bio semester 2 final

Prokaryotic cell

Does not contain nucleus and lacks other organelles, mostly found in bacteria and is unicellular

Eukaryotic cell

larger, contains the nucleus, and contains organelles

Asexual reproduction

produces offspring genetically identical to the parent 

Sexual reproduction

combines genetic material from two parents to generate genetically diverse offspring

specialized cells

• Skin cells

• Blood cells

• Muscle cells

• Neurotic cells

gene expression

• Each cell is different because they all have different functions. Some ways that different types of human cells differ from one another and makes them specifically suited for a particular function is gene expression. 

• Gene Expression: There are different expressions of genes in human cells, all human cells contain the same DNA but have very different structures and functions. Gene expression is the process of which a gene gets turned on in a cell to make RNA and proteins.

DNA replication

• 1. The DNA molecule unwinds and separates into two strands

• 2. DNA polymerase attaches to each strand and starts adding complementary nucleotides

• 3. On the leading strand, DNA polymerase can add nucleotides continuously, following the unwinding DNA strand. On the lagging strand DNA polymerase adds nucleotides in short fragments and eventually the fragments on the lagging strand are joined together by another enzyme called the DNA ligase (glue that sticks small pieces of DNA together)

• The result is two IDENTICAL DNA molecules, each containing one original strand and one newly synthesized strand. 

• Overall, DNA replication is like making a copy of a long twisted ladder (the DNA molecule) which each ring (nucleotide) carefully matched and added to create an exact duplicate

genome

complete set of DNA in an organism, every cell contains a complete copy of the genome and it is needed or a person to develop and grow because it provides all the info for the organism to function

gene

A gene is the hereditary material that is passed from parent to child. Genes are made up of sequences of DNA.

Chromosome

The building blocks of an organism and contains protein that help DNA in proper forms. They are tight threads that hold the genetic instructions for traits like eye color, height, etc. Humans have 46 chromosomes, 23 pairs, in each cell, with one set inherited from each parent. 

Nucleus

The structure in a cell that contains the chromosomes and is where the gene information is stored and is the cell’s “control center”

Binary fission

asexual reproduction within single-celled organisms used to create a copy within themselves creating an identical offspring, mostly in bacteria

mitosis

sexual reproduction that occurs in multicellular organisms like plants, animals and humans where it is responsible for growth, development and tissue repair.

MITOSIS STEPS

• Before a cell divides, it’s DNA is duplicated to form an exact match before dividing into two cells

1. Interphase

• G1 PHASE: The cell grows, carries out its normal functions, and prepares to replicate DNA

• SYNTHESIS: DNA replication occurs, ensuring that each chromosome is duplicated

• G2 PHASE: The cell continues to grow and prepares for cell division and synthesizes proteins and organelles required for mitosis

2. Mitosis 

• Prophase: Chromosomes condense and become visible 

• The nuclear envelope breaks down 

• Spindle fibers begin to form, extending from the centrosomes

• Metaphase: Chromosomes line up along the equator of the cell 

• Spindle fibers attach to the center of the cell 

• Anaphase: Sister chromatids separate and are pulled apart to the opposite sides of the cells by shortening the spindle fibers 

• Each chromatid is now considered an individual chromosome

• Telophase: Spindle fibers disassemble 

• Nuclear envelopes begin to reform around the separated chromosomes 

• Chromosomes begin to decondense 

3. Cytokinesis 

• The cytoplasm is divided, resulting in two separate daughter cells, each with its own nucleus containing a complete set of chromosomes. 

Each step during this process is ensuring that each daughter cell receives an identical copy of the genetic information that was present in the parent cell. 

Differentiation

process by which the cells change in structure and become caring specialized cells, and as cells differentiate they form groups with their own cells which eventually form tissue, and specific organs like the heart.

stem cells

Unspecialized cells that does not have any tissue specific structure

Adult stem cells

Adult stem cells are undifferentiated cells found in differentiated tissues of our bodies that can renew themselves or generate new cells that can replenish dead or damaged tissue.

fertilized eggs

The sperm fertilizes an egg, and it is called the zygote and the zygote goes through a process of becoming an embryo and developing into a fetus.

