Gentics Exam 2 (Full)

Prokaryotic Genome Size

Bigger than viruses, smaller than Eukaryotes

Prokaryotic Genome

single circular chromosome (makes up 90% of the protein-coding sequences)

Prokaryotic Reproduction

Binary fisson, all bacteria would be clones if not for Horizontal Gene transfer

Plasmids

small circular DNA molecules that replicate separately from the bacterial chromosome, replicate more often than the cell cycle, plasmid research is critical for insulin production for diabetes.

horizonal gene transfer

Conjugation, transformation, transduction

Conjugation

plasmids and other DNA are transferred between bacteria during cell-to-cell contact. Only takes place during ideal conditions (Temp, pH, etc).

Transformation

The bacteria picks up other DNA from its environment. Typically it is DNA fragments that can from recombinant chromosomes within the recipient cell. (DONE VERY OFTEN IN THE LAB)

Competent Bacteria

bacteria capable of naturally performing the transformation. Only 80 natural species. However, it is very commonly done artificially with other species in the lab.

Types of In-lab transformation

Chemical, physical, electroporation, combined, other

Can conjugation occur between different species?

Yes, this often promotes antibiotic resistance

In-Lab transformation

Scientist insert a gene of choice to promote the synthesis of specific proteins (common example is adding bioluminescent to they can identify things under a microscope)

Transduction

viruses move DNA from one infected bacteria to a new host bacteria. (Like mosquitos and blood born disease in humans). Transduction is very rare in nature, and only moves small amounts of DNA from host to host.

F-Factor

A plasmid that allows conjugation in E-coli, and can integrate into the bacterial chromosome to from Hfr cells. Plasmids like this often carry genes for antibiotic resistance and can spread through populations or across species.

Hfr cells

A bacterial cell with a conjugative plasmid integrated into its chromosomal DNA, enabling it to transfer chromosomal genes during conjugation more efficiently than F+ cells.

phages can attack bacteria in two ways

Lytic stage, lysogentic stage

lytic stage

phage infects bacteria, uses it to replicate its own proteins until it causes the bacteria to burst (lyses), releasing the new phages that had been developing inside the bacteria.

Lysogenic stage

phage incorporates itself into the genome of the bacteria, where it stays dormant and continues to replicate its own genetic material, Allows the bacteria to survive.

Relationship between lytic and lysogenic

A virus usually either starts lytic and converts to lysogenic after an intense immune response. Or it begins in the lysogenic stage and lye dormant until the immune system is weak. A key example of this is chicken pox/shingles.

Restriction modification

type of bacteria defense against phages: uses restriction enzymes to cute DNA sequences that are foreign. Methylation is used by the cell to prevent the enzymes from cutting its own bacterial DNA.

CRISPR-CAS

essentially a bacterial immune system. After an initial viral attack, the bacteria is able to learn and recognize that virus, by cutting up a small portion of the virus and integrating it into its own genome (spacers). It is inserted into repetitive sections of DNA (palindromes)

palindromes

A sequence of nucleotides in DNA or RNA that reads the same in both directions (5' to 3' and 3' to 5') on complementary strands, often forming a structure that can have biological significance.

Spacers (bacteria)

Short sequences of DNA found in the CRISPR loci of bacterial genomes, derived from past infections by viruses (phages), which serve as a genetic "memory" of those invaders.

A short sequence of DNA in a virus or plasmid that is targeted and cleaved by the CRISPR-Cas system during an immune response in bacteria. It is the sequence that corresponds to the spacer incorporated into the bacterial CRISPR array.

Expression

CRISPR puts previously viral DNA and incorporates it into its DNA (pre-crRNA)

Maturation

pre-crRNA is processed into crRNA which help CAS proteins identify the viral DNA

interference

last step of CRISPR. cr-RNA guides the CAS proteins to viral DNA and the crRNA binds to it. Together they cut up the viral DNA.

