Untitled Flashcards Set

Bio 131-01: Exam 2 study guide 

CH 4: NUCLEIC ACIDS 

THE 4 MOLECULES OF LIFE

• Proteins 

• Carbohydrates 

• Lipids 

• Nucleic Acids 

adenine (A)

• chemical compound that's a building block of DNA and RNA

• Gives energy to cells

• One of four bases that make up DNA, along with thymine (T), guanine (G), and cytosine (C). 

• DNA: Adenine pairs with thymine to form a base pair that connects the two strands of DNA. The sequence of these bases encodes DNA's information. 

• RNA: Adenine is a building block of RNA. 

• Energy: Adenine is part of substances that store and provide energy for cells, such as adenosine triphosphate (ATP). 

• Adenine is a purine, which means it's made up of two carbon-nitrogen rings. 

• Adenine is poorly soluble in water. 

• Adenine is a nutrient found in many multivitamins. 

• Adenine can be created by combining ammonia and hydrogen cyanide molecules in water. 

• Adenine is unusually robust when exposed to ionizing radiation. 

• Adenine can be produced industrially by heating formamide in a sealed flask.

base (nitrogenous base)

• nitrogenous base (nucleobase) organic molecule containing nitrogen that acts as a base in chemical reactions and serves as a fundamental building block of DNA and RNA, forming the "rungs" of the double helix by pairing with complementary bases to store genetic information

• Primary nitrogenous bases are adenine (A), guanine (G), cytosine (C), thymine (T) (found in DNA), and uracil (U) (found in RNA). 

• Structure: ring structure made up of carbon and nitrogen atoms, with the ability to donate a pair of electrons due to a lone pair on one of the nitrogen atoms. 

• Types: Nitrogenous bases are categorized into two types based on their ring structure: purines (double ring) like adenine and guanine, and pyrimidines (single ring) like cytosine, thymine, and uracil. 

• Base pairing: The specific pairing between bases is crucial for storing genetic information, with adenine always pairs with thymine (or uracil in RNA), and cytosine always pairing with guanine. 

• Importance in genetics: Any changes in the sequence of nitrogenous bases (mutations) can have significant impacts on protein synthesis and potentially lead to genetic diseases. 

• Changes in nitrogenous bases, which are the building blocks of DNA, can lead to a variety of genetic diseases including sickle cell anemia, cystic fibrosis, Duchenne muscular dystrophy, Tay-Sachs disease, cancer, and many other disorders as any alteration in the base sequence can result in a mutation, causing a faulty protein to be produced which can manifest as a disease. 

• Mutations: When the sequence of nitrogenous bases in DNA changes, this is called a mutation, which is the primary cause of genetic diseases. 

• Point mutations: A single change in a nitrogenous base pair is called a point mutation, and can lead to significant effects depending on the affected gene. 

• Examples of genetic diseases caused by base mutations:

1. Sickle cell anemia: Caused by a single base change in the beta-globin gene, leading to abnormal hemoglobin protein. 

2. Cystic fibrosis: Results from a mutation in the CFTR gene, affecting chloride ion transport. 

3. Tay-Sachs disease: Caused by a mutation in the HEXA gene, leading to a deficiency of a crucial enzyme. 

complementary base pairing

• specific pairing of nitrogenous bases in DNA (and RNA) where adenine (A) always pairs with thymine (T) and guanine (G) always pairs with cytosine (C), allowing formation of the double helix structure and ensuring accurate replication of genetic information; in RNA, thymine is replaced by uracil (U) when forming complementary pairs with adenine. Adenine (A) always pairs with thymine (T) and guanine (G) always pairs with cytosine (C) in DNA. 

• Hydrogen bonds: base pairs are held together by hydrogen bonds, which are weak chemical bonds that provide stability to the DNA molecule. 

• Importance in replication: Complementary base pairing is essential for DNA replication, as each strand serves as a template to create a new complementary strand. 

• RNA difference:In RNA, uracil (U) replaces thymine (T) when forming complementary base pairs with adenine. 

cytosine ©

• one of the four nucleotide bases found in DNA and RNA, alongside adenine (A), guanine (G), and thymine (T). type of pyrimidine base that forms three hydrogen bonds with guanine, making them complementary pairs in the DNA double helix structure. 

