Lots of bio

• DNA means deoxyribonucleic acid

  • stores genetic info

  • Code for how to make proteins

    • Humans have 80,000-400,000 unique proteins

  • responsible for an organism’s characteristics

  • All of the DNA is called a genome

    • a genome is 3 billion base pairs (bp)

• The monomer is a nucleotide

  • All nucleotides have the same basic structure

    • 5-carbon (pentose) sugar

      • deoxyribose

    • phosphate

    • Nitrogen base

      • Adenine (A), Guanine (G), Cytosine (C), and Thymine (T) for DNA

• DNA is double-stranded and the strands are anti-parallel

  • one runs from 5 prime to 3 prime and the other runs from 3’ to 5’

  • The two strands are complimentary

    • A goes with T (apple in a tree)

    • C goes with G (car in a garage)

• DNA strands are held together between nitrogen bases with hydrogen bonds

  • they are strong enough to hold them together but weak enough to be broken apart for DNA replication

  • like a twisted ladder

    • A and T and C and G bonds are held together with hydrogen bonds

    • the sides of the “ladder” (deoxyribose) and phosphate are held together by covalent (electron sharing) bonds

• DNA has two forms

  • chromatin - loose and unwound

    • easily read and used

  • chromosomes - tightly wound and compact

    • easily transported so nothing is lost

    • wraps around histones, which are proteins, to stay tightly wound

• DNA replication is a semiconservative process

  • means both original strands of DNA will be used and templates for the new strands of DNA

    • The final product is two identical strands of DNA where one strand was the original and the other was built and is new

• steps of DNA replication

  • INITIATION is the first step

    • an enzyme, helicase, will unwind and “unzip” DNA

      • breaks hydrogen bonds between the nitrogen bases

      • forms a structure called the replication fork

  • ELONGATION is the second step

    • Primase puts primers on the DNA strands to let DNA polymerase know where to start building new strands

    • DNA polymerase adds the complementary nucleotides to the exposed strands

      • can ONLY build from 5’ to 3’

    • leading strand - DNA polymerase builds the same way helicase is unzipping

    • lagging strand - DNA polymerase is building in Okazaki fragments, going away from the helicase

  • TERMINATION is the third step

    • DNA is checked for errors

    • Okazaki fragments are stitched together by ligase

  • Central dogma - DNA —> RNA —> Protein

  • Dogma is a principle or set of principles laid down that are indisputably true

  • DNA vs RNA

    • DNA

      • Built of nucleotides

      • Deoxyribose, phosphate, nitrogen base (A, T, C, G)

      • Typically double-stranded in structure

      • Found protected in nucleus

      • Long-term/stable

      • Has Thymine

      • One type

    • RNA

      • Built of nucleotides
        Ribose, phosphate, nitrogen base (A, U, C, G)

      • Typically single-stranded

      • Found inside and outside nucleus

      • Short-term/unstable
        Has Uracil instead of
        Thymine

    • Human genome has 20,000-25,000 genes

• TRANSCRIPTION

  • The way I remember TRANSCRIPTION is first step of Central Dogma is the "C" in Transcription. It comes before "L" that you will see in the second step known as TRANSLATION

    • Starts with DNA and ends with RNA
      RNA Polymerase = the enzyme that unzips,
      reads, and builds single-stranded piece of mRNA (messenger RNA)
      The enzyme knows where to begin unzipping, reading, and building because DNA has locations called promoter regions

    • Occurs in nucleus of eukaryotic cells

    • The DNA strand that runs 3' to 5' from left to right will be used as the template to make the RNA

  • RNA Polymerase starts building RNA at a PROMOTOR and will stop building RNA at a TERMINATOR

    • Final part of Transcription is making sure mRNA is ready to go outside the nucleus that is a wild and dangerous place within the cell.
      Splice (cut out) introns (unused region) and leave exons (used); stitch exons together; this is done by spliceosomes
      Add a protective cap to 5' end of mRNA

    • Add a protective tail to 3' end of mRNA

• TRANSLATION

  • Happens in cytoplasm

  • needs ribosomes

  • Take our mRNA out into the cytoplasm to the ribosome where the ribosome will attach to the 5' cap and look for START (AUG) codon

  • Then read mRNA a codon (three letter sequence) at a time.

