Exam 1 Notes

What are the four types of biomolecules?

1. Carbohydrates (sugars)

   1. They provide energy for humans and structure for plants. Plants are made up of cellulose which are mostly sugars

2. Lipids (fats)

   1. They are for storing energy and structural purposes. Structural for membranes by holding everything a cell.

   2. Hydrophobic molecules

3. Proteins

   1. Made up of amino acids

   2. Do everything that is important in bio

      1. ex: enzymes: transforms things/do work. If something is being changed in a cell, it is due to proteins

4. Nucleic Acids

   1. Used to make proteins

   2. Ex: DNA and RNA

Define biomolecule

a molecule that is produced by a living organism

What is the reason we have DNA?

We make proteins from the information in the DNA

• only have four “letters” to make DNA

DNA is used to make RNA

How do we make proteins?

The collection of amino acids (beads on a string)

What makes up a person?

• 70% water

• 30% protein

Define molecule

The smallest particle in a chemical element or compound and are formed by atoms sharing or transferring electrons

What is life?

The condition that distinguishes animals and plants rom inorganic matter, including the capacity for growth, reproduction, functional activity, and continual change preceding death.

Shared traits between living things

1. Organization

   1. cellular organization

2. Energy

   1. life needs E

3. Homeostasis: the ability to remain in a stale set of conditions

   1. to maintain a stable internal environment despite changes in the external environment

4. Information

   1. biological information is inherited and manifest (show/display)

5. Metabolism

   1. all the chem reactions in the cell

   2. If something is alive, it tends to control the metabolism

6. Growth and reproduction

7. Respond to change

   1. In the cold —> heat up yourself up

8. Evolution

What is life made of?

Cells

What are cells

Cells are the basic units of life

Membrane holding everything inside (how it’s imagined)

Two types: Prokaryotic and Eukaryotic

Prokaryotes

• Bacteria and Archaea

• Single-celled organisms

• No nucleus

• Lack membrane-bound internal structures (organelles)

Eukaryotes

• Animals, plants, Fungi, Protists

• Can be single/multicellular

• Has a nucleus

• Membrane-bound internal structures (organelles)

What are the three major groups of life on earth?

Three different types of cells

1. Bacteria

   1. smal, single celled

2. Archaea

   1. small, single celled, similar structure to bacteria

3. Eukarya

   1. Archaea and bacteria seemed to have merged to create this

Explain the tree of life

• believed that billions of years ago, the first cell on earth started reproducing

• The last common ancestor to everything on earth is LUCA

• LUCA then split into two groups

  • Bacteria and Archaea

• The Eukaryotes (us) formed when these two groups joined together

What do all living things require?

All living systems must acquire and use energy

Importance of structure and function

• Most biomolecules the structure determines the function

• If the structure changes, the function also changes

• Proteins ace as the machinery of living systems

  • Their functions tightly linked to their three-dimensional structure

Importance of Regulation

• Life is highly regulated (NOT RANDOM)

• Cells pick and choose what happens since it can not all be done at the same time

• The higher the importance, the more it is regulated

• Accomplished via inhibition (process of slowing a biological function, action, or reaction, often by a specific molecule or cell-to-cell contact.

• Regulators are regulated

Metabolism

• the sum of all chemical reactions in a cell or organism

  • sustains life by acquiring, transforming, and using energy and matter

• must be highly regulated or energy is wasted

• interconnected enzymatic reactions make up metabolic pathways

Life & Information

• DNA sequences make up most of our hereditary information

Growth and Reproduction

• All cells originate from other cells (reproduction)

• Heavily regulated

• Lack of growth can be lethal

• Uncontrolled growth is cancer

• Extinction results from not reproducing

• Includes copying heredity information

What is the scientific method?

1. Observation and description of a phenomenon

2. Ask questions and get unbiased answers to them

3. Formulate a hypothesis to explain the phenomena

4. Make predictions based on hypothesis

5. Experiment to test hypothesis

What did Watson and Crick win a NP for?

• They won a noble prize for their hypothesis of what a DNA structure looked like

• They said it looked like a double helix

How to design an experiment

• Ideal experiment will only manipulate one variable at a time to test the hypothesis

• Has a dependant variable

• Has an independent variable

• Divided into control and experimental groups

Define independent variable

The variable that is deliberately changed during an experiment

Define dependant variable

Variable that is observed and that changes in response to the independent variable

Define control groups

Are part of experiments that are exposed to the same conditions as the experimental group except for one independent variable

Define experimental group

Are part of experiments that are exposed to the independent variable

Define null hypothesis

• There is no relationship between the two measured variables (phenomena)

• Any differences observed in an experiment are simply the result of random differences

Define negative control

• In an experiment, a group(s) wgere bi ogebinebib us expected

• Ensure that there is no effect when there should be no effect

Define positive control

• In an experiment, a group(s) where the phenomenon is expected

• Ensure that there is an effect when there should be an effect

Eukaryotes vs Prokaryotes

Eukaryotes:

• larger and structurally more complex

• Has a nucleus

• Contain membrane-containing organelles and complex cytoskeleton

• multicellular organisms that are specialized and vary in size, shape, composition, and function

Prokaryotes:

• perform all functions of the organism

• smaller

What is in a bacterial cell?

• Cytoplasm where the DNA is located

  • Called a nucleoid

• Ribosomes

• Plasma membrane

What is in eukaryotic cells?

• Cytoplasm

• Plasma membrane

• Ribosomes

• Nucleus

• Nuclear membrane

• Membrane-bounded organelles

What structures are in Eukaryotes?

