EXAM 2 IB

DNA

the molecule that holds hereditary information

(Deoxyribonucleic acid)

Can be described as a polymer and a polymer is a long molecule made up of tiny units named monomers and the monomers that make up dna are called nucleotides

Phenotypic

Manifestation of the physiological and behavioral traits of an organism like any observable traits

Genotype

Is the genetic information of an organism which are all hereditary traits that can be passed down from one generation to the next

Describe the relationship between the genotype and the phenotype of an organism

The genotype is the genetic information that gets passed down from parents to offspring across generations and the phenotype is the physical manifestation of those traits. It's is why evolution and natural selection is so important because if an organism didn't have the phenotype suited for a specific environment then that genotype wouldn't be passed down.

Environment and genetic factors

Both influence the phenotype and traits are very rarely just genotypical, like they can start out that way but in most cases can be influenced by environment like eye color, skin color and hair type, body type things of that nature are still incredibly influenced by your environment

Before the structure of DNA was discovered, experiments revealed an interesting, but at the time puzzling result - while the amount of the four nitrogenous bases in DNA samples from different species varied, the relative amount of always two bases was always the same. We now understand that this result is a consequence of the base-pairing rules.

In a DNA sample we collected from a flower, we find that 34% of the nitrogenous bases in this organisms DNA is made up of nucleotides that contain the nitrogenous base Guanine (G). Based on what you just learned about base pairing rules, predict what proportion of nucleotides in the genome of this flower contain the nitrogenous base Adenine (A).

16% (There are always the same amount of G and C, and A and T. So if 34% of the DNA sample consisted of G, then 68% had to consist of both G and C combined. This leaves 32% for A and T combined, and since there have to be equal amounts of each, A must make up 16% of this DNA sample.)

Genome

simply put it is the entirety of our genetic blueprint, it is stored on multiple long dna molecules in the nucleus. More detailed explanation is that it represents the sum total of your genetic instructions in the sequence of 4 nucleotide bases (AT and CG)

Nucleotide

Made up of 3 sub units

A phosphate group, a 5 carbon sugar and a nitrogenous base

The sugar and phosphates are arranged in such a way that they easily attach to other sugars and phosphates which is very sturdy and almost like a backbone

Double helix dna

Every molecule is made up of 2 sugar phosphate backbones and each one has the nitrogenous bases that stick out from that backbone

The nitrogenous bases stick out and attach to other ones and looks like the steps to a ladder.

Then the whole thing starts twisting and coiling tg which makes the double helix

4 nucleotide bases

Adenine, Thymine, Cytosine and Guanine

Can be arranged in any (paired) worder and doesn’t modify the structural into the molecule at all

(Think about it like the alphabet that conveys information when put in the correct order)

46 chromosomes

Our genome is not put into one single dna molecule it’s actually divided among 46 chromosomes which is a linear stretch of DNA contains many millions of nucleotide bases and is very coiled

Chromatin

Combo of DNA and histone complexes that is typically wound into a coil called the 30nm fibre

Plants store dna…

In the nucleus of cells and a little bit in mitochondria and chloroplast as well

Only thing that dna codes for…

Is how to make rna and from the rna how to make proteins

Protein

A string of amino acids that can be strung in any sequence together which is the ACTUAL information held in dna not this gene is for making my nose big which is why gene mapping is a thing because certain proteins will map to different areas and even code for more than one thing at once

The manufacture of all proteins happens in the cytoplasm outside the nucleus

Amino acids

There’s 20 that almost every organism uses and then a very rare one that occasionally gets utilized

Each one has extremely different chemical properties that make them react differently even under the same circumstances. Some are hydrophobic, some are polar or non polar some have varying ph values some coil up differently. There so many different variations that can occur which is why the different types of proteins they can make are basically limitless and how we humans have such variation in phenotype

Enzymes

Are how we are able to specify what kind of molecules our body can make

They have the ability to catalyze the reactions that allow us to build all of the organic molecules that are nested to build a cell

Explain how a cell can make a macromolecule such as a lipid from its glycerine and fatty acid subcomponents using the information that is stored in genes along a stretch of a DNA molecule.

A cell can make a macromolecule such as a lipid from its glycerine and fatty acid sub components by utilizing RNA. It acts as a messenger by translating the nucleotide language to the animo acid language and delivering it into the cytoplasm so the production of the lipid can take place.

Central dogma of biology

Answers how we get from the genetic material to the final protein product

It’s the steps of going from dna into making a copy into rna then taking that copy and turning it into the final gene product which is a protein

So simply put DNA→ RNA → protein

RNA

Messenger of genetic material

(Ribonucleic acid)

A copy was made from DNA to the very similar rna and it’s just a short snippet of the information that we want on the very long chromosome from our gene

Leaves the nucleus through little pores in the nuclear envelope and into the cytoplasm

Gene

Stretch of DNA that codes for a protein

Transcription of the genetic information

Is when we go from DNA to RNA

Transcription

Stays in the same “language” of nucleotides and simply transcribes the information from from one language into the language of animo acids

Begins with a bundle of factors assembling at the start of a gene to read off the information that will be needed to make a protein

Splicing

Simple way to describe:Unzipping the double helix and copying one of the two strands

The editing process RNA goes through before it can be translated into a protein

Involves removing the non coding regions (introns) and leaving only the protein coding (exons)

begins with the assembly of factors at the intron/exon borders which act as beacons to guide small proteins to form a splicing machine