PAM (protospacer adjacent motif)

A short DNA sequence immediately following the protospacer in the genome of an invading virus or plasmid, required for the CRISPR-Cas system to recognize and cut the target DNA. Without PAM, bacteria may cut itself

Cleavage / Cleaving

The process of cutting or breaking a DNA, RNA, or protein molecule at specific sites by enzymes or other mechanisms.

MOTIF

A short, recurring sequence or structural pattern in DNA, RNA, or proteins that has a specific biological function or significance.

CRISPR modern relevance

highly relevant in fighting human diseases and developing new gene treatments.

Viruses have...

adaptive anti-CAS / CRISPR proteins to fight back against bacteria retaliation.

Only ____ % of bacteria have CRISPR-CAS

50% ; without CRISPR bacteria is unable to recognize previous viral attacks and must rely on other methods of protection

Potential evolutionary benefits to not having CRISPR - CAS

allows for increased genetic diversity and adaptability (acquire more foreign DNA and integrate it into their genome), maintaining CRISPR is very energy taxing, so less energy cost, avoid autoimmune responses/self destruction

Viral genomes

can be DNA or RNA based, single or double-stranded, some use reverse transcriptase (HIV)

reverse transcriptase

An enzyme that synthesizes complementary DNA (cDNA) from an RNA template, commonly found in retroviruses like HIV.

RNA virus

small genome, high mutation rates

Viruses have a strong natural selection for:

Size, replication speed, small compact genomes

Influenza / COVID

relativley small, single stranded RNA virus, can adapt and rapdily replicate

Giant viruses

700,000+ kb, 500+ genes, affect zooplankton

Viruses can be

circular or linear genomes, but more commonly linear

DNA viruses...

hijack their host to synthesize replication

RNA viruses..

use RNA polymerease to replicate in the cytoplasm of the host

retroviruses

use reverse transcriptase to integrate their DNA into the host genome (HIV)

HIV (AIDS)

a retrovirus that attacks the immune system to the point where a common cold could kill the human host. Transmitted through sex, blood, birth. Infects the CD4, CC5 immune cells.

-Delta 32 mutation in CCR5 gene

a very rare mutation that makes humans resistant to HIV. May have evolved from the Vikings, or survived the plague. This mutation has not grown at the same rate as HIV, and a very small amount of people have this trait (primarily in Europe)

HIV may have come from..

sooty mangabeys (monkeys kept at pets), or hunting chimpanzees

Heredity requirements

must encode lots of information, passes on through generations, able to code for different phenotypes, vary between species and individuals

Johannes Friedrich Miescher

first researcher to isolate nucleic acid (studys on pus)

Albrect Kossel

discovered nitrogenous bases

Aaron Lovene

discovered nucleotides

What distinguished DNA as the hereditary molecule?

In 1952 a radiolabeled phosphorus test proved that DNA was the hereditary molecule and not proteins.

Rosalind Franklin and Maurice Wilkins

discovered DNA structure with X-ray crystalography

James Watson and Francis Crick

(1953) discovered the double helix shape

Components of DNA

Sugar, nitrogen-containing base, phosphate

Nitrogenous bases

purines and pyrimidines

Purines

Adenine and Guanine (2 rings)

Pyrmidines

cytosine, thymine, uracil (one ring)

Phosphates are attached to sugars at

5' and 3' postions

Primary DNA structure

string of nucleotides connected by phsophodiester

Phsophodiester

A covalent bond that connects nucleotides in the primary structure of DNA and RNA by linking the 5' phosphate group of one nucleotide to the 3' hydroxyl group of the next nucleotide.

DNA is

2 stranded, anti parallel

Hydrogen bonds

weak bonds that form between the complementary nitrogenous bases

secondary structure

3D DNA (double helix)

Major and minor grooves

The indentations on the surface of the DNA double helix that result from the twisting of the two strands, providing binding sites for proteins and other molecules.

B-DNA

The most common form of DNA in cells, characterized by a right-handed helical structure and specific dimensions.

