Biology II Exam 3 Review

cell differentiation

the process by which cells with identical DNA become specialized to perform different functions

What does it mean that somatic cells are genetically equivalent?

Almost all body cells contain the same DNA. Different cell types arise because different genes are expressed, not because cells have different genes

four levels of gene expression control

- Transcriptional (DNA level)

- Post-transcriptional (RNA level)

- Translational (protein synthesis)

- Post-translational (protein modification/degradation)

epigenetics

Heritable changes in gene expression that do not involve changes to the DNA nucleotide sequence itself. Includes histone modifications and DNA methylation. Epigenetic changes can be reversed, unlike mutations

histone acetylation

Acetyl groups added to positively charged lysines in histone tails. This loosens chromatin structure, making DNA more accessible and promoting transcription (increased gene expression)

histone methylation

Methyl groups (-CH_3) added to histone tails condense chromatin, making DNA less accessible and leading to reduced transcription (decreased gene expression)

DNA methylation

Addition of methyl groups (-CH_3) to cytosine bases in DNA. Reduces binding of transcription factors, inactivating the gene. Genes more heavily methylated in cells where they are NOT expressed

Can epigenetics modifications be inherited?

Yes-- epigenetic modifications like DNA methylation can be passed from parent cell to daughter cell. Unlike DNA mutations, they can also reversed

transcription factors

Proteins that locate promoters and recruit RNA Polymerase II to express a gene. Required because RNA polymerase cannot initiate transcription alone

difference between general and specific transcription factors

General transcription factors are essential for all transcription by RNA Polymerase II but only low-level transcription. Specific transcription factors interact with control elements to produce high levels of transcription of particular genes

Mediator complex

A protein complex that communicates between regulatory elements (enhancers/silencers) and the transcription initiation complex. it bridges signals from activators/repressors to RNA Polymerase II

activator

Proteins (like transcription factors) that bind enhancer DNA elements to increase gene expression

repressors

proteins that bind silencer DNA sequences to decrease gene expression

proximal control elements

DNA binding sites for transcription factors located close to the promoter. They fine-tune transcription initiation alongside the promoter

enhancer elements

DNA sequences that can be near or far from the gene (thousands of nucleotides up- or downstream). Genes can have multiple enhancers. Activators or repressors bind them to increase or decrease gene expression

how do enhancers act at a distance

DNA-bending proteins loop the DNA, physically bringing enhancer-bound activators close to the promoter region so they can interact with general transcription factors

What modifications produce a mature mRNA?

1) 5' cap added to 5' end

2) Poly-A tail added to 3' end

3) Intron splicing-- introns removed, exons joined. These modification are essential for mRNA stability, nuclear export, and translation efficiency

alternative splicing

A process where exons from the same pre-mRNA can be joined in different combinations, allowing a single gene to produce multiple different proteins. A powerful regulatory mechanism

miRNA

Small non-coding RNAs (~21-23 nucleotides) that bind target mRNAs and either repress translation or promote mRNA degradation. Work through the RISC protein complex

siRNAs

Small interfering RNAs (~20-24 nucleotides), double-stranded. Guide the RNA-induced silencing complex (RISC) to degrade complementary mRNA, preventing protein synthesis

two examples of post-translational regulation

1) Modification and trafficking -- chemically modifying proteins and directing them to correct locations

2) Removal - degrading proteins via proteasome (misfolded/unneeded) or autophagy/lysosome (damaged cell components)

ubiquitylation

Tags the protein with a small ubiquitin protein, marking it for degradation by the proteasome. Also involved in protein localization, cell signaling, DNA repair, cell death, and immune responses

Do most somatic cells in a eukaryote contain the same DNA?

Yes-- almost all somatic (body) cells contain identical DNA. Different cell types arise through differential gene expression, not different DNA sequences

master regulatory genes

Genes that control other genes and help direct processes such as cell differentiation, body formation (morphogenesis), differences in gene expression, and programmed cell death (apoptosis)

morphogen

A signaling molecule that provides positional information to cells in a developing embryo. Cells respond differently depending on the concentration of the morphogen

bicoid

A morphogen found in fruit fly eggs. It is a transcription factor that helps tell cells where they are in the embryo. It is found concentrated at the anterior end and helps establish the head-to-tail body axis

Why do problems with maternal mRNA affect all offspring the same way?

Because maternal mRNAs are deposited in the egg before fertilization. All offspring from that female receive the same maternal mRNA, so any problems with it affect all offspring equally

homeotic genes

Determine which body parts form in specific locations during development. Mutations in homeotic genes can cause body parts to form in wrong locations

hox genes

an important group of homeotic/homeobox genes that are highly conserved across animals. They determine body plan and are organized in clusters. Their expression patterns determine which structures form along the body axis

What do Antennapedia and bithorax mutations show?