Spliceosome

It brings the exons on the ither side of the intron very close tg so it can be cut

The introns form a loop when cut then are released

This process happens for every single intron in the rna and there are multiple Spliceosomes

Afterwards the Spliceosome disassembles

Introns

Non coding regions

Exons

Protein coding regions which are the complete instructions for the protein

Ribosome

Components of a molecular factory lock around the rna that snaked out of the nucleus

Translates the genetic information in the rna into a string of animo acids that will become a protein

Special transfer molecules bring each amino acid to the ribosome and there are different transfer molecules for each one of the 21 amino acids (prob need more information on that seems vague)

inside the ribosome the rna is pulled through, then the code for each amino acid is read off the rna, then the animo acid is added to the grown protein chain and after a few seconds the protein will start to emerge from the ribosome

Gene product

Is a protein aka the specific sequence of animo acids

RNA and dna…

Have mostly similar bases but rna has uracil instead of thymine.

mRNA

Has a single long chain instead of the double helix that dna showcases, string like open structure not many bonds

RNA polymerase

It splits apart the base pairs of dna at the beginning of a gene (gonna need further explaination ngl) “ I watched the video and now I understand more” still need to know the difference between a rna polymerase and a spliceosome

RNA polymerase happens first bc it is just making the rna then spliceosome comes next after that and is the thing that separates that rna between exons and introns

Rules for coding DNA

A → T

C → G

Special coding rules for RNA

A → U instead of T but C → G stays the same

DONT FORGET…. T goes to A still

Triplet code

Is written in words of 3 letters each, 3 bases long and each one codes for a specific animo acid

Codon

each one of the 3 groups of nucleotides and again they code for a particular amino acid

rRNA

ribosomal rna, is rna (made of 2 sub units) that gets folded in on itself along with other proteins and makes up the equivalent of an enzyme

tRNA

Transfer rna

AUG

Starts the protein sequence and codes for the amino acid methionine

3 stop condons

UAA

UAG

UGA

5 prime and 3 prime

Provide a sense of directionality to the blank and gives blank context on read direction to read the sequence from

Sugars in our nucleotides

Have 5 carbons

Genetic code is…

Unambiguous

Mutations

The origin of all genetic diversity that we see on earth is the result of genetic mutations that occurred at some point or another

More specifically it’s when we make a permanent change of one or more nucleotides in our long dna molecule

Important: that change in the nucleotide is really just a random accident that happened (do not believe that an organism needed a particular mutation to do something new and interesting and that’s why mutation happened is so not true)

Substitution mutation (categorized by cause)

one base pair is substituted for a different base pair in the sequence. For instance, if the original sequence read: CATACTTAG, a substitution mutation at the fourth base position from A to C would result in the sequence: CATCCTTAG

Simply substituted one nucleotide for a different nucleotide

“Indels” Insertion or deletion mutation (categorized by cause)

in insertions, one additional base pair gets inserted into a sequence, while in deletions one base pair gets removed. For example, an insertion of A after the 3rd position in the sequence CATACTTAG would result in the sequence CATAACTTAG.

Simply put these types of mutations add or delete nucleotides in the sequence and this can either push the whole sequence down when added or make the whole sequence shorter when deleted

Frameshift mutation (categorized by effect)

push the whole sequence down when added or make the whole sequence shorter when deleted

an indel mutation will often result in a frameshift mutation, because after the insertion or deletion of 1 or 2 base pairs, the reading frame of codons got shifted. This has a very severe consequence for the protein product following that mutation, because every codon downstream of the mutation will have been altered. Note that indel mutations that involve multiples of three base pairs will NOT result in a frameshift mutation, as the reading frame of codons in the rest of the mRNA molecule is preserved.

Silent mutations (categorized by effect)

Have no effect, a mutation did occur and happen but it has no measureable or meaningful effect

If a mutation occurred such that both the original and the altered codon code for the same amino acid, there is no effect - no change to the protein product, and we call the mutation silent. The redundancy of the genetic code results in more than one codon to code for the same amino acid bc there are so many varieties of amino acids some of the nucleotides code for the exact same animo acids so the even though a mistake was made it is overlooked

Missense mutuation (categorized by effect)

One of the amino acids got changed out for a different amino acid

if a mutation resulted in a new codon that codes for a different amino acid, the protein product is altered by that one amino acid at that position. The "sense" of the allele has changed since it changes the amino acid at that position in the protein, so we call it a missense (a mistaken sense). Missense mutations can differ in severity, depending on how important that changed amino acid was for the functioning of the protein.

Nonsense mutation (categorized by effect)

A codon that was meant to be an amino acid now reads as a stop codon and the protein was “truncated” meaning it ended prematurely. We are left with half a protein that is unfinished and the rest of it is missing and this is a horrible mutation with devastating consequences

if a mutation changes a codon so that it now codes for one of the three STOP codons, the final protein product will be truncated. Any part of the protein following this nonsense mutation will be missing. Nonsense mutations tend to have severe consequences on the functioning of a protein, as whole chunks of the protein are missing.

Remember: there is "no sense left" in the protein after a nonsense mutation, because the rest of the protein is missing.

Alleles

Different versions of a protein/gene

Think abt it like making a potato chip

The gene tells you the general instructions of how to make it and these instructions will differ slightly depending on what flavor/allele you want to end up with