UF-BSC2010 Exam 1, BSC 2010 UF Exam 1

Unsaturated Fatty Acids

-not saturated with hydrogen bonds
-double bonds/kinks in carbon chain
-liquid at room temp

Fat's major function

storing energy

Phospholipids

-hydrophilic phosphate head and two hydrophobic fatty acid tails
-major components of cell membranes
-form phospholipid bilayer (hydrophilic heads facing extracellular fluid and cytosol, hydrophobic tails inward)

Anabolic reactions

-construction of complex molecules from simpler ones
-require/absorb energy
-endergonic reactions, free energy of products > reactants

Catabolic reactions

-breakdown of complex molecules to simpler ones
-release energy
-exergonic reactions, free energy of products < reactants

Nucleic Acids made of

-polymers of nucleotide monomers

Nucleic acids function

-store, transmit, and use hereditary information in the form of genes

Types of nucleic acids (major)

Deoxyribonucleic acid (DNA)
Ribonucleic acid (RNA)

DNA function

store information, direct RNA synthesis and control protein synthesis

RNA function

translate DNA into polypeptides (proteins)

Nucleotide

-5-carbon sugar
-phosphate group
-nitrogenous base

Nucleoside

-pentose sugar
-nitrogenous base

Phosphodiester bond

-bind nucleotides (condensation rxn)
-hydroxyl group on 3' carbon and phosphate group on 5' carbon of subsequent nucleotide
-forms polynucleotide backbone

Pyrimidines

-nucleotides with one ring structure
-Cytosine
-Thymine/Uracil (in RNA)

Purines

-nucleotides with two ring structures
-Adenine
-Guanine

RNA structure

-Single stranded
-H-bonds can make it fold back on itself

DNA structure

-two strands (double helix)
-H-bonds form between pyrimidines on one strand and purines on the other
-always three rings b/w carbon backbones of each antiparallel strand

Complementary base pairing rules

DNA: Cytosine and Guanine, Thymine and Adenine
RNA: Cytosine and Guanine, Uracil and Adenine

C-G stronger than A-T

Transcription

the info from DNA transferred to the messenger RNA in the nucleus

Translation

ribosomal complex attaches to mRNA to form a polypeptide (protein)

Central Dogma

DNA transcribed into complimentary strand of RNA, which is translated into a specific sequence of amino acids that results in the creation of a protein

Proteins

-polymers of amino acids
-enzymes, defense, regulation, receptors, storage, structure, movement, transport, gene expression

Amino acids

-20 common ones, proteins made of these
-amino group on one end, carboxyl on the other, variable R group
-nature of side chain determines nature of amino acid

Peptides (oligopeptides)

-short polymers of only 20 or fewer amino acids
-signaling molecules/some hormones

Polar amino acid

has a polar side chain (hydrophilic)

Nonpolar amino acid

has a non polar side chain (hydrophobic)

Cysteine

-SH at end of R group, forms disulfide bridge which helps determine how a protein folds

Gylcine

single H atom in side chain, small enough to fit into tight corners in a protein molecule

Proline

ring structure

Peptide bonds

-covalent bonds b/w amino acids (dehydration)
-polymerization occurs from the amino ends towards the carboxyl end
-grows form the amino terminus to the carboxyl terminus

Primary structure

amino acid sequence that makes up the backbone of the protein

Secondary structure

alpha helices and beta pleated sheets, result of hydrogen bonding b/w repeating parts of the polypeptide backbone

Tertiary structure

refers to bonds between variable groups of amino acids
-disulfide bridge example of R-group interactions that contribute to tertiary structure

Quaternary structure

highest level of protein structure,
-formed by the combination of multiple polypeptides into functional units
-not all proteins have this

Enzymes

-special class of proteins, speeds up rxns without being permanently altered/consumed
-name of enzymes usually end in -ase

Ribozymes

-special kinds of catalytic RNA molecules

Active site

-area in the enzyme where substrates are held
-specific to one kind of substrate

Substrate

-the reactant that binds to an enzyme and is chemically modified by it

Enzyme-substrate complex

formed when two specific substrates bind to the active site

Induced fit

-when a substrate binds to an enzyme's active site, it will bring chemical groups into the appropriate position to enhance their ability to catalyze the rxn
-baseball & catcher's mit

Cofactors

-nonprotein organic compounds/inorganic ions necessary for a catalyzed reaction to proceed

Prosthetic groups

non-amino acid groups that are permanently bound to their enzymes

Coenzymes

enzymes that remove chemical groups from the substrate

Metabolic pathway

step-by-step, enzyme mediated process by which a precursor molecule is converted into a final product

Enzyme inhibitors

-substances that stop and enzyme from doing its job

Irreversible inhibition

inhibitor COVALENTLY binds to the side chain on the active site of an enzyme, blocking substrates form binding to it

Competitive inhibitors

-reversible inhibition
-attach to an enzymes active site so that the substrate cannot bind to the enzyme

Noncompetitive inhibitors

-bind to a site other than the active site and change the enzyme's shape so that the active site cannot accept the substrate molecule any longer
-example of all0steric regulation

Allosteric regulation

-occurs when the function of an enzyme is affected by the binding of some kind of non-substrate regulatory molecule at another site (allosteric site)
-this makes the binding of substrate molecules to its active sire either easier or harder

Allosteric activators

activate enzymatic activity

Allosteric inhibitors

inhibit enzymatic activity

Protein kinases

-enzymes that modify proteins by adding phosphate groups
-increases rates of reaction by phosphorylating allosteric or active sites of other enzymes

Protein phosphatases

enzymes that modify proteins by removing phosphate groups (undoing the work of protein kinases)

Feedback inhibition

-the end product acts as a noncompetitive inhibitor in the first enzyme in a metabolic pathway, shutting down the pathway