A - DNA

A right-handed helical form of DNA that is more compact than B-DNA, characterized by a shorter and wider helical structure, typically observed in dehydrated conditions or in the presence of certain DNA-binding proteins. A-DNA has 11 base pairs per turn and features deeper major grooves and shallower minor grooves compared to B-DNA.

Z - DNA

A left-handed helical form of DNA characterized by a zigzag appearance and an irregular backbone, typically occurring in regions of DNA with alternating purine and pyrimidine bases. Z-DNA is narrower and more elongated than both A-DNA and B-DNA, with 12 base pairs per turn and a more pronounced zigzag configuration, often associated with transcriptional activity and biological processes involving gene regulation

Hairpins

stems and loops in single stranded DNA or RNA

Tertiary structure

how DNA is folded to fit inside the cell (3-D) shape

How long is human DNA?

It can reach the sun and back hundreds of times

Challenges of DNA

has to fit in the cell, to has to be accessible to be copied and transcribed, needs to fold and unfold

Toposiomerase

supercoiling causes by topsiore enzyemes. Makes it more space effcicent

RNA Structure

single stranded, ribose sugar, hairpins

Types of RNA

mRNA, tRNA, rRNA, microRNA, etc

mRNA

messenger RNA; type of RNA that carries instructions from DNA in the nucleus to the ribosome

tRNA

transfer RNA; type of RNA that carries amino acids to the ribosome

rRNA

ribosomal RNA; type of RNA that makes up part of the ribosome

microRNA

A class of small, non-coding RNA molecules, typically 21-25 nucleotides in length, that play a crucial role in the regulation of gene expression by binding to complementary sequences in target messenger RNAs (mRNAs).

RNA activties

protein synthesis, gene regulations, catalysis

Eukaryotic DNA is in the form of

chromatin

Types of chromatin

euchromatin and heterochromatin

Euchchromatin

The less condensed form of eukaryotic chromatin that is available for transcription.

Heterochromatin

highly condensed chromatin, centromeres, telomeres, other suppressed sites. Condensation makes hetero strain darkly in cells.

Histone proteins

package eukaryotic DNA, give DNA the beads on a string appearance

Nucleosomes

histone octamer - 8 histones in 1 balls, further wound by a 30 nanometer fiber

Linker DNA String

the DNA between each nucleosome, not associated with histone proteins

+H1 protein

holds DNA to the histone ball

Histone tails

they are outside the histone ball and can be chemically modified

If enzymes add an acetly group to the histone tails..

it changes the charge from positive to negative (histone is loosened) and the DNA becomes much easier to transcribe

Endometrial histone acetylation

The process by which acetyl groups are added to histone proteins in the endometrium (the inner lining of the uterus), resulting in changes in chromatin structure that can influence gene expression related to reproductive functions.

centromeres

mostly heterochromatin, CENP-A (histone protein) binds to the kineticore

Telomeres

characteristic sequences, repetitive sequences, protect the ends, shortening

Telomere shortening

chromosomes shorten every cell division. chromosome gets too short, cell dies

T-loop

Lasso-like structure at the end of a telomere that serves to protect the termini of a chromosomal DNA molecule from end-to-end fusions and degradation by exonucleases.

Organelles with their own DNA

mitochondria and chloroplasts

Mitocondrial replication

is usually independent of the cell cycle (split and fuse)

Endosymbiosis

bacteria was engulfed by another cell, the bacteria survived, and both benefited through symbiosis. Now we have mitocondria and chrlorplast

Evidence for endosymbiosis theory

organelle size (similar to a bacteria), organelle fission (similar to a bacteria), double membrane (similar to a bacteria), independent ribosomes and proteins, chloroplast resembles a cyanobacteria, circular genomes (bacteria have 1 circular chromosome and plasmids), molecular phylogeny

Primary endosymbiosis

chloroplast evolves from a cyanobacteria

secondary endosymbiosis

a process in eukaryotic evolution in which a heterotrophic eukaryotic cell engulfed a photosynthetic eukaryotic cell which survived in a symbiotic relationship inside the heterotrophic cell