They demonstrate the role of Hox genes in development. Antennapedia causes legs to grow where antennae should be; bithorax causes an extra set of wings. Shows Hox genes control which structures form at specific locations

What happens when developmental genes are gained or lost?

Gaining or losing developmental genes can cause gain or loss of body structures. Ex: changes in Hox gene expression affect limb formation; loss of Sonic hedgehog can prevent hindlimb development

biological evolution

Change in the genetic compositition (allele frequencies) of a population over time, from one generation to the next. Individuals do not evolve-- populations do

What did Darwin and Wallace propose?

The theory of evolution by natural selection-- that heritable traits that improve survival and reproduction become more common in populations over generations

What is homology vs. homoplasy?

Homology: similarity due to shared ancestry (Ex: vertebrate limbs) Homoplasy: similarity due to convergent evolution in unrelated species (Ex: wings in bats and insects)

vestigial traits

reduced or non-functional structures that were functional in ancestors. Evidence of evolutionary change (ex: human tailbone, whale pelvic bones)

natural selections

environment selects for traits that improve survival/reproduction

artificial selection

humans intentionally select for desired traits in breeding programs

four mechanisms of evolution

1) mutation

2) gene flow

3) genetic drift

4) natural selection

mutation

creates new genetic variation

natural selection

differential survival/reproduction based on heritable traits

What is required for natural selection to occur?

1) Variation must exist in heritable traits

2) Variation must affect survival/reproduction (fitness). Natural selection acts on existing variation-- it does NOT create variation

adaptation

a heritable trait that increases an organism's ability to survive and reproduce in its environment

fitness

the reproductive success of an individual relative to others in the population

3 types of natural selection

1) directional selection

2) stabilizing selection

3) disruptive selection

direction selection

favors one extreme phenotype

stabilizing selection

favors intermediate phenotype, reduces variation

disruptive selection

favors both extremes, increases variation

microevolution

change in allele frequencies in a population over generations. Natural selection is the only mechanism that causes adaptive evolution

genetic drift

random chance events that alter survival and reproduction, thus changing allele frequencies. Most significant in small populations. Tends to reduce gentic variation through loss of alleles

founder effect

When a few individuals become isolated from a larger population and establish a new populatin. The new population's allele frequencies do not represent the original population, reducing genetic variation

bottleneck effect

A drastic reduction in population size due to a random effect. Results in a gene pool that no longer reflects the original population. Reduces genetic variation; some alleles may be lost or disproportionately represented. Can cause harmful alleles to become fixed

gene flow

The movement of alleles between populations through migration. Can increase or decrease the fitness of a population by introducing new alleles or removing alleles

Hardy-Weinberg principle

A mathematical model stating that allele and genotype frequencies in population will remain constant from generation to generation if no evolutionary forces act on it. If a population meets H-W criteria, it is NOT evolving

5 conditions for Hardy-Weinberg equilibrium

1) no mutations

2) random mating

3) no natural selection

4) very large population size

5) no gene flow

If any condition is violated, the population can evolve

phylogeny

A diagram showing the evolutionary history of a specie sor group of species. Shows patterns of descent, NOT phenotypic similarity. Does not show when species evolved or how much change occurred unless noted

binomial nomenclature

the scientific naming system using two parts: genus and species, part of the taxonomy classification system

clade

a group that includes an ancestor and all of its descendants on a phylogenetic tree

basal taxon

a taxon that branches off early in the history of group-- it diverged before other members of the group diverged from each other

sister taxa

groups that share an immediate common ancestor-- they are each other's closest relatives on the phylogenetic tree

outgroup

A taxon that is closely related to but not part of the group being studied. Used as a reference point to determine which characters are ancestral vs. derived

homology

similar traits due to shared ancestry (divergent evolution)

analogy

similar traits due to convergent evolution-- unrelated species develop similar adaptive traits in response to similar environments

homoplasy

a phenotype or characteristic that is similar between unrelated organisms due to convergent evolution, not shared ancestry. Ex: wings in bats and insects

shared ancestral characters

traits that originated in an ancestor of taxon

shared derivated characters

evolutionary novelties unique to a particular clade or taxon

maximum parsimony

The principle of choosing the phylogenic tree that requires the fewest evolutionary changes to explain the data. The simplest explanation consistent with the evidence

molecular homologies

Similarities at the DNA or protein level used to build phylogenetic trees. The length of a branch in a molecular tree can reflect the number of genetic changes that occurred