Bio 1 exam 2

The polypeptide backbone of antibodies (and all proteins) contains N and C joined in which of the following ways?

-N-C-C-N-C-C-N-C-C- Which of these atoms correspond to a SINGLE amino acid? What other (two) atoms not shown here are also considered to be part of the 'polypeptide backbone'?

Carbs: Summarize the different roles carbohydrates play in organisms, and give examples of each.

-sugars and 'sugar polymers' -monosaccharides = building blocks -disaccharides, oligosaccharides (3-50), polysaccharides (50+) -glyscosidic linkages FUNCTIONS: 1) energy source (monosaccharides) 2) C source (monosaccharides) 3) storage of energy (polysaccharides) 4) structural (polysaccharides)

Units of weight: grams vs. Daltons: "How much does one molecule/one mole of this molecule weigh?"

1 Dalton--Remember that 'grams' are used to describe the weight of everyday objects. 'Daltons' are used to give the weight of single atoms, parts of atoms, or molecules. 'Grams' give the weight of

1) Why is the plasma membrane referred to as a 'mosaic'? 2) How are integral and peripheral membrane proteins positioned differently in the plasma membrane?

1) -the plasma membrane is mosaic becuase it contains a diverse set of proteins - some proteins are EMBEDDED some aren't: INTEGRAL (embedded) PERIPHERAL (on one side) -proteins have specific ORIENTATION receptor proteins cell-cell recognition 2) integral proteins are embedded in the plamsa membrane whereas peripheral proteins are on the sides

Carbs: 1) Contrast starch and cellulose with regard to: A. their make-up, and B. their 3-D structures. 2) Of what value are their structural differences to plants? 3) Can humans break them down for energy?

1) starch is an alpha glucose in plant cells that is built with excess glucose is broken down with the enzyme amylase. contains some branching. cellulose is a beta gluclose in plant cells that makes part of the plant cell wall, wood, and cotton. it is the most abundant organic compound. it is UNDIGESTABLE by amylase. it is not helical OR BRANCHING. chains form weak intermolecular interactions. H bonds. 2) cellulose is mostly linear chains of glucolse molecules while starch is present in both linear and branched chains. Cellulose is stronger than starch. 3) Humans can break down starch but not celluose because they do not have the enzyme for beta linkages. cellulose acts as a fiber in the intestinal tract other beta glucose: chitin (structural, glucose deriviative, form h bonds, exoskeletons, cell wall fungi) and peptidoglycan (cell wall bacteria)

1) Explain the difference between 1° active transport and 2° active transport (cotransport). 2) What type of transport protein is required for active transport? 3) How is ATP important for each? Give specific examples of both types.

1) - 1º active transport: used to concentrate ions. ion pumps. EX. NA+/K+ pump - 2º active transport: involves the movement of two substances... a molecule and an ion. AKA cotransport. driven by the ion! EX. a Na+ driven glucose transport protein 2) a carrier protein is required for active transport 3) ATP is important to move the molecules across their gradients

1) What is a polymer? 2) Name and describe the chemical reactions that are used to make and break biological polymers, as done in lecture. 3) Which of the four classes of biological molecules form polymers? 4) What of the four may be macromolecules?

1) A polymer is a substance or material consisting of very large molecules, or macromolecules, composed of many repeating subunits. MOLECULAR 'CHAINS' built from similar or identical building blocks 2) dehydration (biosynthesis): removes a water molecule to make polymerrs. *requires and enzyme and energy.* Hydrolysis (digestion): adds a water molecule to break down polymers. *requires and enzyme and releases energy.* occurs inside and outside of the cell. food-> monomers -> new polymers (hyrdolysis) (dehydration) There are four classes of biomolecules that constitute all living matter: carbohydrates, lipids, proteins, and nucleic acids. 3) LIPIDS can NOT form polymers 4) Carbs, protiens, and nucleic acids can be macromolecules NOT LIPIDS While they have different structures and functions, they are all composed of long complex chains of molecules (polymers) made up of simpler, smaller subunits (monomers).

Create a table in which you compare and contrast all the modes of passive and active transport discussed in class. Include the following: simple diffusion facilitated diffusion 1º active transport 2º active transport direction (up/down gradient) membrane protein (yes/no) specific/nonspecific source of energy a specific example

1) DIFFUSION: no energy input - PASSIVE transport - moves with, DOWN the, gradient - a gradient has potential energy. no input of energy but energy is involved because net movement. - SIMPLE diffusion (small, non polar substances) - FACILITATED diffusion (polar, charged substances) (specific) - CHANNELS: an integral membrane protein completely spanning the membrane. it contains a hydrophilic pore that recognizes one type of solute. EX. ions (Na+, K+, Ca+) and aquaporins (water) - CARRIERS: an integral membrane protein. its structure CHANGES SHAPE to allow one type of solute to pass through EX. monosaccharides, amino acids, glucose transporter 2) moving ACROSS: energy input - ACTIVE transport - moves against, UP the, gradient - requires an input of energy... ATP - requires a carrier protein - 1º active transport: used to concentrate ions. ion pumps. EX. NA+/K+ pump - 2º active transport: involves the movement of two substances... a molecule and an ion. AKA cotransport. driven by the ion! EX. a Na+ driven glucose transport protein

1) Summarize the structure and function of the rough ER and the Golgi apparatus. 2) Include the role of chaperones, vesicles and Golgi enzymes in your answer.

