferentiated

Nuclear Reprogramming

- reverses differentiation by resetting a differentiated cell to an ________________ stem cell

- requires that the epigenetic changes present in the differentiated cell's DNA be reversed

- 2 methods: Somatic Cell Nuclear Transfer (SCNT), Direct Programming

enucleation

Nuclear Reprogramming: Somatic Cell Nuclear Transfer (SCNT)

1. nucleus from a differentiated cell is removed & inserted into an oocyte or zygote from which the original nucleus has already been removed through __________________

2. transcription factors present in cytoplasm of oocyte or zygote then reprogram the differentiated nucleus back to a stem cell state

- this process is technically challenging

induced pluripotent

Nuclear Reprogramming: Direct Programming

stem cell-associated transcription factors are introduced into a differentiated cell, which reprograms the nucleus to create an ____________ ______________ stem cell (iPS), which is unable to generate a complete embryo or adult animal

cloning

nuclear reprogramming, particularly through SCNT, is closely associated with __________

reproductive cloning & therapeutic cloning both involve nuclear reprogramming

Reproductive

__________________ Cloning

- creates a genetically identical copy of an individual organism

- begins with SCNT

- results in a complete individual which is genetically identical to the individual from which the differentiated nucleus came

-potential to allow for reintroduction of extinct species

- potential to replicate important lines of livestock

Therapeutic

_____________ Cloning

- does not result in a complete individual

- produces patient-specific tissues that can be used in medical treatments

- similar to initial steps of reproductive cloning

- potential to provide patients with rejection-free organs and tissues and treatments for individuals with autoimmune diseases

induced pluripotent

because of ethical concerns associated w/ human embryos & therapeutic cloning, there is now considerable focus on ____________ ______________ stem cells, which are not derived from embryos & may provide solutions to some issues

evolution

________________ is the change in populations of organisms over time

- change in allele frequencies in populations

- happens at population level, not individuals

- is a result of any process that changes the genetic composition of a population over time

- historical record of change through time

genetic variation

___________ ______________ = different alleles of genes present in population

- variation in populations can be studied at different levels: morphology, genes, proteins, genomes

- genotype + environment → phenotype

evolutionary biology

main focus on ___________________ ____________ is to understand the evolutionary mechanisms = factors that cause allele frequencies to change over time

4 mechanisms: mutation, gene flow, genetic drift, selection

Mutation

Evolution Mechanisms: _______________

- any change in base sequence of DNA

- ultimate source of variation; gives rise to different alleles

- rare & not primary cause of changes in allele frequency within a population

gene flow

Evolution Mechanisms: _________ _______

- movement of alleles from 1 population to another

- can occur when an individual moves to join a new population, or when gametes in immature stages of plants are carried to new locations via wind or other organisms

- can occur when individuals of different populations mate

- can lead to new alleles being introduced into a population or shift in allele frequency

genetic drift

Evolution Mechanisms: ____________ ________

- change in allele frequencies due to random chance

- largest effect in small populations

- can cause 2 small populations that become isolated to significantly differ genetically

founder effect

Evolution Mechanisms: genetic drift - _____________ __________

when a new population is established by a small number of individuals, it is unlikely that they carry all the alleles found in the parent generation

frequent in island populations

bottleneck effect

Evolution Mechanisms: genetic drift - _________________ __________

- when a small number of individuals are contributing gametes to the next generation, the alleles they carry may not represent all the alleles found in the parent generation

- population losing genetic variation from drastic reduction in size

- common causes: diseases, natural disasters

selection

Evolution Mechanisms: ___________

number of offspring an organism leaves behind is affected by phenotype & behavior

Darwin suggested that natural selection leads to evolution

fitness

3 required conditions for evolution to occur by natural selection

1. variation: individuals within a population are variable

2. differences in survival & reproduction: in every generation, some variants are more successful at surviving & reproducing than others = higher "____________"