Commitment step

-first reaction in the metabolic pathway
-shut down in feedback inhibition

Isozymes

enzymes that catalyze the same reactions, but that have different physical properties and compositions

Cell theory

-all organisms consist of one or more cells
-cells are the smallest functional unit of life
-all cells arise from pre-existing cells

Plasma membrane

-"outer barrier"
-selectively permeable
-

Prokaryotic and Eukaryotic both have

-DNA
-ribosomes
-cytosol
-plasma membrane

Prokaryotic cells

-oldest cells
-no membrane bound organelles
-one circular chromosome in nucleoid region
-most have cell wall-peptidoglycan (sugars & amino acids)
-flagella

Eukaryotic cells

-membrane-bound organelles
-larger than prokaryotic
-multiple, complex chromosomes
-double-nuclear membrane (nuclear envelope)

3 major parts of eukaryotic cells

-nucleus
-cytoplasm
-plasma membrane

Nucleus

-DNA replication and transcription occurs here
-enclosed in nuclear envelope
-dense region (nucleolus)
-shape maintained by nuclear lamina

Chromosomes

-made of condensed chromatin, which consists of a complex of DNA and proteins
-contain genetic info

Nuclear envelope

-double membrane
-contains nuclear pores that regulate the flow of materials to the rest of the cell

Nucleolus

-dense region
-ribosomal RNA (rRNA) made

Ribosomes

-made of rRNA and a protein complex
-not membrane bound (free floating in cytoplasm-pro&eu or attached to rough ER-eu)
-protein synthesis
-protein complex takes mRNA (messenger RNA) and translate the code into an amino acid sequence to build polypeptides

Cytoplasm

everything within the cell except for the nucleus or nucleoid region

Endomembrane system

-performs metabolic functions and regulates protein traffic within the cell
-endoplasmic reticulum, Golgi apparatus, nuclear envelope, lysosomes and plasma membrane

Endoplasmic reticulum

-continuous with the outer membrane of the nuclear envelope
-biosynthetic factory of the cell, produces various molecules

Rough ER

-studded with ribosomes
-used to make proteins
-once made, proteins modified in lumen of rough ER and tagged for delivery
-proteins sent out into cell via transport vesicles

Smooth ER

-used to make lipids, polysaccharides, steroids and phospholipids
-detoxifies small molecules

Golgi apparatus

-receives the products of the endoplasmic reticulum, modifies them, and ships the modified products either to the rest of the cell or outside the cell via transport vesicles
-polysaccharide synthesis in plants
-cisternae: membranous sacs evolved from the ER
-cis: same side, trans: opposite side

Lysosomes

-sacs of hydrolytic enzymes that break down large molecules
-intracellular digestion
-animal cells only

Phagocytosis

-cells take in macromolecules, plasma membrane engulfs material forming phagosome

Primary lysosome

-emerges from trans side of golgi apparatus

Secondary lysosome

-when phagosomes combine with primary lysosomes
-the hydrolytic enzymes digest the contents of the phagosome

Autophagy

-lysosomes that selectively destroy old cell parts

Not part of endomembrane system

-mitochondria
-chloroplasts

Mitochondria

-powerhouse of the cell
-cellular respiration occurs here
-cells convert energy to ATP through redox reactions
-double membrane
-cristae: highly folded
-innre membrane divides the mitochondrion into the inter membrane space and the mitochondrial matrix

Chloroplasts

-kind of plastid that contains photosynthetic pigments that convert light energy to chemical energy
-double membrane

Chlorophyll

-photosynthetic pigment that gives plants their green color

Thylakoids

-saclike membranes that are interconnected to form stacks of grana
-lumen inside of these

Stroma

-fluid that exists outside the thylakoid membrane
-synthesis of carbohydrates here

Similarities between mitochondria and chloroplasts

-both involved in energy conversion
-neither part of endomembrane system
-double membranes
-independent DNA and ribosomes
-proteins made by free ribosomes

Peroxisomes

specialized organelles that use enzymes to break down the toxic by-products of metabolism

Glyoxysomes

specialized organelles where stored lipids are converted into carbohydrates
-plants only

Vacuoles

-plants & fungi
-storage: waste and toxic products
-structure: central vacuole increases in size when water enters
-reproduction
-catabolism: breakdown of waste products
-osmotic balance

Cytoskeleton

-network of microtubules, microfilaments and intermediate filaments that branch throughout the cytoplasm
-gives cells their 3-D shape and assist in transport of organelles
-dynamic

Microfilaments

-solid rods made of actin (protein)
-smallest
-fix organelles in place, support the cell's shape
-dynamic instability: can be broken down and subsequently be reorganized

Intermediate filaments

-thicker than microfilaments but thinner than microtubules
-help anchor the nucleus and other organelles
-position and she more permanent

Microtubules

-thick, hollow rods with walls made of tubulin (globular protein)
-guide organelle movements and separate chromosomes during cell division

Cilia

-made from microtubules
-bend in beating motion due to dynein

Flagella

-longer than cilia
-move in snakelike motion

Cell walls

-plants
-protects from infection
-maintains shape and volume
-prevents from taking in excessive amounts of water
-made of polysaccharide, proteins and lignin

Extracellular matrix

-gel like matrix of glycoproteins
-support, adhesion, movement, regulation, filtering of materials, orientation of cell movement

Cell junctions

-connections between cells formed by specialized structure that "glue" adjacent cells together

Plasmodesmata

made of fused vacuoles that allow cytoplasm to flow from one cell to another
-make the plant one continuos system

Tight junctions

-animal cells
-seal off adjoining cells preventing extracellular fluids from moving across a cell layer

Desmosomes

-affix cells together in strong sheets, but allow some materials to move in the extracellular matrix