1) ER: makes lipids and proteins for the membrane!!!! ER products either remain in the ER or leave. transport vesicles travel from the ER to the golgi. RER: covered in ribosomes, makes proteins, contains chaperones. SER: no ribosomes, makes lipids, detoxifies drugs, stores glycogen. GOLGI: multiple flattened sacs, each contains a unique set of enzymes, recieves/transmits/buds off vesicles, processes (chemically changed them) then sorts and ships ER products (lipids and proteins). follows two critical routes: to the cell membrane (SECRETION) or to organelles called LYSOSOMES. 2) Chaperones are proteins that guide proteins along for the proper pathways for folding. they protect proteins when they are in the process of folding, shielding them from other proteins that might bind and hinder the process. Transport vesicles help move materials, such as proteins and other molecules, from one part of the call to another. golgi enzymes catalyze the addition or removal of sugars from cargo proteins, the addition of sulfate groups, and the addition of phosphate groups

1) Describe way(s) that each of the following substances cross the plasma membrane as discussed throughout the lecture: Na+, K+, O2, CO2, water, glucose, cholesterol, and a cell-sized food particle. 2) If a transport protein is involved, what type of transport protein? 3)Which mechanisms require an additional input of energy? (Another table!)

1) Ions and water = channels glucose and cholesterol = carriers cell sized food particle = endocytosis 2) 3)

1) Explain the functions of lysosomes in the cell. 2) Include in your answer the terms hydrolase and food vacuole (a.k.a. a phagosome). 3) Where do lysosomal hydrolases come from? 4) What prevents the hydrolases from breaking down the organelle they originate in?

1) LYSOSOMES: mebrane-bound sacs containing HYROLYTIC ENZYMES (hydrolysis enzymes), can fuse with vesicles/food vacuoles originating from the plasma membrane ex. amoebas and macrophages. also breaks down organelles: AUTOPHAGY. 2) VACUOLES: membrane-bound sac with specific functions. 1. central vacuole 2. FOOD VACUOLE: buds in from the cell membrane. ex. protists, amoebas. phagosomes degrade biological material. Hydrolase are the acidic enzymes in lysosomes 3) From the trans face of the golgi stack and are formed first as primary lysomes then become enzymes 4) the membrane prevents the aggressive enzy,es from destroying cellular structure

1) Where are proteins of the cell membrane constructed? 2) What determines a protein's position in the membrane? 3) In what way are membrane proteins 'asymmetrical'? (Refer to Figure 7.10)

1) The proteins of the cell membrane are constructed in the ER-- RER produces proteins, SER produces lipids and processes through the golgi 2) Their primary structure and orientation determines a proteins position in the mebrane 3) proteins are 'asymmetrical' by the arrangement of proteins, lipids, and their associated carbs that are built by the ER and Golgi

1) Explain what is meant by a concentration gradient when dealing with a membrane. 2) How does a substance's concentration gradient influence its diffusion? 3) How does it influence the diffusion of another substance? (See Figure 7.11)

1) The region along which the density of a chemical substance decreases 2) The difference in the concentration of a substance between two areas is called the concentration gradient . The bigger the difference, the steeper the concentration gradient and the faster the molecules of a substance will diffuse. The direction of diffusion is said to be 'down' or 'with' the concentration gradient. 3)

Nucleic Acids: 1) What is the basic structure of a nucleotide? 2) How are nucleotides assembled to make polynucleotides? 3) Name three structural differences between DNA and RNA.

1) a nucleotide has 3 parts: a pentose sugar, phosphate, aand nitrogenous base. 2) 13 or more nucleotides make polynucleotides 3) DNA uses deoxyribose sugar and RNA uses ribose sugar 3 bases in each but DNA uses thymine and RNA uses uracil # of chains: RNA is single chained but DNA has 2 nucleotides to form a double helix

1) What do ribosomes do in cells? 2) What 2 types of macromolecules are ribosomes constructed from? 3) What is the difference between free and bound ribosomes?

1) a ribosome is a macromolecular complex that constructs polypeptides. contains 2 subunits. contains rRNA and decodes mRNA. 2) Ribosomes are highly complex molecules thaat are constructed from a protein and nucleic acid. 3) cytosolic (free) ribsomes are in the cytosol and are not attached to any other structure. they produce PROTEINS used INSIDE the cell itself. make proteins for cytosol, mitochondria, and chloroplasts. ER surface (bound) ribosomes produce PROTEINS that are EXPORTED from the cell to be used elsewhere in the EMS and for secretion. -ER -GOLGI -lysosome -cell membrane

Protiens: 1) What is the basic structure of an amino acid? 2) Why do different amino acids have distinct chemical properties? 3) How are amino acids assembled to make polypeptides? 4) Summarize the structural features of a polypeptide chain.

1) basic structure of amino acid: amino group + and carboxyl group - attached to a central alpha carbon contains H atom contains a variable group (R group or side chain) 2) different R groups= different chemical properties 3) amino acids make proteins and proteins are assembled to make polypeptides through peptide bonds 4) polypeptide chains contain a backbone composed of N-C-C-N-C-C-N and is polar with no charge. the side chains are the R groups that determine their properties

1) Describe the structural features of mitochondria and chloroplasts. 2) How are these organelles believed to have originated? 3) What evidence supports the endosymbiont theory?

