BIO 421 Exam 1: genes to genomes 2

1. coding

2. regulatory

3. duplications and deletions​

• DNA replication​

• Transposition

• meiosis

• Horizontal transfer

1. Changing amino acids that are being coded can change structure or shape of protein and how it interacts with others... in turn, altering function ​

2. Dictate where and when a gene is expressed ​

3. Entire extra copies of genes that are duplicated or entire genes that are deletions ​

How do these changes in the genome occur: ​

Everytime that DNA does replication there is a risk of error ​

Transposons bring genes to other places in the genome ​

Meosis BIG driver in evolution! Can have a huge duplication or deletion if meiosis does not happen in the correct alignment ​

HGT – passing of genes between different species ​

What are different types of genetic changes that may alter gene function? ​

1. Gene mutations that affect the protein _____ sequence​

2. Mutations within ____ regions (promoters for example)​

3. Gene ______

How do these changes in the genome occur?​

• Errors in ______

• _____​

• Errors during crossing over in ____​

• ______ (rare—maybe?)​

• DNA polymerase

• small

• coding

• expression

• divergence

DNA replication errors​

• Caused by______ making mistakes during DNA replication​

• Typically creates single base-pair substitutions or ____ insertions/deletions​

• Depending on location:​

• - Can affect ____ sequence​

• - Can affect gene _____​

• A major cause of nucleotide sequence ____ over evolutionary time​

Trying to create base pairing but its not perfect! ​

Can experience "spliiage" where is accidently skips a few bases or adds a few new ones that are not needed – usually small changes (less than 10 bp) ​

Effect can vary ​

Depends on if it occurs in a coding sequence – can change amino acid or have a stop/start codon ​

Gene expression – regulatory mutations ​

Mutations do not have to be a big deal! If its in a noncoding section then it will occur as normal! - nonimportant regions

duplications and deletions​

Biggest

repeitive

Unequal crossing-over during meiosis:​
Short repetitiveDNA sequencesare most likely remnants of transposons that are no longer active​

unequal cross-overs lead to ______

Larger changes! ​

_____ reason for whole gene mutations ​

Homologus chromomoes exchange parts... leads to better genetic diversity ​

Align based on sequence similarity ​

Can be problematic because when there are areas of _____ sequences... they can align on repetitve sequence instead of where they are suppose to!

Will not receive equal pieces! ​

One copy is going to receive too many... and the other will receive too little (no copies!) ​

One normal and one duplication​

One deletion and one normal "arm" ​

Answer: Yes ​

Immediatley after duplication... they are identical ​

Not enough evoltuinary time has occurred for them to have different functions... so they will produce the same proteins ​

Over evolutionary time though... they will diverge! ​

Would you predict that two genes that are the result of a duplication have the same function immediately after duplication?

redundancy

selective pressure

drift

Duplicated genes will acquire mutations resulting in genes with novel functions (Divergence):

​

Duplication creates ______ ​

The _______ decreases (bc if one gene cannot do it... its okay the other one can!) ​

Can free both of these copies to have mutations and ___ away from each other ​

• diverge

gene clusters

Over many generations duplicated genes will acquire mutations resulting in genes with novel functions:

• Genes that are related and near each other on the chromosome.. Flanked by repeitive DNA ​

• Duplications can keep occuring... can have 4 or 8 copies! ​

• Several copies of closely related genes... but they ____ evolutionarily to have different functions! ​

***for genes to be "flanked" means they have specific DNA sequences—known as flanking regions—directly adjacent to their 5′ (upstream) or 3′ (downstream) ends

It is common that if genes are flanked by short repetitive DNA sequences gene duplications can result in the presence of “______” – a group of highly related genes with different functions.​​

Hemogolbin

Heme

• 4 oxygen

• one

The hemoglobin gene family evolved from a series of gene duplication events​:

______ – allows you to carry oxygen in blood ​

_____ group to bind oxygen

• We have 4 chain hemoglobin... which have different types of globin that can bind _____ molecules ​