  • tRNA will drop of the correct amino acid

  • Move to next codon and build a strand of amino acids (protein)

  • Translation will finish when you reach a STOP
    codon

• What is a mutation?

  • A change in the DNA sequence of an organism

  • Mutations can be positive, negative, or even neutral

  • Example: Hemophilia (mutation in clotting factor proteins of blood)

  • Example: Eye color (mutation in pigment that gives our eyes color)

  • Example: Dark fur color in Rock Pocket Mice (mutation in the pigment that determines fur color)

• Common mutagens (sources of mutations)

  • Radiation

    • UV Radiation

    • X-Rays

  • Chemicals

    • Cigarette Smoke

    • Benzoyl Peroxide

    • Nitrate and Nitrate Preservatives

    • Barbecuing

  • Infectious Agents

    • Human Papillomavirus (HPV)

    • Helicobacter pylori

• Point Mutations = A single change in a nitrogen

  base in DNA

• Frameshift Mutations = adding or deleting a nitrogen base that leads to the codons shifting how they are being read

  • Insertion Frameshift Mutation - inserting a nitrogen base into DNA where it wasn't before leading to a shift in the codons being read

  • Deletion Frameshift Mutation - deleting a nitrogen base from DNA leading to a shift in the codons being read

  • These types of mutations are more likely to lead to bigger and more noticeable change where they occur!

• DNA and its expression are highly controlled

  • In humans, all cells (except sperm and egg) have the same full set of DNA

  • Each cell type only uses the genes of the DNA that are relevant to their
    functions

  • The parts not useful to a cell's function will be made inaccessible to be transcribed and translated

• Histone Acetylation speeds up transcription

  • Chromatin vs. Chromosome

  • DNA tightly wraps around histones

  • DNA is negatively charged

  • Histones are positively charged

  • Acetyl group = -COCH3

  • If you add these to the tails of histones... histones become NEUTRAL in charge

  • DNA will loosen its wrapping around histones

  • Make it easier for RNA Polymerase to come in and transcribe

• DNA methylation slows transcription down

  • Methyl group = -CH3

  • These will attach to promoter regions of DNA and block RNA Polymerase from getting there to start transcription

  • Methyl groups also promote other enzymes to remove acetyl groups from histone tails

  • DNA will start to tightly wind back around histones

  • DNA becomes inaccessible and hard to read because it is tightly wound

• What is biotechnology?

  • The usage of known biological processes for industrial and other purposes.

  • It can include genetic manipulation, producing
    antibiotics, forensic crime scene investigations, and medical treatments to name a few

• What is Polymerase Chain Reaction

  (PCR)?

  • Sometimes referred to as a process that is like a "DNA
    Copy Machine"

  • You can make billions of copies of a DNA fragment outside a cell in the lab that can be used for many things...

  • Crime scene investigations

  • Medical research

  • P = Polymerase - the enzyme that is going to "build" the copies of DNA

  • C & R = Chain Reaction - this process is a chain reaction of steps done over and over in cycles

• PCR steps

  • Step 1 - Denaturation

  • DNA is exposed to temperature of 95 degrees Celsius

  • Separates DNA strands

  • Step 2 - Annealing

  • Add primers to DNA

  • Requires a lowering of temperature to 50 degrees Celsius

  • Step 3 - Extension

  • DNA Polymerase builds new DNA
    strands

  • Occurs at a temperature of approximately 72 degrees Celsius

  • This is for research, crime scene investigations, genetic testing, and agriculture

• WHAT IS GEL ELECTROPHORESIS

  Sometimes called DNA fingerprinting

  • Used a lot in crime scene
    investigations, paternity testing, and research

  • Allows researchers to separate DNA based on size and charge

  • Can compare samples to identify similarities and differences

• BASICS OF GEL ELECTROPHORESIS

  • Preparing a gel

  • Made of agarose (seaweed)

  • The gel has wells (openings where you load/put each of your DNA samples)

  • Cutting DNA samples with the same restriction enzyme (DNA scissors)

  • Ex: A restriction enzyme may cut anywhere in DNA that has the sequence ACCA

  • Loading DNA samples

  • Going to require the usage of a micropipette

  • Running the gel w/DNA (applying electrical current)