• Chemical symbol: C

• Function: Building block of DNA and RNA

• Base pairing: Always pairs with guanine (G)

• Type of base: Pyrimidine 

DNA (deoxyribonucleic acid)

• molecule found inside cells that carries the genetic instructions needed for an organism to develop and function, acting as the blueprint for life; it is crucial because it holds the information passed from parents to offspring, determining traits like eye color, hair color, and other characteristics, and is unique to each individual making it useful in fields like forensics and medicine. 

• Structure: DNA is a double-stranded helix, formed by two strands of nucleotides twisted around each other, with each strand consisting of a sugar-phosphate backbone and nitrogenous bases (adenine, thymine, guanine, and cytosine) that pair together according to specific rules (A with T, and C with G). 

• Function: DNA stores genetic information in the sequence of its bases, which can be "read" by the cell to produce proteins that carry out various functions. 

• Replication: DNA has the ability to replicate itself, creating an exact copy of the genetic information before cell division to ensure each new cell has a complete set of DNA. 

• Genes: DNA is divided into sections called genes, which code for specific proteins. 

• Mutations: Changes in the DNA sequence (mutations) can occur, sometimes leading to variations in traits or diseases. 

• Inheritance: During reproduction, each offspring receives half of their DNA from their mother and half from their father.

Genes

• segments of DNA that contain instructions for making proteins. Passed down from parents to offspring and determines a person's physical traits. 

• Genes are located on chromosomes in the nucleus of cells. 

• Genes are made up of sequences of DNA, which are made up of chemical building blocks called nucleotides. 

• Different sequences of nucleotides create different codes for different genes. 

• Genes that make proteins are called protein-coding genes. 

• Changes in genes can lead to genetic disorders. 

Types of genes:

• Complementary genes: Two genes that interact to produce a specific trait 

• Duplicate genes: Also called paralogs, these genes descend from a common ancestor 

• Polymeric genes: These genes have relatively low immunogenicity and cytotoxicity 

Studying genes:

• The study of genes, genetic variation, and heredity is called genetics.

• Researchers are studying genetic testing to identify changes in a person's DNA that may indicate a risk of developing a disease. 

genome

guanine (G)

nucleosides

nucleotide

phosphodiester bond

RNA (ribonucleic acid)

thymine (T)

Nucleic acids

• polymers specialized for the storage, transmission, and use of genetic information. #4 in the molecules of life 

• DNA = deoxyribonucleic acid (Deoxyribose)

• RNA = ribonucleic acid (Sugar ribose)

• 5 carbon sugars (pentoses)

Nucleotides 

• monomers that make up nucleic acids

• nucleoside = nucleobase + ribose or deoxyribose

• nucleotide = nucleoside + phosphate group

• linked together in condensation reactions to form phosphodiester linkages.

• The phosphate groups link the 3′ carbon in one sugar to 5′ carbon in another sugar.

• Nucleic acids are said to grow in the 5′-to-3′ direction

 Linking Nucleotides Together 

Pyrimidines- Single ring DNA bases (Uracil is RNA base)

Purines- double ring DNA bases 

Oligonucleotides - about 20 monomers (a.k.a. 20-mer, or 20 bases): RNA “primers” to start DNA duplication, RNA that regulates gene expression (RNAi), etc.

Polynucleotides, or nucleic acids (DNA and RNA): can be very long—up to millions of monomers (kilobases – kb).

• Human genome: approx. 3 billion base pairs (that’s 2 x 3 billion bases) 

             To convert billion base pairs to kilobases, simply divide the number of base pairs by  1,000.

6,000 kilobases

DNA bases: 

§Adenine (A)

§Cytosine (C)

§Guanine (G)

§Thymine (T)

• RNA has Uracil (U) instead of thymine.

(1 ring, only in RNA)

Complementary base pairing

purines pair with pyrimidines by hydrogen bonds

• A with T (or U in RNA)G with C

§Adenine (A)

§Cytosine (C)

§Guanine (G)

§Thymine (T)

   Uracil (U)

DNA

• two strands of a DNA molecule form a double helix

• All DNA molecules have the same structure; diversity lies in the sequence of base pairs

• (DNA is an informational molecule: information is encoded in the sequences of bases)

DNA transmits information in multiple ways

Replication: DNA can reproduce itself (replication).

