Biology: Key Concepts of Midterm 1

Key Concepts of Midterm 1

• Covers cells, organelles, chemical reactions, enzymes, macromolecules, and enzyme function

Matching Definitions

• Hydrocarbons are organic molecules of only hydrogen and carbon
• Functional groups are clusters of atoms that change the properties of organic molecules
• Hydrophobic substances are insoluble in water
• Isomers are compounds sharing a chemical formula but differing in atomic connectivity
• Polymers are large molecules with many linked subunits

Synthesis

• Synthesis joins many monomers to form a polymer
• This process involves anabolism and dehydration synthesis

Macromolecule Breakdown

• Breakdown into component monomers involves catabolism, degradation, and hydrolysis

Organic Molecules and Monomers

• Carbohydrates are made of glucose monomers
• Lipids are made of triglyceride monomers
• Proteins consist of amino acid monomers
• Nucleic acids consist of nucleotide monomers

Carbohydrates

• A simple carbohydrate corresponds to a single glucose molecule
• A disaccharide corresponds to two simple sugars covalently bonded
• Glycogen is defined as a large, highly branched network of glucose molecules
• Cellulose is defined as a long, strong, linear chain of glucose molecules

Starch vs Glycogen

• Starch and glycogen both consist of linked glucose monomers
• Starch contains long chains, in contrast to glycogen, which is highly branched
• Plants store energy as starch
• Animals instead, store energy as glycogen

Fats

• Fats are typically solid at room temperature because they are saturated
• Saturated fats have fatty acid tails with single bonds, allowing tight packing
• Oils liquid at room temperature are unsaturated
• Unsaturated fats have fatty acid tails with double bonds, preventing tight packing

Phospholipids

• Phosphate groups, glycerol, and fatty acids contribute to monomers of a phospholipid

Cell Membranes

• Cell membranes are bi-layered mats of phospholipids

Steroids

• Steroids include estrogen and cholesterol

Lipids

• Lipids do not provide short term energy storage
• Lipids do provide insulation, long term energy storage, are structural components of cell membranes, and they also act as chemical messengers

Amino Acids

• Amino acids have an amine group and a carboxyl group present

Polypeptides

• Amino acids connect in polypeptides via peptide bonds

Protein Structure

• Pleated sheets and alpha helices are examples of secondary protein structure
• Primary protein structure is a string of amino acids connected by peptide bonds
• Secondary protein structure is the folding or coiling of a polypeptide string
• Tertiary structure folding is defined as the three-dimensional folding pattern of a protein
• Quaternary is defined as structure combining two or more folded proteins to form a large protein

Protein Functions

• Proteins are contractile, defensive, and play a role in metabolism and structural roles

Nucleic Acids

• DNA and RNA are made of long chains of nucleotide monomers

Nucleotide Composition

• Nucleotides consist of a pentose sugar, phosphate group, and nitrogenous base

Nucleic Acid Components

• DNA does not contain the sugar ribose
• Some nucleotides of DNA contain thymine
• RNA does not contain deoxyribose
• Some nucleotides of RNA contain uracil
• Both DNA and RNA can contain guanine

Base Pairing

• Cytosine pairs with guanine in both DNA and RNA
• Adenine pairs with thymine in DNA
• Adenine pairs with uracil in RNA

Complementary Base Pairing

• The complementary base pairing to the DNA sequence AAC TGA CGT TAG is TTG ACT GCA ATC

DNA Location

• DNA is found in the nucleus, mitochondria, and chromosomes

DNA Structure

• DNA is a double stranded alpha helix of two anti-parallel but complementary strands
• Strands held by hydrogen bonds between complementary bases: A with T, and C with G

RNA types

• Messenger RNA (mRNA) is created by copying a section of DNA and carries this copy to the cytoplasm
• Transfer RNA (tRNA) carries amino acids to the ribosome during translation
• Ribosomal RNA (rRNA) is created in the nucleolus and is a large component of ribosomal subunits

RNA vs DNA

• RNA and DNA contain nucleotides and are nucleic acids
• DNA contains thymine and forms a double helix for storing genetic information
• RNA contains uracil, and it has multiple forms (mRNA, tRNA, rRNA) with multiple functions

ATP

• ATP is a nucleic acid
• The sugar in ATP is ribose
• The ATP stores energy in the bonds linking phosphate groups, especially between the 2nd and 3rd phosphate
• It releases energy by breaking this bond, creating ADP and inorganic phosphate

Enzymes

• Enzymes work with lipids(fats/oils) with the assistance of Lipo and ASE
• Vegetable stir fry provides a quick and long energy source due it's simple carbohydrates