1) convert energy from one form to another not a part of the EMS - have their own DNA and ribosomes - do not bud off or fuse to vesicles mitochondrion uses sugar to make ATP -outer membrane -inner membrane -cristae -matrix -2 membranes -~2-8 um chloroplast uses light to make sugar -stroma -inner and outer membranes -granum -thylakoids -2 membranes -~5-10 um 2) endosymbiont theory: membrane of larger cell engulfed smaller cell= DOUBLE MEMBRANE 3) the shape/size, double membrane, semi-antonumous, modern day examples

Nucleic Acids: 1) Explain the structural features of the DNA double helix. 2) Why are its strands said to be complementary?

1) deoxyribose nucleic acid: 3 bases. thymine=DNA. 2 nucleotides for helix-> "base pair" joined by H bonding A-T G-C 2) because the bases fit perfectly, g complements c and a complements T and U (for RNA)

1) List all organelles whose membranes are considered part of the endomembrane system. 2) What functions does the EMS serve for the cell?

1) endomembrane system: system of membranes INDIRECTLY joined by transport vesicles (all can bud off and fuse with vesicles). this contains the ER, golgi, lysosomes, 'food' vacuoles, and the cell membrane.. 2) manufactures, sorts, ships, exports, imports, and recycles biomolecules

Protiens: 1) What determines the conformation of a protein? 2) How do variations in the environment influence a protein's conformation?

1) enviromental factors, different amino acids, based off of primary structure 2) water, pH, and temperature influence a proteins conformation. noncovalent bonds withh break aand unfold if boiled.

Lipids: 1) What are the structural features of fats? 2) What is meant by saturated vs. unsaturated fats? 3) What are oils?

1) fats are made from 3 fatty acids + 1 glycerol joined by an ester linkage hydrophobic non polaar partial charge fats have more energy nutrients then carbs or proteins functions: cushions organs, insulation 2) saturated fats contain saturated fatty acids -animal fats -SOLID at room temp because the saturated fatty acids allow them to be packed efficiently unsaturated fats contian one or more unsaturated fatty acid -describes plant and fish fats -LIQUID at room temp because the C-C double bond creates a kink 3) OILS are UNSATURATED fats

Lipids: 1) What are the structural features of a fatty acid? 2) Draw the structure of a methyl group. 3) Explain the difference between saturated and unsaturated fatty acids. 4) Explain cis vs. trans double bond configurations. Which configuration is most common in natural foods? 5) What determines the omega number of a fatty acid?

1) fatty acids are the simplist lipid acidic negative carboxyl group on one end, methyl group on other 2) 3 H bonded to C. 3) length can vary depending on saturation level: saturated= straight, no c-c double bonds unsaturated= bent, has one or more c-c double bonds 4) cis configurations are isomers to trans configurations cis has 2 carbon groups on the same side where trans has the carbon groups on different sides ONLY CIS are found in cells and nature trans are made by food processing= TRANS FATS 5) the number of carbons away from the methyl end of the chain. if the double bond is 3 carbons away, it is omega-3 fatty acid

Carbs: 1) What is the basic structure of a monosaccharide? 2) Explain the terms triose, pentose, and hexose. 3) What type of structure do biological monosaccharides typically have? 4) Give examples of ways in which monosaccharides differ leading to different isomers. 5) Explain the difference between alpha and beta glucose.

1) functional groups found in monosaccharides: hydroxyl and carbonyl Ring and long chain 2) Triose (3), pentose (5), and hexose (6) relate to the number of carbons. 3) ????? 4) glucose, fructose and galactose all are monosaccharides and isomers 5) A is when OH is below the ring and B is when OH is above the ring. (ants on the ground, birds in the sky) alpha glucose= starch plants make built with excess glucose one monomer at a time humans hydrolyze with amylase (enzyme that breaks down starch) glycogen animals make stored mainly in liver and muscle ~1 day supply beta glucose= cellulose (FIBER!) structure major part of cell wall makes up wood, cotton most abundant organic compound undigestable by amylase not helical OR branchin chains for intermoleculear weak interactions

Nucleic Acids: 1) How does DNA indirectly run cellular operations? 2) Explain what is meant by 'DNA → RNA →protein'. 3) How is it that different genes are able to encode proteins with different 1º structures?

1) it contains the biological instructions (genes) that make each species unique. The genes in DNA transcribe to RNA (mRNA) then proteins through translation, tRNA, and ribosomes 2) DNA to RNA decodes to a protein 3) gene splicing prior to mRNA

Carbs: 1) How are monosaccharides assembled to make polysaccharides? 2) What are disaccharides and oligosaccharides?

1) monosaccharides are assembled to make polysaccharides through dehyration reaction (which produces water, requires an enzyme and energy) and glycosidic linkages 2) disaccharides are monosaccharides joined together by 2 links and oligosaccharides hace 3-50 links

1) Explain the structure and function of the nucleus as described in lecture and your textbook. 2) Include in your answer a description of the nuclear envelope and nuclear pores. 3) Name 2 places genes are found in animal cells, and 3 places genes are found in plant cells.