Transcription: DNA sequences can be copied into RNA (transcription). 

Translation: The RNA can specify a sequence of amino acids in a polypeptide (translation).

• Transcription plus translation = expression

The central dogma of molecular biology 

• states that genetic information flows in one direction only, from DNA to RNA to protein, meaning that the sequence of bases in DNA determines the sequence of amino acids in a protein, and this process occurs through transcription (DNA to RNA) and translation (RNA to protein); this is considered the fundamental principle of how genetic information is expressed in living organisms. 

• Directionality: Information only moves from DNA to RNA to protein, not in reverse. 

• Transcription: The process where DNA is copied into a messenger RNA (mRNA) molecule. 

• Translation: The process where the information in mRNA is used to build a protein chain. 

• Francis Crick: The scientist who proposed the central dogma. 

• DNA replication and transcription depend on base pairing.

• DNA replication involves the entire molecule only relatively small sections of the DNA are transcribed into RNA.

Genome 

• The complete set of DNA in a living organism (genome) 

• Not all the information is needed at all times; sequences of DNA that encode specific proteins are called genes.

DNA replication and transcription 

CH 5 CELLS: PART 1 

Cell Theory  

First unifying theory of Biology)

• Cells are the fundamental units of life

• All organisms are composed of cells

• All cells come from preexisting cells

Conclusion of “cell theory” (The functions of all cells are similar, but not identical) 

Specialization 

• (Meaning Below) BOTH have nuclei, cytoplasm, lipid bilayer, organelles Look different 

Oocytes (Human eggs) 

• Largest human cell (by volume) 

• 150 um (diameter) very small human eye can barely see it 

The scale of life 

Why are cells so small?   

(Advantage to being small) 

• High surface area to volume ratio is a must 

• Volume determines the amount of chemical activity in the cell per unit time (Larger cells have more chemical activity) 

• Cell surface area limits the amount of resources and waste products that can cross the cell boundary per unit time 

• Most cells are 10-20 “um” in size ( Cant see them to the naked eye, have to use microscopes)

µm (or "um") 

• unit of measurement called a micrometer, equal to one millionth of a meter, or one thousandth of a millimeter, ( very small unit used to measure microscopic objects like bacteria or the thickness of a hair)

Microscope 

Magnification: Allows object to appear larger than actual size (Magnifies the object) 

Resolution: Allows for clearer picture of magnified object (Minimum distance two objects can be apart and still seen as two objects)

Low resolution: Blurry/ everything blur together/ low detail 

High resolution: Less blurry/ able to see more detail/ distinct between objects 

Light Microscopes: Use glass lenses and light  (Resolution of 0.2 UM)

Electron Microscopes: Electromagnets focus on electron beam (Resolution 0.2 nm)

The plasma Membrane 

• Outer surface of every cell (similar or same structure in all cells) 

• Made up of double layer of phospholipid bilayer with embedded proteins and other molecules)

• (selectively permeable barrier) allows certain substances to pass through while blocking others,acting like a gate that controls what enters and exits a cell, maintaining the cell's internal environment (Homeostasis) by carefully regulating the movement of molecules across it. 

• Important in communication and receiving signals 

• Can contain proteins for binding/ adhering to adjacent cells 

 lipid bilayer 

• thin, flexible double layer of lipid molecules that forms basic structure of a cell membrane

• Acts as a barrier to separate the inside of a cell from its environment, keeps the cell's components contained while allowing controlled movement of substances in and out

• Like a sandwich" where the "bread" is made of the hydrophilic (water-loving) heads of the lipid molecules and the "filling" is made of their hydrophobic (water-fearing) tails that face each other in the middle. 

Collagen fibers 

• Protein strands that provide structure and elasticity to connective tissues in the body, main component of skin, tendons, ligaments, and bones. 