Embryonic stem cells

type of stem cell and they have the ability to differentiate into many different cell types in the body, and they have the potential to become any cell type, such as nerve, muscle or blood cells.

embryo

Unborn organism in the very early stages of development and made up mostly of stem cells and forming specialized ones.

Cell specialization

process of which the cells in a multicellular organism become specialized to perform specific functions.

Differentiation

• Series of changes that occur in a cell as it becomes specialized to perform a specific function within body

• Initially each cell starts out as a stem cell and as development progresses cell undergo differentiation, where they acquire distinct structures, functions and characteristics

DNA is the “cookbook” for protiens

• DNA: instruction manual/ recipe book or the cell, and contains all the genes, which are the individual recipe for making proteins 

• Gene: specific sections of DNA that contain the instructions for making proteins. Each gene is like a recipe in the cookbook. 

• Proteins: these are the finals products synthesized based on the instructions provided by genes and carry out various functions in the cell 

• In order to “cook” the dish, you must turn the gene on and they are turned on at different times and in different cells, depending on what the cell needs.

• Essentially, cells turn on different genes to make the proteins they need for their specific tasks

regulation of cell cycle

Regulation of the cell ensures the cells divide at the right time, place and under the right conditions and control progression through the cycle by activating or inhibiting various checkpoints

what is cancer caused by? MUTATIONS!!

 In the checkpoints of each phase, check for errors before moving onto the next step. If there is a mutation in a gene for a protein that controls a checkpoint, this can lead to cancer.

• Cancer arises from defects in the mechanisms that regulate the cell cycle, such as mutations in genes that control cell division or DNA repair. 

• These mutations can cause cells to bypass checkpoints that normally prevent abnormal growth and division leading to tumor formation

what is DMD

• DMD is a genetic disease in which you lack a protein which is dystrophin, a muscle-bonding protein and they lack it because of a gene mutation

• Dystrophin acts as a stabilizer during muscle contraction to prevent contraction-induced damage.

• An absence of dystrophin causes the muscular dystrophies, a group of inherited diseases in which the muscle damaged leads to muscle degeneration

Why does DMD usually only affect boys

Parts of the body like the muscle and respiratory systems are impacted by DMD because it makes the muscles weaker and dystrophin is sort of like a glue for muscles

Three types of muscles

• There are three types of muscles; smooth, cardiac and skeletal

• Smooth- calf, stomach

• Cardiac- heart

• Skeletal- skull

• The type of biomolecule our muscles are made up of are proteins 

• Actin and myosin work together to make the muscle contract; the myosin grabs onto the actin and pulls it which is what moves the muscle

types of proteins (TESDSC)

• Transport proteins are what cause osmosis and diffusion

• Enzymes break down food 

• Structure is can be the skeletal structure of your body

• Defense proteins are antibodies

• Storage proteins are stored in tissue 

• Communication proteins are the messengers of the cell

DNA codons

A DNA triplet is a group of 3 bases on the DNA strand, and when we read it as groups of 3 they are amino acids that make up a protein

transcription

• Transcription is the process by which genetic information encoded in DNA is copied into the messenger RNA (mRNA)

• (mRNA) is a molecule that carries genetic information from the DNA in the cell nucleus to the ribosomes in the cytoplasm, where it is used as instructions 

• During transcription, the enzyme RNA polymerase binds to a specific region of the DNA and unwinds the double helix. Then, RNA polymerase synthesizes the mRNA molecule by pairing the RNA nucleotides with the complementary strand (ATCG- UAGC) 

• A binds with T in DNA, and A binds with U in RNA

• This resulting mRNA carries the genetic information from the DNA to the ribosomes in the cytoplasm, where it serves as a template for protein synthesis during translation. 

3 steps of transcription

• Initiation : in this stage, the ribosome gets together with the mRNA and the first tRNA so translation can begin.

• Transcription begins with the binding of RNA polymerase to a specific region in the DNA

• The DNA double helix unwinds 

• RNA polymerase then starts synthesizing a complementary RNA strand using on of the DNA strands as a template 

• Polymerase is a special kind of enzyme that helps build long chains of molecules

• Elongation : in this stage, amino acids are brought to the ribosome by tRNAs and linked together to form a chain.