  • Separation of DNA pieces

  • DNA is negatively charged and will travel to positive once electricity is applied

  • Bigger pieces travel less distance that smaller pieces

  • Visualizing results

  • Sometimes involves staining of samples with a dye

Enzymes are:

- Proteins

- catalysts, which speed up reactions by a lot and do this by lowering activation energy which is the energy needed for a reaction to occur

- specific

- reusable

- affected with environmental conditions

- and often end in -a s e like lactase

Enzymes have active sites, which are locations where they interact with reactants, Substrates, in a reaction

- these sites are Special in shape, like lock and key, which means you can't use just any.

- and they aren't used up in reactions

- they denature if environments are not in their optimal range which means best conditions and can include:

- temp

- Salinity

- pH

- these can change the active site shape which means no product

Homeostasis is maintaining a stable, internal environment, energy is expensive

Can assist in:

growth development

- move materials

- build new molecules

-responding to the environment

-temperature regulation

Energy forms are:

- light

electricity

-heat

- can also be found in the bonds that keep molecules together

-A T P stores and releases energy and is the currency of cells

-A T P is Adenosine triphosphate and is made up of:

- Adenine

- ribose

- 3 phosphate groups which are negative

• There are two main types of inhibitors:

Non-competitive Inhibitors and competitive inhibitors

- Competitive inhibitors compete For access to the active site and prevent enzymes to catalyze reactions efficiently

- These would not stop a reaction from occurring completely because it would require an inhibitor to be in EVERY active site but it can still slow down a reaction

- Non-competitive inhibitors bind to an enzyme on a site called the allosteric Site that then causes the shape of the active site to change

- With an active site that is a different shape, it can't speed up the reaction because the reactants aren't the right they are not permanent and are reversible

-allo means different, so it is a different site to change the active site

- Photosynthesis: The process by which plants, algae, and even some bacteria convert LIGHT energy to chemical energy (GLUCOSE).

- Another name for a plant, algae, and/or bacteria that can photosynthesize is Autotroph (can make its own food)

- Other organisms obtain their chemical energy by consuming other living things and are called heterotrophs

Chloroplasts:

• Specialized structures that make photosynthesis possible

• Stroma - fluid portion of chloroplasts

• Thylakoids - sac-like membranes where photosynthesis takes place

• a stack of thylakoids is called a granum

• Contain pigments whose job is to absorb sunlight (example:
  chlorophyll)

CHLOROPHYLL IS A PIGMENT

• Pigments = light capturing structures

• Found in the membranes of thylakoids

• Most well-known photosynthesis pigment is chlorophyll

• look at light absorption spectrum and determine what colors of light chlorophyll absorbs best

Chemical equation:

6CO2+6H2O → C6H12O6 + 6O2, carbon dioxide and water are converted into glucose and oxygen with help of light

Light-dependent reactions

• Occurs in thylakoids

• Requires light

• Produces ATP and
  NADPH

Light-independent reactions (Calvin
Cycle)

• Occurs in stroma

• Does not require water

• Uses ATP and NADPH to do functions

Light dependent reactions follow these steps:

• Light hits a photosystem and excites electrons

• The electron follows the Electron Transport Chain (ETC) to the second photosystem

• The other electron that was in the second photosystem follows another ETC to NADP+ creating NADPH

• While that happens, hydrogens travel from the outside to the inside of the thylakoid membrane

• They come back up through ATP Synthase, spinning it and creating ATP

• To recycle, Water is broken apart for the electron, the hydrogen joins the others and oxygen becomes a byproduct

Light Dependent reactions (Calvin Cycle) works as follows:

• Carbon Fixation

  • 3 molecules of CO2 join to RuBP (5 carbon sugar) by rubisco

• Reduction

  • The 6 carbon compound is split into two 3 carbon molecules because it was unstable at the beginning

  • They split and reform using energy from ATP and NADPH from the light dependent reactions

  • The six 3 carbon molecules are known as G3P

  • There is a net gain of three carbons, which form one half of a glucose molecule

    • Once the process is done TWICE, then one full glucose will be formed when they connect

• Regeneration

  • Using ATP, (Making it ADP and a phosphate) The remaining 5 G3P molecules are rearranged to create RuBP

BROAD OVERVIEW OF THE ENTIRE PROCESS PHOTOSYNTHESIS:

• The Light Reactions (Phase 1) capture the energy in sunlight and convert it to chemical energy in the form of ATP and NADPH through the use of photosystems, electron transport chains, and ATP
  Synthase

• The Calvin Cycle (Phase 2) uses the energy transformed by the light reactions along with carbon dioxide to produce glucose.