Structure: 

• Made up of bundles of collagen molecules (large in diameter and appear white in color)

• Flexible but inelastic individually

Fibronectin 

• glycoprotein that helps cells stick together and move, important for wound healing Plays a critical role in tissue engineering

• Helps with cell adhesion, migration, and differentiation

• found in blood plasma, connective tissue, and on cell surfaces. 

• Helps cells stick together and move, Helps organize the cytoskeleton, Helps cells progress through the cell cycle, Helps cells grow and survive, Helps cells differentiate, Helps maintain homeostasis of the extracellular matrix, Helps regulate cell-matrix and matrix-matrix interaction

• Binds to integrins, collagens, fibrins, and glycosaminoglycans 

• Acts as a mechanical link between matrix proteins in the extracellular matrix and cell cytoskeleton 

• Binds to a large number of matrix components and substrates 

Mosaic  :  Lipid bilayer embedded within proteins 

Fluid: Many of the proteins can “move” in this sea of lipid 

• Plasma membrane fits fluid mosaic model 

(STRUCTURE OF PLASMA MEMBRANE)

Embedded cholesterol:  A lipid that's found in cell membranes, it helps maintain fluidity and stabilizes proteins. Cholesterol helps membranes move around easily in a cell membrane over a wider range of temperatures

• low temperatures: it prevents phospholipids from packing too tightly together

• High temperatures: reduces how easily lipids/ proteins in a cell membrane can move around

Protein structure:
Cholesterol stabilizes the structure of proteins embedded in the membrane. Can affect the protein's binding capacity, signal transduction, and affinity state. 

Fluidity :  ( viscosity of the cell membrane's lipid bilayer): How easily the lipids and proteins in a cell membrane can move around

Transmembrane protein:  Hydrophobic/ hydrophilic forces determine the orientation of proteins in the plasma membrane 

Function of plasma membrane molecules 

Carbohydrates Chains: provide a fingerprint for the cell so it can be recognized by other cells 

Cholesterol: Helps membrane retain its flexibility 

Receptor proteins: Bind to external chemicals to regulate processes within the cell

Recognition proteins: provide a fingerprint for the cell so it can be recognized by other cells 

Transport proteins: Provide a passageway for molecules to travel in and out of a cell (carry materials in and out of cells)

Enzymatic proteins: Accelerate intracellular and extracellular reaction on the plasma membrane 

PROKARYOTIC VS EUKARYOTIC CELLS 

PROKARYOTIC CELLS 

Cytoplasm:  Made of cytosol (liquid component) and filaments/ particles 

Cytosol: Water with dissolved ions, small molecules, and soluble macromolecules 

Ribosomes: RNA and proteins (protein synthesis)

Rigid Cell wall: Most prokaryotes have a rigid cell wall outside the plasma membrane 

Flagella: In a prokaryotic cell is a whip-like structure that acts as a "motor" to allow the bacteria to move around, functioning like a propeller to propel the cell through its environment (Main way a prokaryotic cell can swim)

Pili: (Some bacteria contain Pili) hairlike structures projecting from the surface, help bacteria adhere to other cells. Some pili can help share genetic information from one bacterial cell to another 

Fimbriae: shorter than Pilli, help cells adhere to surfaces like animal cells 

Cytoskeleton: System of protein filaments that maintain cell shape and play roles in cell division (Cytoskeleton is different in prokaryotes vs eukaryotes) 

EUKARYOTIC CELLS 

• Complex cells means much larger than prokaryotic cells (up 10 times larger than prokaryotic cells) 

Compartmentalization: Eukaryotic cells specialize and form tissues and organs of multicellular organisms 

Nucleus (Nuclear envelope): membrane enclosed nucleus. Protein lined pores allow matteria to move in and out 

Chromatin: DNA plus associated proteins 

Nucleolus: Condensed region where ribosomes are formed 

Peroxisome: Metabolizes waste 

Endoplasmic Reticulum:

• Rough (ER): Associated with ribosomes, makes secretory, and membrane proteins 

• Smooth (ER): Makes lipids 

Cytoskeleton (Microtubules): Form the mitotic spindle and maintain cell shape 

Centrosome: Microtubule organizing center 

Intermediate filaments: Fibrous proteins that hold organelles in place 

Microfilaments: Fibrous proteins that form the cellular cortex 

Plasma membrane: 