1) nucleus contains a nuclear envelope, nucleolus, and chromatin. It is fully enclosed in the nuclear membrane and contians the majority of the cells genetic material which is organized as DNA molecules, along with proteins to form chromosomes 2) nuclear envelope, or nuclear membrane, is made up of two lipid bilayer membranes (inner and outer) that surrounds the nucleus. the nuclear pores are a set of large complex proteins that allow small molecules and ions to freely pass or diffuse in and out of the nucleus. they also lalow necessary proteins to enter the nucleus from the cytoplasm. 3) two places genes are found in animal cells: mitochondria and nucleus three places genes are found in plant cells: chloroplast, nucleus, aand mitochondria

1) Which types of cells have cell walls? 2) Referring to information from lecture, the textbook, and/or the lab notebook, give the polysaccharide component of each. 3) Which type of cell has an extracellular matrix? 4) What purpose(s) do these structures serve?

1) plants, prokaryotes, fungi, and some protists 2) plants cell walls: cellulose, starch prokaryotes cell walls: peptidoglycan fungi cell walls: chitin protist cell walls: cellulose 3) animal cells 4) extracellular matrix provides support and anchorage for the shape of the cells, regulates, and determines cells dynamic behavior including cell survival, cell proliferation, cell polarity, cell differentiation, cell adhesion, and cell migration. Plant cells are already strong enough.

Protiens: 1) Describe the four levels of protein structure. 2)What is the chemical basis of each?

1) primary (1°) structure, secondary (2°) structure, tertiary (3°) structure, and quatranary (4°) structure. folding occurs spontaneously based on the primary structure. enviromentaal factors affect the conformation: water, pH, temperature 2) primary (1°) structure: results from COVALENT bonding between amino acids the order of amino acids in a protein is determined by the order of monomers in the DNA (gene) for that protein. Genes specify the primary structure of proteins a polypeptide folds in a precise way based on its primary structure... established by: COVALENT BONDS secondary (2°) structure: characterized by LOCALIZED FOLDING of the polypeptide two types: COILS (alpha helices) and SHEETS (beta pleated sheets) -depends on the protein secondary structure is found in ALL proteins so it is held together by the h-bonding between BACKBONE ATOMS (O and H) established by: NONCOVALENT BONDS: H-BONDS tertiary (3°) structure: overall 3D structure fromed by the polypeptide involves R groups "R group has entered the chat" nonpolar amino acids cluster in the interior of proteins. they interact with eachother by HYDROPHOBIC interactions. also H BONDS, IONIC BONDS, VAN DER WAALS, & a covalent bond (?) established by: NONCOVALENT BONDS denaturation: disrupts weak interatctions only. what will happen when boiled? noncovalent bonds break and unfold. quatranary (4°) structure: -hydrophic, h-bonds, ionic bonds, van der waals, DISULFIDE BONDS (covalent bond, disulfide bridges) ALL PROTEINS HAVE 3 OR 4 STRUCTURE

1) What makes prokaryotic and eukaryotic cells different from one another? 2) What features do ALL cells have?

1) prokaryotic cells: no membrane bound organelles DNA in nucleoid ~1-5 um bacteria & anchaea eukaryotic cells: membrane bound organelles most DNA in nucleus ~10-100 um protist plants animals fungi MEMBRANE BOUND ORGANELLES: -compartmentalization (ordering of events such as DNA>RNA>protein, control of the pH, segregation/concentration of nutrients) -membranes provide function (with enzymes) (all contain aqueous solutions, either 1 or 2 membranes, number depends on the cell) 2) a plasma membrane (transports nutrients, structure and receptors), cytosol, DNA, ribosomes (make proteins), nutrients, 1000s different enzymes

1) How does the chemistry of phospholipids and membrane proteins determine the structure of the cell membrane (i.e. the fluid mosaic model)? 2) Which chemical interaction holds a membrane together? 3) How thick is the cell membrane?

1) the chemistry of phospholipids and membrane proteins determines the structure of the cell mebrane because their are embedded, or transmembrane, proteins that are polar, charged, and hydrophilic or nonpolar and hydrophobic. the phospholipids are hydrophilic on their heads and hydrophobic on the tails. 2) HYDROPHOBIC interactions 3) the cell membrane is 7-8nm thick

Carbs: 1) Discuss the polysaccharides glycogen and starch with regard to the following features, noting any differences: 1) their make-up, 2) their 3-D structures, 3) in which organisms they are found, and 4) where they are stored in the organism. 2) Why is branching an important structural feature for glycogen and starch?

1) the polysaccharides glycogen and starch are alpha glucose -animals = glycogen -> stored mainly in *liver and muscle* -> ~1 day supply -> C6H10O5 3d structure: 5 swigglies more branched more ends easier for enzymes to find ends and breaka down polymers -plants = starch -> built with excess glucose -> one monomer at a time -> in starch-storing tissues within leaves -> C6H10O5 3d structure: 3 swigglies less branched less ends need amylase to break down 2) branding is an important structural feature because it determines how easily the polymer can break down. More branching = more surface area = more ends for enzymes to attach to

1) Where in a cell are the proteins made by free ribosomes found? 2) Where all are proteins made by bound ribosomes found? (Proteins contain molecular 'address labels' that send them to different destinations!)

1) the proteins made by free ribsomes are either transported into the nucleus/mitochondria or remain in the cytosol 2) the proteins made by bound ribosomes are imported to the ER and a polypeptide is 'threaded' into the ER. proteins stay in the ER or leave to travel to other parts of the EMS by transport vesicles.