3. heritability: variations among individuals are passed from parent to offspring

natural selection

this is the process that occurs when environmental conditions affect which individuals produce the most offspring

outcome depends on both fitness & allele frequency; a strong fitness effect can act quickly on even small differences in allele frequencies

selection

when evolutionary forces interact, they can either work together or in opposition

example: mutations & genetic drift often counter _____________

gene flow can either promote or prevent evolutionary change

if less favorable alleles are continuously being introduced into a population through migration, it can hinder their removal through selection

reproductive

evolutionary fitness is a combination of survival, mating success, and number of offspring per mating

_______________ success

selection favors phenotypes with greatest fitness

equilibrium

Hardy-Weinberg Principle

proportions of genotypes in a population will remain constant assuming

(1) no mutation takes place

(2) no genes are transferred to or from other sources

(3) mating is random

(4) population size is very large

(5) no selection occurs

when the proportion of genotypes does not change, the population is said to be in Hardy-Weinberg _______________ = no evolutionary forces are acting on it

allopatric

2 major categories of species isolation

1. sympatric: species live in the same geographic location & often utilize different parts of the habitat

2. _____________: species live in different geographic locations and are often separated by some sort of physical barrier

morphological

Sympatric species

- usually have visible ____________________ differences

- some may look the same, but have different mating calls or behaviors

gene flow

Allopatric species

members of geographically distant populations must still experience some ________ ___________ to continue to be the same species

subspecies

_______________ are populations of the same species in different locations that have distinct differences

fertile

members of the different subspecies must be able to produce ____________ offspring together to be considered part of the same species

reproductive isolation

_______________ _______________ is when individuals either will not mate with each other, cannot mate with each other, or produce sterile offspring

critical aspect of speciation

pre-zygotic

mechanisms of reproductive isolation can be _____________ (prevent zygote from forming) or post-zygotic (prevent fertile offspring from being produced)

ecological isolation

Pre-zygotic isolation mechanisms

this pre-zygotic isolation mechanism is when species that live in the same area may use different areas of the environment and not encounter each other often

behavioral isolation

Pre-zygotic isolation mechanisms

this pre-zygotic isolation mechanism is when differences in courtship rituals and mating calls prevents different species from accidently mating

temporal isolation

Pre-zygotic isolation mechanisms

this pre-zygotic isolation mechanism is when species capable of mating in lab may not mate in nature because they have different growing/breeding seasons

mechanical isolation

Pre-zygotic isolation mechanisms

this pre-zygotic isolation mechanism is when there are structural differences in reproductive systems of some plant & animal species, which prevent mating

prevention of gamete fusion

Pre-zygotic isolation mechanisms

this pre-zygotic isolation mechanism is important for animal species that shed gametes into water & plants that rely on wind or pollinators to transfer pollen

hybrid inviability

Post-zygotic isolation mechanisms

this post-zygotic isolation mechanism is when the embryos will not develop properly & may not be born at all or die shortly afterwards

hybrid infertility

Post-zygotic isolation mechanisms

this post-zygotic isolation mechanism is when hybrids do survive, but are sterile

fertile offspring

Biological Species Concept

- species = groups of actually or potentially interbreeding natural populations which are reproductively isolated from other such groups

- to be the same species, must be able to produce _____________ _________________

complications

- individuals we classify as separate species will mate & produce fertile offspring

- cannot be applied to asexual or dead organisms

- difficult to apply to geographically isolated populations

overestimates

Phylogenetic Species Concept

- species should only be applied to groups of populations that have been evolving independently from other groups of populations

- does not require knowledge about ability of allopatric populations to interbreed

- can be applied to sexual, asexual, alive, and dead organisms

complications

- _______________ number of species

- species may not always be descended from a single ancestor

reinforcement

__________________ takes incomplete pre-zygotic isolation differences and amplifies them when previously isolated groups come in reproductive contact again

drives speciation

speciation

given a long enough time period, any isolated population will diverge due to genetic drift

if divergence leads to traits which cause reproductive isolation, ______________ will occur

adaptive radiation

______________ ______________ = a group of species which have recently evolved from a common ancestor by adapting to different parts of the environment

- can lead to diversity