Exam 1 Biology 1 UTD

1.) What is the framework of most biological molecules

Carbon bonded to other carbon molecules, or other types of atoms

2.) What are hydrocarbons and their characteristics?

Covalently bonded hydrogens and carbons with nonpolar properties (Bonds have considerable energy)

3.) What are functional groups?

Small, reactive groups of atoms that give larger molecules specific chemical properties

4.) Name the different functional groups (Covalently bonded):

a.) Hydroxyl: enables alcohol to form linkages through dehydration synthesis

b.) Carbonyl: major building block of carbohydrates, & participate in supplying energy for reactions

c.) Carboxyl: gives organic molecules acidic properties because it releases protons in solution

d.) Amino: act as organic bases because they accept protons in aqueous solutions

e.) Phosphate: act as weak acids in solutions because of release of proton solution

f.) Sulfhydryl: converted into a covalent linkage called disulfide linkages

5.) What are isomers?

Molecules with the same molecular or empirical formula, but different chemical structures

6.) Name the different kinds of isomers:

a.) Structural isomers: arrangement of atoms is different (Ex: fructose vs. glucose)

b.) Stereoisomers: differ in how groups are attached (Ex: galactose and glucose)

c.) Enantiomers: mirror image molecules with a chiral carbon (Ex: L-sugars and D-sugars)

7.) What are monomers and polymers?

Monomers are chemically similar subunits that ultimately build polymers through polymerization

8.) What is dehydration synthesis?

Formation of large molecules by the removal of water (Monomers joined to form polymers)

9.) What is hydrolysis?

Breakdown of large molecules by the addition of water (Polymers broken down into monomers)

10.) What ratio is present within carbohydrates?

Molecules have a 1:2:1 ration of carbon, hydrogen, and oxygen (Good energy storage molecules)

11.) What is a monosaccharide?

Simplest carbohydrate composed of a basic six-carbon skeleton (Enzymes distinguish between isomers)

12.) What is the difference between alpha-glucose and beta-glucose?

There is carbon-one with hydroxyl group facing down (Alpha-glucose), or facing upwards (Beta-glucose)

13.) What are disaccharides?

Two monosaccharides linked by dehydration synthesis (Used for sugar transport and energy storage)

14.) Name the different disaccharide linkages and molecules:

a.) Maltose: two alpha-glucose molecules (Alpha 1->4 linkage)

b.) Sucrose: glucose and fructose molecules (Alpha 1->2 linkage)

c.) Lactose: glucose and galactose molecules (Beta 1->4 linkage)

15.) What are polysaccharides?

Long chains of monosaccharides linked through dehydration synthesis (Linear, or branched molecules)

16.) Name the different polysaccharides, linkages, and functions:

a.) Amylose: a plant starch with alpha 1->4 linkages (Energy storage)

b.) Glycogen: found in animal tissues with alpha 1->4 and 1->6 linkages (Energy storage)

c.) Cellulose: primary fiber in plant cell walls with beta 1->4 linkages (Structural support)

d.) Chitin: fiber within arthropods and fungi with beta 1->4 linkages (Structural support)

17.) What are the monomers of nucleic acids such as DNA and RNA?

Nucleotides (Composed of sugar + phosphate + nitrogenous base)

18.) What is a nucleoside?

A nitrogenous base + five-carbon sugar (Lacks the phosphate group)

19.) Name the types of nitrogenous bases:

a.) Pyrimidines: nitrogenous base with one carbon-nitrogen ring (Uracil, thymine, cytosine)

b.) Purines: nitrogenous base with two carbon-nitrogen rings (Adenine, guanine)

20.) What is the main difference between ribonucleotides and deoxyribonucleotides?

There is either hydrogen at the 2' carbon (Deoxyribose) or a hydroxyl group (Ribose)

21.) What is a phosphodiester bond?

Forms between the 5' carbon (Phosphate group) of one nucleotide and the 3' carbon (Sugar) of another

22.) Describe the function and structure of DNA:

Encodes information for amino acid sequences & contains double helix (Connected by hydrogen bonds)

23.) What is the difference in hydrogen bonds for the different complimentary base pairs?

Adenine and thymine have only two hydrogen bonds; guanine and cytosine have three hydrogen bonds

24.) What is complementary base pairing?

Pairing of A—T or G—C to determine sequence of DNA (DNA replication uses these rules as a template)

25.) Describe the structure and function of RNA:

Single polynucleotide strand that uses information from DNA to sequence amino acids (Contains ribose)

26.) What are some other nucleotides?

a.) ATP: primary energy currency of the cell (Produced by Krebs cycle)

b.) NAD+ and FAD+: electron carriers for many cellular reactions

27.) What are some functions of proteins?

Transport, storage, enzyme catalysis, defense, motion, and regulation

28.) What is the structure of proteins?

Composed of amino acids (Monomers) to form chains of polypeptides connected by peptide bonds

29.) What is the basic structure of an amino acid?