Termination :in the last stage, the finished polypeptide is released to go and do its job in the cell

Translation

• Initiation:

  • mRNA binds to a ribosome

  • tRNA (transfer RNA) carries the amino acid methionine, or the “initiator” to start codon AUG on the mRNA

  • Ribosomes bring together the mRNA and tRNA with the help of initiation factors

• Elongation:

  • Ribosome moves along the mRNA 

  • tRNA molecules carry the amino acids bind to the ribosome, matching their anticodons with the codons on the mRNA

  • Peptide bonds form and create a POLYPEPTIDE CHAIN 

  • The ribosome moves to the next codon, shifting the tRNAs and mRNA

• Termination 

  • When a stop codon is reached on the mRNA, a release factor bands to the ribosome

  • This causes the release of the polypeptide chain from the last tRNA in the ribosome

  • The ribosome releases mRNA and tRNA

• A protein is formed!!!

Overall, translation converts the nucleotide sequence of mRNA into the amino acid sequence of a protein, following the genetic code. Each three-nucleotide codon on the mRNA corresponds to a specific amino acid or a termination signal, ensuring that the correct sequence of amino acids is assembled to form the final protein product.

Polypeptide chain

• Polypeptide chain is a string of amino acids connected by peptide bonds 

• Poly means many, and peptide refers to protein 

• Polypeptide chain is the building blocks of proteins or amino acids and the make up proteins

Mutations

• A beneficial DNA mutation will benefit the protein and change the structure and function of the protein

• A harmful mutation prevents the protein from being able to function properly 

• Mutagen- A mutagen is anything that can cause a mutation in a cell. An example can be smoking cigarettes, because it will change the proteins from working properly. 

• The difference between a point mutation and frameshift mutation caused by a deletion: Point mutations change a single nucleotide, and frameshift mutations are additions or deletions of nucleotides that cause a shift in the reading part. The frameshift mutation leaves to a more defective protein because more is changed and adding and deletion form a completely new protein. 

• The specific mutation that causes DMD is a frameshift mutation

Codons

• A codon is a sequence of three DNA or RNA nucleotides that corresponds with a specific amino acid or stop signal during protein synthesis. 

• Codons are found in mRNA.

• A stop codon is what halts the process of protein synthesis when the protein is ready.

gel electrophoresis

• Gel electrophoresis is a technique used to separate and analyze molecules, like DNA and RNA or proteins based on their size and charge 

• A gel is in a rectangular mold and contains small pores through which molecules can migrate. 

• DNA molecules have negative charge 

• The gel used in gel electrophoresis is typically made up of agarose

• The gel in the wells of a gel electrophoresis machines have a negative charge 

• DNA travels to the positive side after being placed in the well

Gene editing

• Genetic diseases are caused by mutations in the DNA, which leads to incorrect amino acids being added to a protein. This results in a defective protein that can’t do its job. 

• Gene editing works by cutting pieces of DNA using CRISPR to see which DNA needs to be replaced and they replace the faulty gene with a healthy one

• CRISPR is a long functioned bacteria immune system, and it uses two main components of short snippets of repetitive DNA sequences

• The second is Cas, or CRISPR proteins which chop up DNA like molecular scissors. 

• When a virus invades the bacterium, cas proteins cut out a segment of the viral DNA to stitch into the bacterium’s CRISPR region

• To manipulate CRISPR to cut the DAN segments they’d like, scientists first design a guide RNA (gRNA) to match the gene they want to edit and attach it to cas9

• Like the viral RNA  in the CRISPR  immune system, the gRNA directs Cas9 to the target gene, and the proteins molecular scissors snip the DNA

• Once the DNA is cut, the cell will try to repair it by joining the ends together

MEIOSIS

• Prophase 1: the chromosomes condense, and the nuclear envelope breaks down and crossing over occurs. 