1) Explain how water diffuses across membranes (i.e. osmosis). 2) Explain the different ways animal cells, plant cells, and protists deal with the problem of osmosis, as discussed in lecture and the lab class.

1) water diffuses across the membrance from the region of lower soltue concentration to that of higher solute concentration until solute concentrations are equal. diffusion of water across a selectively permeable membrane (water goes to the area with MORE solute) hypertonic: a solution that contains more dissolved particles than is found in normal cells and blood. hypotonic: has a lower concentration of solute than another solution. 2) osmoregulation is a primary example of the homeostasis all life must maintain.... protists= contractile vacuoles bacteria= cell walls plants= cell walls animals= solute balance: equal in and out, no net movement

The primary structure of antibodies includes numerous cysteine amino acids. Referring to Figure 5.17 in your book, determine the approximate molecular weight (the weight of one molecule) of this amino acid. (Fyi: the atomic weight of sulfur is 32 Daltons.)

121 Daltons Fyi, antibodies have hundreds of amino acids in each of their 4 polypeptides, for a total MW of ~150,000 Daltons (150 kD). A very large macromolecule, but its weight is still given in Daltons.

Which level of structure is held together by COVALENT BONDS (only/always)?

1° These covalent bonds are known as ______________ ___________.

Which level of structure is held together ONLY by h-bonds?

2° Which THREE atoms of the polypeptide backbone help to form the h-bond? (Circle them on the chain in the earlier question!)

Of the 20 amino acids that antibodies are made from, how many are classified as 'basic'?

3 Notice that all three of these amino acids have an AMINO GROUP within their side chain. As covered in Chapter 4, the amino group is basic at cellular pH, accepting a proton (an H+) and obtaining a + charge. Which functional group is found in the two 'acidic' amino acids? What charge do these obtain? All proteins function by interacting with other molecules, and it is their partial and full charges that allow them to form ionic bonds with those molecules.

Carbs: List the 3 monosaccharides and 3 disaccharides commonly found in our diets.

3 monosaccharides: glucose fructose galactose 3 disaccharides: sucrose= glucose + fructose maltose= glucose + glucose lactose= glucose + galactose all are isomers: C12H22O11

Of the twenty amino acids that antibodies are made from, how many are classified as 'charged'?

5 Remember that amino acid classification is based solely on the side chain or 'R' group. Every amino acid is technically charged, due to its ionized amino and carboxyl groups, but only five are classified as 'charged'. Also remember that the 'polar' amino acids are all polar but uncharged.

Nucleic Acids: Explain what a gene is, what it's made of, what it's used for, and where it is found.

A gene is an informational unit consisting of a region of DNA Specifies a CHARACTERISTIC by encoding a protein (eye color) It is made of nucleotides

Which of the following statements best describes some aspect of the function of a protein that cotransports glucose and sodium ions into the intestinal cells of an animal?

A substance that blocks sodium ions from binding to the cotransport protein will also block the transport of glucose.

Covalent bonding: orbitals and hybridization "How many atoms in this molecule have undergone sp3 hybridization?"

C normally forms 4 covalent bonds H normally forms 1 covalent bond O normally forms 2 covalent bonds N normally forms 3 covalent bonds Carbon, oxygen, and nitrogen undergoes SP3 hybridication whenever they form SINGLE COVALENT BONDS ONLY Hydrogen does not undergo SP3 hybridization because it only has 1 orbital. the position of electrons in s and p orbitals are______ whereas in sp3 orbitals they

List the two types of membrane transport proteins and explain how each works. Explain how these proteins are 'specific'.

Diffusion-> passive-> facilitated-> - CHANNELS: an integral membrane protein completely spanning the membrane. it contains a hydrophilic pore that recognizes one type of solute. EX. ions (Na+, K+, Ca+) and aquaporins (water) - CARRIERS: an integral membrane protein. its structure CHANGES SHAPE to allow one type of solute to pass through EX. monosaccharides, amino acids, glucose transporter

All proteins are synthesized by ribosomes in the cell. Some ribosomes float freely in the cytosol, while others are bound to the surface of the endoplasmic reticulum. Most proteins made by free ribosomes function in the cytosol. Proteins made by bound ribosomes either function within the endomembrane system or pass through it and are secreted from the cell. Which of the following proteins are synthesized by bound ribosomes?

ER protein, lysosomal enzyme, insulin

Nucleic Acids: Summarize the different roles nucleic acids play in organisms, and give examples of each.

FUNCTIONS: 1) information storage (genes) (polynucleotides) 2) USABLE energy (ATP) (nucleotides) the order of nucleotides in a gene determines the order of amino acids in a protein= primary structure

How does phospholipid structure relate to the selective permeability of the plasma membrane? : Nonpolar molecules (hydrocarbons, O2, CO2)

Hydrophobic can cross lipid bilayer easily no transport protein required

Which one of the following statements about the endomembrane system is correct?

Proteins that will be secreted from the cell are likely to be found in closed spaces bounded by membranes of the endomembrane system. Proteins that will be secreted are always enclosed by some membrane of the endomembrane system until they are secreted.

An amino acid is CLASSIFIED (polar, nonpolar, charged) based on the chemistry of its _____.

R group Be able to group amino acids based solely on their structures, by the RULES posted under Quiz #4.

Lipids: 1) How does the structure of cholesterol differ from that of a fat? 2) For what types of products does cholesterol serve as a precursor?