• marine worms, insects, and primitive fish only have ___​

***This means that evolutionarily... we used to have one but we evolved to have 4 based on duplications! ​​

• transposons

• genes or regulatory elements

• duplications

Mobile genetic elements: transposons​

• _____ are genetic elements that can change positions within the genome ​

• They can jump into _______, disrupting them​

• Sometimes when they move they take nearby sequences with them, creating _____​

• ****Not as common as unequal crossing over during meiosis​

Less common contributor to gene mutations... but can still cause them! ​

"jumping genes" - move locations ​

This can cause all sorts of disruptions ​

If it jumps into a coding sequence it can have a frame shift which can cause a stop codon ​

Can create duplications since they can bring sequences that is near them as well ​

rare

unrelated

conjugation

Horizontal Gene Transfer may also contribute to genetic diversity:

Most ____!! ​

One speicies is going to aquire genes from an ____ species ​

***Happens in prokaryotes and other single celled organisms ​

****If not, it can be a eukaryote and a small unicellular organism or a bacteria! ​

Common in bacteria! (through _____!) ​

cell endocytosis (takes up) bacterial cell and degrades it.... but sometimes the genetic material stays in the cell and gets to the nucleus

• single

• 0.1-1%

In bacteria horizontal gene transfer occurs by conjugation:​

Bacteria use conjugation to do HGT ​

Eukaryotes cannot do this with other species (can only reproduce with their own species) so how does it occur??? ​

Still an open question.. But hypothesis that the _______​

VERY theoretical

Conjugation is less common but can still occurin eukaryotes​:

• Mounting genomic evidence suggests that horizontal gene transfer can occur in eukaryotes​

• Most common in ____-celled eukaryotes ​

• Estimates vary, but between _____ of genes in some single-celled eukaryotes maybe from HGT​​

Answer: duplication of genes to create extra copies that can acquire new functions (A) ​

****#1 mechanism that creates new genes ​

De novo option: does not really happen ​

HGT – depends! Single-celled... possible! Multi-cellular... probably not! Not the most significant contribution ​
​

which of the processes listed below contributes significantly to the evolution of new protein-coding genes?

Answer: 20 micrometers ​

1,000 micrometers in 1 mm ​

1,000 nm in a um​

What is the typical size of a human cell?

• surface area to volume

• movement; membranes

10 um and 100 um

move things around and do chemical reactions

What is the typical length of a human cell?​

• Cell size is constrained by _____ ratio​

• This is important for ____ of molecules and exchange of molecules across _____​

Cannot see things below 1 mm in size with the naked eye ​

Most plants and animals are between _____​

***Exist in a restricted range bc they are restricted in a surface area to volume ratio! ​

In order to do the work of the cell... you need to ________​

*****Larger the cell volume the harder this is! (harder it is for enzymes to find their partners!) ​

• Specialization

Cells come in many different shapes and sizes​

• Euk multi-cellular organisms can come in many different shapes and sizes ​

• _____ helps them form specialized functions ​

read and comprehend

Evolution of internal compartments – 2 independent mechanisms:

Invagination: in an ancent pro cell... it became part of the cell ​

Engulfment: ancent pro/euk cell... engulfed a fully functioning organism and become organelle (endosymbiosis!) ​​

• nucleus, ER, golgi,endosomes, lysosome​

1. double

2. vesicle transport​

3. extracellular

The endomembrane system formed via invagination​:

• Endomembrane system =________

• Evidence:​

1. Nuclear envelope has a ____ membrane​

2. These organelles are connected or communicate via _____

3. The interior environment of the endomembrane system is more similar to the _____ environment than the intracellular one​

Endomembrane system – thought to evolve through invagination ​

All communicate with eachother and transfer part of membrane through vesicle transport ​