• Metaphase 1: pair of homologous chromosomes move to the middle the cell 

• Anaphase 1: homologous chromosomes move to the opposite poles of the cell 

• Telophase 1 and cytokinesis: chromosomes gather at the poles of the cells and the cytoplasm divides 

• Prophase 2: A new spindle forms around the chromosomes 

• Metaphase 2: chromosomes line up in the middle 

• Anaphase 2:  centromere divide and chromatids move to the opposite poles of the cells

• Telophase 2 and cytokinesis: A nuclear envelope forms around each set of chromosomes and the cytoplasm 

haploid cells

• Haploid cells contain half the total number of chromosomes, 1 of every kind (23 chromosomes)

• Haploid cells are formed by the process of meiosis and haploid cells are only used for sex cells. 

• Daughter cells are considered haploid

Since meiosis consists of a single phase of DNA replications and undergoes two cell divisions which results in 4 haploid cells.

Diploid cells

• Diploid cells the normal number of chromosomes, 2 of every kind (46 chromosomes) 

• Parent cells are considered diploid

Gamete cells

• Gamete are haploid cells and each cells carry only one copy of each  (1) chromosome

• Gamete cells are reproductive cells and in females they are called egg cells and in males they are called sperm cells.

Independent assortment

Independent assortment: During metaphase 1 of meiosis, mothers and fathers chromosomes line up in a random assortment

• Independent assortment is like shuffling a deck of cards, where each chromosome pair gets randomly divided into sex cells. 

Crossing over

Crossing over: the chromosomes exchange pieces of DNA making more space for genetic variation 

Crossing over is when chromosomes exchange pieces of DNA, mixing up the genetic code. Lastly, during fertilization, an egg and sperm join, creating a new combination of genetic material that's a mix of both parents. These processes make each person unique, like a genetic puzzle with pieces from both mom and dad.

Homologous chromosomes

• Homologous chromosomes are pairs of chromosomes that carry the same genes, one inherited from each parent and play a key role in genetic inheritance and variation. 

• During meiosis homologous chromosomes undergo pairing, crossing over and separation which ensures genetic diversity in sexually reproducing organisms.

Random variation

Random variation: random combination of one egg and one sperm

Homozygous

same (CC or cc)

heterozygous

Cc - different

Monozygotic twins

twins that shared the same egg and sperm cell but was split 

dizygotic

twins that did not share the same sperm and egg cell and had completely different egg and sperm cells

melanin mc1r gene

• The MC1R gene provides instructions for making a protein called melanocortin 1 receptor and this receptor plays an important role in normal pigmentation 

• The OCA2 gene makes a protein that makes melanin

• Mutations in the OCA2 and MC1R gene have been linked to conditions such as albinism and fair hair, light colored eyes 

• Tyrosinase is a gene that codes for a protein that is responsible for the first step in melanin production, and because it is the first step having a mutation on the TYR gene can cause the alleles to disrupt the normal production of melanin

eumelanin

• dark skin

• Populations with dark skin pigment evolved in climates with a lot of sunlight and dark skin pigmentation protects people against skin cancer and getting sunburnt

pheomelanin

• light skin

• Populations with light skin pigment evolved in climates of a little sunlight and light skin pigmentation protects people against vitamin D deficiency

Incomplete dominance

Incomplete dominance is instead of displaying the dominant trait only, it shows a display a blending of the two traits

Codominance

Codominance is pairs of alleles that are both expressed equally in the phenotype of a heterozygous individual

X-linked heritage

X-linked inheritance- males always inherit an X-linked trait from their mother  and a mutation in the copy of the gene on the single X chromosome causes the condition because they only have one X chromosome

Patterns for X-linked Recessive Inheritance

• 100% incidence of affected sons from an affected mother suggests X-linked recessive

• Affected fathers will pass their traits to all their daughters, who will be carriers but will not express the trait; son of the affected fathers will not inherit the trait since they inherit their Y chromosome from their father, not their X chromosome

• Affected mothers can pass the trait to both sons and daughters, but sons are more likely to express the trait as they only have one X chromosome. Daughters will only express the trait if they inherit the affected X chromosome from both parents. 