STEROIDS 1) cholesterol (also an alcohol) contains 4 linked hydrocarbon rings. 2) cholesterol serves as a precursor through steriod hormones, bile, vitamin D, and it also makes up the membrane ex. cholesterol-> preg..something -> progest...something-> testoserone-> estrogen = products of one reaction become reactants for others until the cell is satisfied

Which of the following results is most likely result if a portion of an animal's blood is replaced with distilled water?

The animal's red blood cells will swell and possibly burst because the blood has become hypotonic compared to the cells.

Which of the following statements best describes how unsaturated fatty acids increase membrane fluidity at lower temperatures?

The double bonds form kinks in the fatty acid tails, preventing adjacent lipids from packing tightly.

Which of the following statements best explains how the membranes in winter wheat are able to remain fluid in extremely cold temperatures?

The membranes contain an increased proportion of unsaturated phospholipids.

What happens when two solutions separated by a selectively permeable membrane reach osmotic equilibrium?

Water molecules move between the two solutions, but there is no net movement of water across the membrane Water molecules are constantly in motion and will continually move across the membrane. However, becuase the solutions are in equilibrium, there is not net movement across the membrane.

channels

allow water molecules and small ions to flow quickly across the membrane provide a continuous path across the membrane are integral membrane proteins transport solutes down a concentration or electrochemical gradient provide a hydrophilic path across the membrane

DIFFUSION: orange dye move independently of purple dye

always

Protiens: Are the terms protein and polypeptide synonymous? Explain.

amino acids are protein's monomer. polypepetide are protein's polymer. A protein is one or more polypeptides folded into a specific conformation so a polypeptide is made up of proteins. amino acids -> proteins -> polypeptide

Which functional groups are present in this polypeptide?

amino group, carboxyl group, hydroxyl group, sulfhydryl group be sure you can identify them all! Which ONE behaves as an acid at cellular pH? Which one a base?

Why does the surface area-to-volume ratio place a limit on the size of cells?

as radius gets larger, volume increases much quicker than surface area. surface area is squared where as volume is cubed. Plants are able to get so big because they have a central vacuole that decreases volume.

All proteins are composed of _____.

atoms and amino acids Only some proteins have quaternary structure, so 'several polypeptides' is not a correct answer.

Covalent bonding: atoms, covalent bonds, and molecules: "How many atoms/bonds are found in this molecule?"

atoms-- count all the elements covalent bonds-- nm to nm bonds molecules-- the entire thing

lysosomes

autophagy (removes unnecessary or dysfunctional components) (cancer cells) macromolecule digestion

Acidic and basic functional groups: "Which of these molecules contains a functional group that is basic and therefore bears a full charge as shown, at cellular pH?"

basic functional groups: amino + acidic functional groups: carboxyl - phosphate - polar: hydroxyl carbonyl sulfhydryl nonpolar: methyl

Which type of secondary structure is most common in antibodies—alpha helices or beta strands?

beta strands There are a few helices in antibodies but mostly strands, which are the segments of polypeptide that make up a beta sheet. This can be seen in the structure shown at http://www.samper.pl/strony/Feder_Marcin/antibody.htm.

Which level of structure is held together by NONCOVALENT BONDS?

both 2° and 3° Specifically, which noncovalent bonds (i.e. weak interactions) hold together each level? (One answer can be found in the next question!) The take-home: polymers are formed by covalent bonding, while conformation is established through noncovalent bonding (intramolecular weak interactions). Noncovalent bonds also allow two different molecules to interact with each other (intermolecular weak interactions). These are the two reasons weak interactions are essential for biology, which we listed back in Chapter 2 (with our signal-receptor example)!

the POLYPEPTIDE BACKBONE contains which of the following atoms?

carbon, hydrogen, oxygen, nitrogen The backbone is shaded in the structural formula on the right above. It includes the repeating pattern of "N—C—C", but also the H bonded to N and the O bonded to the second C.

What are cell junction proteins, and why are they important for multicellular organisms?

cell junctions are proteins structures that act as glue to stick the plasma mebrances of adjacent cells together. the junctions are found in multicellular animals and are crucial to the physical intergity of the organisms TISSUES

Which of the following organelles often occupy the majority of the volume of a plant cell?

central vacuole

3 types of vacuoles—central, contractile, and food—were discussed in either lecture or the textbook/lab course. Summarize the functions of each.

central vacuole: functions as a reservior, waste dump, storage region, and keeps cell in shape (volume to surface area concept-- allows them to get bigger) contractile vacuole: controls intracellular water balance by accumulating and expelling water in and out of the cell. this allows cells to survive under hypotonic stress (pond water) food vacuole: contains food for cell and perform digestion for the cell

Based on the specific rules for classifying amino acids, how would you classify this amino acid?

charged Remember that each amino acid is classified into only ONE GROUP: nonpolar, polar (but uncharged), or charged.