They can also send vesicles to fuse with plasma membrane... says that they membranes are all similar! ​

pH and content is similar to extracellular environment than what is happening in the cytosol ​

englufed

Mitochondria and cholorpast

• anaerobic

• Symbiosis

• aerobic

1. size

2. vesicle trafficking

3. binary fission

4. circular

5. bacterial

6. introns

• fix nitrogen​

• 2024

• DNA

Mitochondria (& chloroplasts) may have evolved from engulfed bacteria = endosymbiotic theory:

Free living prokayrtoic bacterium was ____ by cell and evolved to become an organelle ​

________​

​

• This suggests that the ancestral eucaryotic cell was cable of engulfing things.​

• One theory is that the ancestral eukaryotic cell may have been _____ and that a symbiotic relationship with an organism able to use oxygen to make energy was beneficial. ​

• _____ refers to the intimate association that results long-term selective advantage. ​

• But this original hypothesis stirred lots of controversy, especially since it sets a new paradigm for how ____ eukaryotes arose. ​

Evidence that Mitochondria & chloroplastshave prokaryotic origins​

1. Are same ___ as prokaryotic cell​

2. Do not participate in _____ that connects the organelles of the endomembrane system​

3. Divide by _____, independently from the rest of the cell​

4. Have their own DNA that is ____, not linear.​

• Sequence of many mitochondrial/chloroplast genes resembles ____ homologs​

• Genes do not have ___

The evidence!! ​

****Divide independently, which is separate from the rest of the cell cycle ​

****DNA is circular... not linear like eukaryotic DNA ​

****Euk genes have introns... pro do not ​

​

• ​​Previously only bacteria were thought to be able to _____

• 2024: discovery of a nitrogen-fixing organelle in a marine algae​

• A new example of endosymbiosis!​

Previously thought that cholorplast and mitochondria were only examples ​

Disovered a 3rd example in ____! ​

Algae could fix nitrogen.. Thought it could only do it in bacteria... but saw they had a nitrogen fixing organelle ​

Organelle has its own ____! So thought to be part of the endosymbiosis theory ​

Compound light microscope

• live

• transparent and colorless (low contrast)​

• refractive index​

• differential interference contrast (DIC)

Microscopy allows researchers to study cells​:

Modern _______​: Can be used to view fixed or living specimens ​

• Cheap, accesible, and easy to use ​

• Useful for ____ cell behavior ​

Visualizing cells with light microscopy​

• Most cells and tissues are_______

• Cellular components differ from each other in______

• Optical techniques such as phase -contrast and ________ can be used to view living, unstained cells

**Caviots/struggles: cells and tissues are transparent... so there is low contrast and hard to tell things apart ​

Different cellular components can reflect light differently ​

DIC – can make this contrast better ​

1. Fluorescent molecules/fluorophores

2. high energy state

3. longer wavelength(less energy)

Fluorescence microscopy​

1. _______ absorb light(energy) of a specific color (wavelength) ​

2. Fluorophores are excited by a particular wavelength of light into a _____. ​

3. The photon is emitted as light of a _______.​​

4. The chemical properties of the fluorophore determine its excitation and emission wavelengths.Many different fluorophores are available.​

**Emit light... so get incredible contrast (either glowing or not glowing!) ​

• jellyfish

• blue; green

Naturally

sequence

GFP tagging of proteins​

• A natural protein fluorophore expressed in ____​

• Absorbs ____ light and emits (fluorescent)____ light​

• DNA sequence can be fused to other genes and reintroduced into cells​

• Its discoverers won the 2008 Nobel Prize inChemistry​

Protein fluorophores!! ​

_____ occuring proteins that act as fluorphores (means you don't have to try and bind them to something... they are naturally occuring!) ​

Encoded by genetic ____ ​

*****Can take genetic sequence and put it into other organism ​

• GFP; promoter; tagged

• multiple

Genetically tagging proteins to image proteins in vivo:

• Can take DNA of protein and attach a copy of ___ for it, put a ____ on, and the cell can now express a ____ version, making the protein glow ​

• ****Can do this without disrupting the function of the protein (most of the time!) ​

Many genetically-encoded fluorophores are now available​:

• Can tag ____ proteins within a cell ​