DEFINITION OF CELLULAR RESPIRATION

• The controlled release of energy from food (commonly glucose) in the presence of Oxygen.

• The chemical reaction of cellular respiration is the REVERSE of photosynthesis

• Cellular Respiration and Photosynthesis are said to be COUPLED

• What one produces the other needs

• C6H12O6+602 —> 6CO2+6H2O+Sunlight (opposite of photosynthesis equation)

Happens in four steps

1. Glycolysis

2. Pyruvate Conversion

3. Krebs Cycle (Citric Acid Cycle)

4. Electron Transport Train/ATP Synthesis

MOST OF CELLULAR RESPIRATION HAPPENS IN MITOCHONDRIA

• Outer Membrane

• Inner membrane

• Space between membranes is called intermembrane space

• Matrix = Fluid of mitochondria

• Cristae = folds of inner membrane

CELLULAR RESPIRATION

STEP 1:

• Glycolysis

• Glyco-= glucose

• -lysis = to break

• Happens in CYTOPLASM of cell

• Glucose → 2 pyruvate molecules

• Investment - spend 2 ATP

• Payoff - produce 4 ATP

• OVERALL = +2 ATP

• Also creates electron carriers called NADH

PYRUVATE CONVERSION

STEP 2:

• This process occurs in the intermembrane space of

occurs when oxygen is available

• 2 pyruvate → 2 acetyl coA molecules

• Molecules produced in this step - carbon dioxide, NADH, and acetyl coA

KREBS CYCLE/CITRIC ACID CYCLE

STEP 3:

• Occurs in the matrix of mitochondria and only occurs when oxygen is

• The final breakdown of what is left from what was glucose

• Products formed = carbon dioxide, NADH, FADH2 and 2 ATP

ELECTRON TRANSPORT CHAIN/ATP SYNTHESIS

The electron transport chain (ETC) is located in the inner membrane of the mitochondria and its main purpose is to produce energy in the form of ATP.

Step 1: Electron Donation

NADH and FADH₂, which are made during glycolysis and the Krebs cycle, donate their electrons to the ETC. When they do this, NADH becomes NAD⁺ and FADH₂ becomes FAD.

Step 2: Electron Flow

The donated electrons move through a series of protein complexes in the ETC. This movement releases energy, which is used to pump hydrogen ions (H⁺) from the mitochondrial matrix to the intermembrane space, creating a concentration gradient.

Step 3: ATP Production

The hydrogen ions then flow back into the matrix through a protein called ATP synthase. This flow provides the energy needed to convert ADP into ATP.

Step 4: Water Formation

At the end of the chain, electrons combine with oxygen (the final electron acceptor) and hydrogen ions to form water (H₂O).

Final Products

From the ETC, around 34 ATP molecules and water are produced. The carriers, NAD⁺ and FAD, are recycled to be used again in earlier steps of cellular respiration.

FERMENTATION

What if oxygen isn't available for cellular respiration?

Step 1 (Glycolysis) of Cellular

Respiration will always occur in the cytoplasm WITH or WITHOUT oxygen.

• Pyruvate conversion, Krebs Cycle, and ETC & ATP Synthesis will not be able to occur.

• A process called fermentation will occur to allow only a small amount of ATP to be produced

Lactic Acid Fermentation

Typically occurs in animals and some bacteria

• This is the type of fermentation that humans do when cells have limited or no oxygen available

• Example: muscle cells during intense exercise

• This type of fermentation is also responsible for yogurt, cheese, and pickles

ALCOHOLIC FERMENTATION

• Occurs in plants, yeasts, and some bacteria

• 2 Pyruvate + 2 NADH → 2 NAD* + 2 CO2 + 2 Ethanol

• Wine, beer, bread