• Mitochondria

• Cytoskeleton

• Nuclear Pore

• Nucleolus

• Endoplasmic Reticulum

• Ribosomes

• Plasma Membrane

• Golgi

• Centrioles

What is the function of the mitochondria

• “Powerhouse of the cell”

• Produces ATP via cellular respiration

Define ATP and its purpose

• Adenosine triphosphate is the primary molecule for storing/transferring energy in all living cells

• Consists of an adenine base, ribose sugar, and three phosphate groups

Define cellular respiration

The metabolic process in which cells convert biochemical energy from nutrients into ATP, releasing waste produced ike water and CO₂

What is the function of the cytoskeleton?

• structural support

• transport

• cell movement

What is the function of the nuclear pore?

• regulated transport between the nucleus and cytoplasm

• A way to enter/exit the nucleus

What is the function of the nucleolus?

rRNA synthesis and ribosome assembly

What is the function of the nucleus?

Genome storage and transcription

What is the function of the endoplasmic reticulum (ER)?

• Protein and lipid synthesis and modificaton

• Made out of membranes next to the nucleus

• Some parts have ribosomes

What is the function of the ribosomes?

• Make proteins

• Partly made out of proteins but mostly made out of RNA

What is the function of the plasma membrane?

• Selective barrier controlling entry and exit of the cell

• Outer membrane of the cell

  • EVERY cell has this

What is the function of the golgi?

• Modifies, sorts, and ships proteins and lipids

• Internal structure made out of membranes

What is the function of the centrioles?

• organize microtubules for cell division and motility

What is found in plant cells?

• Central vacuole

• Tonoplast

• Chloroplasts

  • Carry out photosynthesis (converting light energy into chemical energy, sugar)

• Plasmodesmata

• Plant cell wall

  • made out of cellulose

Info on Mitochondria

• Used to be bacteria/prokaryotes

  • Own genome

  • Own ribosomes

  • Double membrane (inner/outer)

• Produces most ATP

• Important in metabolism

• Lynn Margulis was the first to propose that mitochondria and chloroplast used to be free-living cells

Info on Plasma Membrane

• Outer boundary of the cell

• membranes are largely lipids

  • Controls what enters/leaves the cell

• Includes proteins

• Without a membrane, there is no cell

What is the Fluid Mosaic model of membrane Structure?

• Term that describes how we think membranes look/behave

• Mosaic because there’s a bunch of things thrown into it

• Fluid because it’s not a solid structure

Info on the nucleus

• Center of most eukaryotic cells

• Stores/protects genome

• Keeps most of the DNA

• Surrounded by double-membrane

• Site of RNA synthesis

• Separates transcription from translation

• Contains nuclear pores and the nucleuolus

How to create RNA?

• Use DNA as a template by reading the information and making the RNA contain similar information

• Process called transcription that occurs in the nucleus

Info on the Nuclear Pores

• Located in the nucleus

• Passageway that allow things to move in/out of the nucleus

Info on the nucleuolus

• The nucleus of the nucleus

• The darker stain than the rest of the nucleus

• Site of ribosomal rna synthesis (rRNA)

  • Producing structural parts of the ribosomes

Info on Ribosomes

• Make proteins

• Use info from RNA to produce proteins

• Two sites:

  • Cytoplasm: free ribosomes

  • ER: for secretion for membranes

    • Proteins that are often modified and exported from cell

Info on the endoplasmic Reticulum (ER)

Two types:

• Rough ER: ribosomes attached to it. Some proteins are made here

• Smooth ER: lacks ribosomes; some lipids are made here

Site of modifications of proteins and lipids

Info on the Golgi Apparatus

• Made out of membranes with hollow parts inside

• A lot of the membranes that make up golgi come from the ER and then are further motified

ER and Golig interactions

• Protein and lipid production/modification in the ER

• Even more modification for proteins and lipids in the golgi

Protein Targeting to Organelles

• Proteins need to be transported around the cells

Info on the cytoskeleton

• Maintains structure of the cell and determines its shape

• Defining features of eukaryotic cells

• Made up of mostly long fibrous proteins

What are microtubules?

• Seperate genetic material into two different groups into two different cells

• Seen during cell division

• Like “highways” for motor proteins

Define motor proteins

• Proteins that help things move along a cell and usually interact with the cytoskeleton

• proteins with two feet like structures that “walk” along the microtubules

• Kinesin (motor protein) uses E from ATP to walk along the microtubules, carrying cargo

• Dynein functions similarly but in the opposite direction

• Myosin functions similarly but interacts with actin filaments

Info on the centrioles

• Look similar to microtubules

  • Think as short microtubules

• Creates a part of our cell where microtubules grow out of

• Important part of cell division

  • separating the chromosomes when cells are dividing

• DON’T contain membranes

Electron Microscopy

• Old school

• Pictures come out in black/white

• Highest resolution, allowing for images for tiny structures

Fluorescence Microscopy

• Type of light microscopy

• Dye cells so when certain wavelengths are on cells, different structures glow with different colors

• How most microscopy is done today

Typically need two different molecules to accomplish this, doing it with one is extremely rare

Types of molecules:

• Dapi: binds to DNA, gives off a blueish color

• Phalloidin: types of poison, binds to actin and prevents it from being remodeled which eventually kills this cell

What is Immunohistochemistry

• Type of light microscopy where you use antibodies

• How to do this:

  • Have an antibody bind to the structure you want to highlight

  • Bind a secondary antibody to the first antibody. This antibody is connected to another compound that turns it to a different color

What are antibodies?

• Proteins that are part of the immune system

• Binds to foreign objects in you (virus, bacteria) and tries to destroy them

• Y shaped structures

• Binds to antigen

• Proteins that bind to one specific thing

Green Flouresent protien (GFP)

• Originally found in jellyfish

• Biologist had taken this gene out of jellyfish to use for multiple different purposes