Lysosome: Digests food and waste materials 

Golgi apparatus: Modifies proteins 

Cytoplasm: 

Mitochondria: Produce energy 

Vacuole: Membrane-bound organelle that stores water, nutrients, and waste products in plant and animal cells

Ribosomes:  Sites of protein synthesis 

• Occur in prokaryotic and Eukaryotic cells (have similar structure) NOT SAME

• Contain ribosomal RNA (rRNA) & more than 50 protein molecules

Ribosomes in Prokaryotic cells: Free floating in cytoplasm 

Ribosomes in Eukaryotic cells:  Free in cytoplasm, attached to mitochondria and chloroplasts 

Nucleus: Usually largest organelle, contains DNA, site of DNA replication, where gene transcription is turned on or off, assembly of ribosomes begins in region of nucleus called “NUCLEOLUS”

• Nucleus, surrounded by nuclear envelope (Pores control the movement of molecules across the envelope)

• In nucleus DNA combines with proteins to form chromatin in long thin threads (Chromosomes) 

Chromatin: Condenses DNA into more compact structure so it can fit in the cell nucleus 

Condensed DNA: Chromosomes 

Nucleolus: within nucleus, contains dense matter, where ribosomes are assembled 

Ribosomes: Assembly plants for building proteins (move from nucleolus into cytoplasm)

CHAPTER 5 CELLS: PART 2 

The endomembrane system 

Mnemonic "Never Eat Green Leafy Vegetables, Please!"

Never- Nucleus

Eat- Endoplasmic Reticulum (Rough & Smooth)

Green- Golgi Apparatus

Leafy- Lysosomes

Vegetables- Vesicles

Please- Plasma Membrane

Plasma membrane:

Nuclear envelope:

Endoplasmic reticulum: Network of interconnected membranes in cytoplasm (large surface area)

Smooth Endoplasmic Reticulum (SER):

• More tubular (no ribosomes)

• helps detoxify harmful substances, like alcohol and drugs, by breaking them down into water-soluble compounds that can be eliminated from the body. 

• The SER contains enzymes that break down harmful organic chemicals

• The SER can double its surface area to detoxify substances

• Once detoxification is complete, the SER returns to its normal size

-Example-

• Breaks down Products of natural metabolism, Ethanol from drinking too much alcohol, and Barbiturates from drug overdoses. Breaks down carbs in animal cells 

• Synthesis of lipids & steroids 

Rough Endoplasmic Reticulum (RER)

• Ribosomes are attached 

• Newly made proteins enter RER lumen where they are modified, folded and transported to other regions 

Golgi apparatus: Composed of flattened sacs (Cisternae) & small membrane enclosed vesicles 

• Receives proteins from RER so that they can modify them 

• Concentrates, packages, sorts proteins

• In plant cells: polysaccharides for cell walls are synthesized here

• Contains “Cis” and ‘Trans” face 

• Cis face: receives vesicles (piece of Endoplasmic reticulum breaks off from the “ER”)  

• Trans face: vesicles break off from golgi apparatus and move to plasma membrane or other organelles 

• Cis-close to nucleus 

• Trans-close to cell membrane 

Lysosomes:

Process: (Tiny membrane surrounded vesicles shuttle substances between the various components)

1. Proteins synthesized on the ribosome 

2. The proteins are modified in the ER (Endoplasmic Reticulum)

3. Proteins are packaged in the ER 

4. Proteins are tagged in the Golgi 

5. Proteins distributed through the vesicle 

The cell cycle: 

“Go Sally Get Married”

Go- G1 (First gap)

Sally- S (DNA synthesis)

Get- G2 (Second gap)

Married- M (Mitosis)

Mitosis Phases (PMATC):

"Pass Me A Taco Chef”

• Pass = Prophase

• Me = Metaphase

• A = Anaphase

• Taco = Telophase

• Chef = Cytokinesis 

Lipid:  Fat-like substances that don't mix with water. They store energy, help make cell membranes, and can act as messengers in the body. Basically, lipids are important for energy, structure, and signaling

• Fats and oils for energy.

• Phospholipids for cell membranes.

• Steroids like cholesterol for hormones.