High Glycemic Index

• High glycemic index carbs contain simple carbs, easily digested for insulin

Vitamins

• Vitamins are coenzymes and help enzymes work

Enzyme Action

• Proteins have active sites that recognize other molecules, enabling enzymes to function like a lock and key

Amino Acids

• An essential amino acid cannot be synthesized by the organism and must be obtained through diet

Cell Components

• Fatty acids are structural components of the cell membrane
• Phosphate is required for cells to make proteins, enzymes, amino acids, bone, ATP and phospholipids, nucleic acids, and carbohydrates
• The glucose concentration is expected to be hypotonic outside of the cell, due to glucose transportation

Cellular Respiration

• Cellular respiration occurs in all organisms during the night and day, where cell respiration produces ATP, and ATP is the main cellular energy
• Muscle cells produce the greatest amount of ATP

Enzyme Definitions

• An endergonic reaction requires a net input of energy to occur
• The active site is location on an enzyme where a substrate binds
• Denaturation is a change in shape of an enzyme due to environmental factors, reducing functionality
• An enzyme an organic molecule that increases the rate at which a chemical reaction takes place

Enzymes

• Enzymes greatly increase the rate of a chemical reaction
• Enzymes require a co-enzyme or co-factor
• Enzymes have an active site which fits the 3-D shape of the substrate

Enzyme Interference

• High temperatures which cause an enzyme to lose its shape is called denaturation
• A molecule which binds to the enzyme and changes the shape of the active site is called non-competitive inhibition
• A molecule which binds to the enzyme in the active site is called competitive inhibition

Cell Theory

• All cells arise from pre-existing cells
• The cell is the basic unit of life

Cell Size

• Cells are small due to the need to maintain an adequate surface area to volume ratio
• Organisms grow by increasing the number of cells so each cell maintains its surface area to volume ratio

Neccessary Cell Components

• A plasma or cell membrane
• A watery interior
• Genetic material

Cell Types

• Prokaryotic cells have DNA in the cytoplasm and no membrane bound organelles
• Eukaryotic cells are relatively large, have a nucleus, and membrane bound organelles

Eukaryotic Cells

• A single-celled organism found deep in the ocean has its own mitochondria and rough and smooth endoplasmic reticulum, the presence of membrane bound cell organelles determines that the organism is a eukaryote

Eukaryotic Membranes

• Eukaryotic plasma (cell) membranes contain:
• Phospholipids
• Glycoproteins
• Cholesterol

Plasma membrane

• Phospholipids: Form the majority of the structure and provide a barrier due to the hydrophobic nature of the interior of the bilayer
• Cholesterol: Maintains fluidity
• Glycoproteins: Transport across the membrane, cell adhesion, cell recognition
• Glycolipids: Cell receptors to help cells attach

Cell transport

• Osmosis: The movement of water across a semi-permeable membrane from high to low concentration of water.
• Diffusion:The movement of substances from an area of high concentration to an area of low concentration
• Active Transport:The movement of a substance from an area of low concentration to an area of high concentration with a necessary input of energy
• Facilitated transport: The movement of a substance across the cell membrane from an area of high concentration to a low concentration, with the necessary help from a membrane transport protein.
• Endocytosis: The entrance of a large molecule into the cell by invagination of the cell membrane.

Transport categorization

• passive transport: Osmosis, Exocytosis, Diffusion
• active transport: Protein pumps

Osmosis Vs Diffusion

• Osmosis and Diffusion: Both move molecules from an area of high concentration to an area of low concentration.
• Osmosis:is the movement of water, and movement through a semi-permeable membrane.
• Diffusion: movement of any solute.

Active transport Via protein pumps Vs Facilitated Transport

• Both: require membrane proteins.
• Active transport Via protein pumps: Requires energy and requires molecules to move substances against the concentration gradient.
• Facilitated Transport: Does not require energy and the molecules move with the concentration gradient.

Terminology

• Water is moving through the plasma membrane from an area with a low concentration of solutes to an area of high concentration of solutes= Osmosis
• A cell is expelling wastes from a storage vesicle through the plasma membrane= exocytosis

Types of Tonicity

• Hypertonic solution: Water moves out of the cell
• Isotonic solution: No net movement of water
• Hypotonic solution: Water moves into the cell -Hypertonic: There are more solutes outside of the cell than inside the cell.