Patterns for X-linked Dominant inheritance

• 100% incidence of affected daughters from affected father suggests X-linked dominant 

• Affected fathers will pass the trait to all their daughters but to none of their sons as male inherit their X chromosome trait from their mother 

• Affected mothers can pass the trait to both sons and daughters, but sons are more likely to express the trait as they only have one X chromosome. Daughters will only express the trait if they inherit the affected X chromosome from both parents

Autosomal traits

it is passed down equally between males and females

X linked:

if the trait is determined by genes located on the X-chromosome, it will affect males more than females.

Why can organisms decode the information in each others genes

Organisms can decode the information in each others genes because the way organisms process codes from DNA and make protein are the same. Since they read the codes the same way they can decode the information of each others genes. 

anatomical evidence

Anatomy - Cetaceans show the most physical/anatomical similarities to mammals through their ankle bones, limbs, and more. We can see what they most relate to because of the patterns in bone structure and limb evolution in anatomy.

Fossil evidence

Fossils - Fossils point out the bones, also mentioning the ankle bones, and how many bones in the limbs they have and the similarities of those bones. Fossils help see the evolution of limbs versus fins as well.

Embryonic evidence

Embryos - Modern cetaceans lack hind limbs, even though their earliest embryos contain hind limbs. We can compare other embryos to see patterns in hind limbs as well and use that to find their closest living relatives.

DNA evidence

We use DNA to see how many genes match with each other when comparing organisms. While comparing the DNA of a hippopotamus and a cetacean, we can see that their DNA in their genes match almost completely.

How do mutations and allele shuffling increase variation within a population?

• With things like mutations and allele shuffling, this increases variation

• With more variation, the trait can become more favorable and more suited to the enviorment

biological fitness

Fitness is how fit an organism is in the environment that they live in so: 

• The ability to survive to reproductive age

• Finding a mate in the environment 

• Producing offspring 

• If your genotype is passed on in future generations

The more offspring an organism produces during its lifetime, the greater its biological fitness

things that can help determine if two organisms are the same or different species

1. Based on reproductivity: members of different species won’t or cannot mate with another, and if they do the resulting offspring are often sterile 

2. Using DNA evidence, you can compare the amino acid sequences and see how closely related two organisms are

3. Evidence from embryos

Directional, stabilizing and disruptive selection

• Stabilizing

  • The intermediate trait is favored

• Directional

  • One of the extremes is favored

• Disruptive 

  • Both extremes are favored 

    • Can lead to new species

geographic barrier

physical separation of populations of organisms due to geographical barriers

behavioral barrier

When species are reproductively isolated from others due to differences in behavior

temporal behavior

Temporal isolation means ‘isolated in time’ so the organisms breed during different times, for example some birds breed during spring and some during fall or summer.

small population

When a small group of individuals from a larger population forms a new population, genetic diversity decreases, increasing the chance of genetic drift and potentially leading to unique evolutionary changes.

Non-random mating

Organisms choose mates based on specific traits, influencing the distribution of genetic traits within a population over time.

Mutation

Random changes in the DNA sequence can introduce new genetic variations into a population, which can be inherited and contribute to evolutionary change.

gene flow

Movement of individuals or their genes between populations can introduce new genetic variation, reducing differences between populations and maintaining genetic diversity.

natural selection

Environmental pressures favor individuals with certain advantageous traits, leading to their increased survival and reproduction, which ultimately drives evolutionary change within a population.

PEPPERED MOTHS- variation

Before the industrial revolution, there was variation in the color of peppered moths in England. Some were light-colored, and some were darker. This variation existed naturally within the population.

PEPPERED MOTHS- overproduction

Peppered moths produce many offspring, more than can survive. This leads to competition among the offspring for resources like food and space.

PEPPERED MOTHS- competition

The light-colored moths were well-suited to blend in with the light-colored trees in the pre-industrial environment. However, when the industrial revolution occurred, soot from factories darkened the trees. This created a new environment where the lighter moths stood out more, making them easier targets for predators.

PEPPERED MOTHS- adaptation

In response to the changing environment, moths with darker coloration had an advantage. They were better camouflaged against the darkened trees, making them less likely to be eaten by predators. As a result, these darker moths were more likely to survive and reproduce, passing on their advantageous dark coloration to future generations.

allopatric

something geological keeping them from mating and over time, they get more genetic differences

sympatric

happens in the same area, but there is something else preventing it from happening