Phospholipids vary in the small molecules attached to the phosphate group. The phospholipid shown in the figure has a __________ attached to phosphate.

choline group

Covalent bonds: polar vs. nonpolar: "Which of the molecules shown has [xx number] polar covalent bonds? (Note: Count double bonds as TWO covalent bonds.)"

covalent bonds-- nm to nm bonds - 1 line = 1 bond - 2 lines = 2 bonds - 3 lines = 3 bonds

1) Name the three types of cytoskeletal fibers, the type of protein each is built from, and the diameter of each fiber. 2) Which two fiber(s) participate in cell division, and what do they do?

cytoskeleton: - a netwrok of fibers spanning in the cytosol - gives the cell shape/support - made of protein! - provides MOTILITY, TRANSPORT -DYNAMIC 1) microfilaments: actin, 20 um intermediate filaments: keratin, 10 um microtubules: tubulin, 10 um 2) microfilament: create pseudopodia, ANIMAL CELL DIVISION. form a contracting ring microtubules: guide vesicle movement, CELL DIVISION. form the mitotic spindle

endocytosis

decreases the surface area of the plasma membrane forms vesicles from inward folding of the plasma membrane transported substances never physically cross the plasma membrane requires cellular energy

Based on the figure above, which of these experimental treatments would increase the rate of sucrose transport into a plant cell?

decreasing extracellular pH

The presence of cysteine in antibodies is a hint that their conformations gain added stability from the presence of _____.

disulfide bonds Proteins that are secreted from the cell such as antibodies are the ones that usually contain disulfide bridges. This is because outside the cell they require additional help to maintain their tertiary and/or quaternary structures. Notice that lysozyme, which is found in saliva, also contains disulfide bonds!

A single antibody actually contains four polypeptides, which are connected to each other covalently by _____.

disulfide bonds The only covalent connection than can occur between separate polypeptides of a protein are disulfide bonds. Peptide bonds are what hold together each individual polypeptide. In antibodies, which are a type of secreted protein found outside of cells, both the 3° and the 4° structure gains added stability from disulfide bonds. Glycosidic linkages and phosphodiester bonds have nothing to do with proteins.

List the functions performed by membrane proteins.

enzymatic functions transportation signal transduction cell recognition intercellular joining attachment

A phospholipid also has two "tails" made up of two __________ molecules, which consist of a carboxyl group with a long hydrocarbon chain attached.

fatty acid

One difference between eukaryotic and prokaryotic cells is that eukaryotic cells

have membrane-enclosed organelles, which are lacking in prokaryotic cells. If you had trouble with this question, review the following material: All cells share certain characteristics that allow cells to perform all activities required for life. All cells have both a membrane (the plasma membrane) that acts as a selective barrier and DNA, which is the cell's genetic material. Eukaryotic cells have added complexity with extensive, elaborately arranged internal membranes that divide the cell into compartments called organelles.

Because the phosphate group and its attachments are either charged or polar, the phospholipid head is _________, which means it has an affinity for water.

hydrophilic

How does phospholipid structure relate to the selective permeability of the plasma membrane? : ions (Na+, K+, Ca2+, Cl-)

hydrophilic have difficulty passing the hydrophobic part ransport proteins required to cross efficiently

How does phospholipid structure relate to the selective permeability of the plasma membrane? : polar molecules (water, sugar)

hydrophilic have difficulty passing the hydrophobic part transport proteins required to cross efficiently

Because the C-H bonds in the fatty acid tails are relatively nonpolar, the phospholipid tails are ____________, which means they are excluded from water.

hydrophobic

If plant cells are grown on media containing radioactively labeled thymine for one generation, radioactively labeled macromolecules will be detected in which of the following organelles?

in the nucleus, mitochondria, and chloroplasts... where the DNA is

exocytosis

increases the surface area of the plasma membrane requires fusion of vesicles with the plasma membrane secretes large molecules out of the cell transported substances never physically cross the plasma membrane requires cellular energy

Which of the following molecules can cross the lipid bilayer of a membrane directly, without a transport protein or other mechanism?

lipids, water, carbon dioxide, oxygen

Asbestos is a material that was extensively used in construction for decades. One risk from working in a building that contains asbestos is the development of asbestosis caused by the inhalation of asbestos fibers. Cells will take up asbestos by phagocytosis, but are not able to degrade it. Toxicity most likely results from accumulation of asbestos in which of the following organelles?

lysosomes

Explain membrane fluidity. What factors influence fluidity?

membrane fluidity is how easily substances can get in and out of a cell. how tightly packed the phospholipids are depends on the saturation. fluidity is essential because is allows for slight permeability and for the membrane proteins to function. an example of homeostasis as temperature increases, so does fluidity. unsaturated fatty acids will create kinks and cause an increase in fluidity. EX. single celled life alter the types of fatty acids because they are victims of their enviroment: if temperature goes up, saturated fatty acids are added.

A particular cell contains the following molecules and structures: enzymes, DNA, ribosomes, plasma membrane, and mitochondria. Based on this composition, it could be a cell from which of the following organisms?

nearly any eukaryotic organism

DIFFUSION: purple dye moves ONLY from side B to A

never

Based on the specific rules for classifying amino acids, how would you classify this amino acid?

non polar This is because the side chain contains only C and H, which are joined by nonpolar covalent bonds.