The Nucleus

• The Nucleus: Contains DNA, Comprised of a double phospholipid bilayer
• The Nucleolus: Ribosomal subunits, rRNA
• Ribosomes: produced in the nucleolus, can be found in multiple places in the cell, Protein synthesis

locations of ribosomes:

• Inside mitochondria
• Attached to the rough endoplasmic reticulum

Rough Vs Smooth Endoplasmic Reticulum

• Both: made up phospholipid bilayer, are part of the endomembrane and are continuous with each other and the nuclear envelope
• Rough ER: attached ribosomes,is involved in protein synthesis, directly attached to the nuclear envelope.
• Smooth ER: No attached ribosomes, lipid synthesis

Golgi appparatus

• The golgi apparatus: receives proteins from the rough ER and lipids from the smooth ER, can add sugar to either of these substances forming glycoproteins or glycolipids, packed these substances into vesicles to be secreted through the plasma membrane..
• glycoprotiens enter vesicles that will leave the Golgi Apparatus

Lysosomes

• Differ from vesicles in that they have a double phospholipid membrane and have digestive enzymes
• Lysosomes are similar to vesicles in that they are small, membrane-bound organelles used for storage/transport and both part of the endomembrane system.
• Functions: Digestion of nutrients, Removal of unneccesary embryonic tissues, Breakdown of old non-functioning organelles.

Vesicles vs a Vacuole

• Vacuoles are only found in plant cells and are for the express purpose of storing water.
• Vesicles are smaller, may store a variety of substances, and are found in both animal and plant cells.

Mitochondria function

• The mitochondria is the site of cellular respiration, where glucose and oxygen are converted into carbon dioxide and water
• The mitochondria does not use energy from the sun to create glucose from water and carbon dioxide

Cytoskeleton structures

• Microtubules
• Intermediate filaments
• Cilia
• Centrioles

Organelle collaboration

• glycoprotiens: Ribosome, Rough ER, Golgi Apparatus, Vesicle
• Creation of glycolipids: Golgi apparatus and smooth ER
• Creation of proteins: Ribosomes and rough ER
• Break down of harmful bacteria taken in by phagocytosis: Lysosome and vesicle
• Create of glucose and then the breakdown of glucose to use as energy: Chloroplast and mitochondria

Enzyme Inhibitor Molecule.

The inhibitor molecule would block the active site stopping the reaction.

Enzymes

• Enzyme reaction rates are affected by temperature or pH

Emulsification

• Emulsification is a physical process

Location

• They absorb the macromolecules/nutrients via the capillary net/blood vessels and lipids/fats and water via Lymph vessel

Two Protease Enzymes

• Pepsin, trypsin respectively which starts digestion in the stomach, so pH = 2..

DNA components

• is made of nucleotide

DNA replication

• Helicase: Unzipping of the DNA ladder
• DNA Polymerase: Assembly of the new complementary strand of DNA
• Ligase: Repair of the sugar-phosphate backbone prior to re-coiling Bonding the template can be accomplished using each DNA strand which the DNA Polymerase uses to bond complementary bases to the template strand
• The process of DNA replication, where 1 DNA strand is split and a new half is created onto each of the original halves making each copy of 1 DNA consist of a new strand and an old strand from the original it considered semi-conservative.

Protein synthesis

• Translation comes before transcription.
• In the process of transcription, a molecules of mRNA is produced using DNA as a template.

transcription , DNA replication does not occur

Translation stages

• mRNA binds to the small and large subunit of the ribosome
• A stop codon is reached and so the polypeptide is released
• tRNA bring the appropriate amino acid to the codon and adds it to the growing protein Amino acids are joined via peptide bonds during protein synthesis

Segment

• If a segment of DNA reads: AAA CCC GGG TTT, the corrosponding mRNA, produced during transcription reads reads: UUU GGG CCC AAA

Mutation types

• Frameshift: AAA GGU becomes AAAA GGU
• Point: AAA GGU becomes AAA GGG
• Inversion: AAA GGU becomes UGG AAA

Mutation

• A point effects only changes a single codon and thereby changes a single amino acid
• A frameshift changes every single codon down stream from it, so it changes multiple amino acids in a protien.
• The point mutation would be least likely to affect an organism.

Cell Membrane

• two layers of phospholipids (lipid inside like jelly, and the phosphates on external surfaces like the bread in a sandwich).
• lumps is the protein
• polysaccharides used to identify cells

cellular process imagery

• exocytosis= the arrow shows a vesicle, moving to and joining with the cell membrane, and releases contents
• Diffusion / semipermeable membrane = proteins are too large to move through the membrane, water will move into the Solution A through osmosis to to equilibrate
• Endocytosis: chemicals are moved by forming vesicles that trap the chemicals.

diagrams:

• single ring = glucose/saccharide/carbohydrate, E-shape = lipid, molecule with Nitrogen is a amino acid