Nucleic Acids: Define the following terms: nucleic acid, nucleotide, nucleoside, purine, pyrimidine, mRNA, and ribosome.

nucleotides: 4 different ones. a nucleotide has 3 parts: a pentose sugar, phosphate, and nitrogenous base. nucleotides can have 1, 2, or 3 phosphates attached. negative because phosphate groups. Nucleic acid: molecules made up of nucleotides. organic compound smaller that polynucleotides. ex. nucleic acid DNA consists of 2 polynucleotide chains polynucleotide: contains different nucleotides, different ones have difference sequences. the phosphate end is on 5' and the hydroxyl end is on 3'. backbone: -"P-sugar" from each nucleotide -negatively charged -two different ends: 5' and 3' phosphodiester bond: joins nucleotides to for polynucleotides DNA & RNA: types of phosphodiester bonds, made from nucleotides and ARE nucleic acids nucleoside: a compound commonly found in DNA or RNA, consisting of a purine or pyrimidine base linked to a sugar *purine: DOUBLE nitrogenous base (ring shaped chemical), NEGATIVELY CHARGED pyrimidine: SINGLE nitrogenous base (ring shaped chemical)* mRNA: messenger RNA carries the genetic info copied from DNA into the form of code words ribosome: two functions- decoding the messange and the formation of peptide bonds..

DIFFUSION: there is no net movement of purple dye

only at equilibrium

DIFFUSION: concentration gradients exsist that drive diffusion of both dyes

only before equilibruim is reached

DIFFUSION: there is a net movement of orange dye from side A to B

only before equilibruim is reached

phospholipid has a "head" made up of a glycerol molecule attached to a single ________, which is attached to another small molecule.

phosphate group

smooth ER

poison detoxification lipid synthesis calcium ion storage

Based on the specific rules for classifying amino acids, how would you classify this amino acid?

polar This is because the side chain contains an O, which forms two polar covalent bonds (with C and with H) leading to partial charges.

Which of the four levels of protein structure does an antibody have?

primary, secondary, tertiary, and quaternary Remember that ALL proteins have the first three levels of structure; only some have the fourth.

A cell with a predominance of rough endoplasmic reticulum is most likely involved in which of the following processes?

producing large quantities of proteins for secretion

Golgi apparatus

protein modification and sorting cisternal maturation

rough ER

protein synthesis

identify the path a secretory protein follows from synthesis to secretion: Proteins that are secreted from a eukaryotic cell must first travel through the endomembrane system.

protein synthesis: ER -> cis golgi -> medial golgi -> trans golgi -> plasma membrane : extra cellular space

The liver is involved in detoxification of many poisons and drugs. Which of the following structures is abundant in liver cells and primarily responsible for detoxification processes?

smooth endoplasmic reticulum

Describe 3 functions performed by the SER that were discussed in lecture.

the SER makes lipids, detoxifies drugs, stores glycogen.

carriers

undergo a change in shape to transport solutes across the membrane transport primarily small polar organic molecules are integral membrane proteins transport solutes down a concentration or electrochemical gradient provide a hydrophilic path across the membrane

Antibodies—like any protein—would be expected to have a tertiary structure that is held together by what/which type(s) of intramolecular chemical interaction(s)?

van der Waals interactions, hydrogen bonds, hydrophobic interactions, ionic bonds Besides the four weak interactions, 3° structure may also be stabilized by...? (This is true for the 3° structure of antibodies!)

Which type(s) of intermolecular chemical interactions allow an antibody to interact with an antigen? (Hint: "Antibody/Antigen Interaction - A Closer Look" at url 'c')

van der Waals interactions, hydrogen bonds, ionic bonds, hydrophobic interactions Remember from Chapter 2 that biological molecules typically interact by WEAK INTERACTIONS and not covalent bonds (Ex: a hormone and its receptor, or an enzyme and its substrate).

Lipids: Summarize the different roles lipids play in organisms, and give examples of each.

what atoms are found in lipids? CHo lipids= NO macromolecules= NO polymers however do have dehydration reactions HYDROHPOBIC FUNCTIONS: 1) energy source 2) storage 3) structural 4) cell-to-cell signalling (some hormones) 5) cell chemsitry (some vitamins) vitamins and hormones that are HYDROPHOBIC are LIPIDS lipids are fatty acids, fats, phospholipids, steroids, fat-soluble vitamins

Protiens: Summarize the different roles proteins play in organisms, and give examples of each.

what proteins are found in amino acids? CHON proteins are built from amino acids: 20 different ones.... different by their R groups 6 are polar but uncharged (contains O...& others) 5 are charged (2 acidic with O- and 3 basic with NH+) 9 are nonpolar (all C's and H's some S and N) two functional groups found in EVERY amino acid: *AMINO GROUPS + CARBOXLY GROUPS -* polypeptide -amino acid + peptide bond = polypeptide -contains many different a.a.s. -different ones have different sequences a protein: one or more polypeptides, folded into a specific conformation functions: 1) energy source/ C source 2) storage 3) structural support 4) intercellular signaling--> sometimes lipids sometimes proteins 5) movement 6) transport 7) defense 8) ENZYMES --> most important

Lipids: 1) What are the structural features of phospholipids? 2) Explain how—based on their structures and dual natures—phospholipids behave in an aqueous environment. 3)How are they important to cells?

what type of lipid surrounds cells? needs to be hydrophobic but fat is not good enough so we need.... PHOSPHOLIPIDS 1) phospholipids are made from 2 fatty acids, 1 glycerol, 1 phosphate, 1 additional chemical phospholipids are AMPHIPATHIC with hydrophilic heads and hydrophobic tails 2) phospholipids behave in an aqueous enviroment because their outside is hydrophilic but the inside is hyrdophopic 3) phospholipids are important to cells because they make up the cell membrane