Central carbon atom, amino group, carboxyl group, single hydrogen, and variable R group

30.) Categorize the different amino acids (20):

Nonpolar:

1.) Valine (Val, V)

2.) Leucine (Leu, L)

3.) Isoleucine (Ile, I)

4.) Glycine (Gly, G)

5.) Phenylalanine (Phe, F)

6.) Proline (Pro, P)

7.) Tryptophan (Trp, W)

8.) Alanine (Ala, A)

9.) Methionine (Met, M)

Polar:

1.) Serene (Ser, S)

2.) Cysteine (Cys, C)

3.) Tyrosine (Tyr, Y)

4.) Asparagine (Asn, N)

5.) Glutamine (Gln, Q)

6.) Threonine (Thr, T)

Negatively charge amino acids:

1.) Aspartic acid (Asp, D)

2.) Glutamic acid (Glu, E)

Positively charged amino acids

1.) Arginine (Arg, R)

2.) Histidine (His, H)

3.) Lysine (Lys, K)

31.) What is a disulfide linkage?

Linkage between the sulfhydryl groups of two cysteine amino acids after oxidation (Covalently bonded)

32.) What is a peptide bond?

Formed by dehydration synthesis between amino group and carboxyl group of two different amino acids

34.) Name the different structures of proteins:

a.) Primary structure: sequence of amino acids (Determines the function of a protein)

b.) Secondary structure: alpha-helices and beta-sheets stabilized by hydrogen bonds

c.) Tertiary structure: determined by disulfide linkages and hydrogen bonds (Function/solubility)

d.) Quaternary structure: arrangement of subunits into a protein with multiple polypeptide chains

35.) What is a random coil?

Irregularly folded arrangement that allows for movement within the major parts of the protein

36.) What affects the conformation of a protein?

Disulfide linkages, interaction of polar and nonpolar groups, hydrogen bonds, and electrostatic forces

37.) What are motifs?

Common elements of secondary structure capable of determining structure of unknown proteins

33.) What is the difference between the N-terminal and C-terminal?

N-terminal is the end of an amino acid (No linkage) and c-terminal allows for linkage of new amino acids

38.) What are domains?

Functional units within the large structure of a polypeptide (Have many different functions)

39.) Name some different protein combinations:

a.) Lipoproteins: proteins + lipids (Form cell membranes)

b.) Glycoproteins: carbohydrates + proteins (Enzymes, MHC's, antibodies)

c.) Nucleoproteins: nucleic acids + proteins (Form chromosomes)

40.) What are chaperones?

Proteins that help a protein fold correctly (Cystic fibrosis is an example of a deficiency)

41.) How do chaperones fold proteins?

Unfolded polypeptide enters, and is enclosed by a cap (Folding occurs, and the cap is released)

42.) What is denaturation?

Protein loss of structure and function because of environmental conditions (Temperature, pH, etc.)

43.) What is the significance of Anfinsen's experiment?

Showed that the conformation of protein is found within the amino acid sequence (Ribonuclease)

44.) What are lipids?

Group of molecules that are insoluble in water because of high proportion of nonpolar bonds (C—H)

45.) What are some different kinds of lipids?

a.) Neutral lipids: energy storage molecules (Nonpolar)

b.) Oils and fats: liquid or solid at biological temperatures

c.) Fatty acids: contain a single hydrocarbon chain with a carboxyl group

46.) What are triglycerides?

Formed by dehydration synthesis between a three-carbon glycerol & three fatty acid chains (Nonpolar)

47.) What is an ester linkage?

A covalent bond between the carboxyl group (Fatty acid) and hydroxyl group (Glycerol) in a triglyceride

48.) Name the two kinds of fatty acids:

a.) Saturated fatty acids: found in solid animal fats (Contain only single C—C bonds)

b.) Unsaturated fatty acids: found in vegetable oils (Contain double C—C bonds)

49.) What is hydrogenation?

Plant oils being converted into saturated fats (Unsaturated fatty acids are much healthier)

50.) What is atherosclerosis?

Build up of plaques within the coronary arteries (Caused by the excess buildup of cholesterol)

51.) What are phospholipids?

Composed of glycerol (Polyalcohol), two fatty acids (Nonpolar), and a phosphate group (Polar)

52.) What are the four different types?

a.) Phosphatidyl serene

b.) Phosphatidyl choline

c.) Phosphatidyl inositol

d.) Phosphatidyl ethanolamine

53.) How is the phospholipid bilayer constructed?

One end is exposed to the aqueous environment (Polar) and the other is contained inside (Nonpolar)

54.) What is a micelle?

Lipid molecules that orient with hydrophilic end towards water, and hydrophobic end away from water

1.) What is the difference between genetic material in prokaryotes and eukaryotes?

Contained within a circular molecule called the nucleoid (Prokaryotes) vs. a nucleus (Eukaryotes)

2.) Who discovered cells?

Robert Hooke in 1665

3.) Who proposed cell theory?

Schleiden and Schwann

4.) What are the tenants of cell theory?

All organisms are composed of cells

Cells are the smallest living unit of all living organisms

Cell arise by division from preexisting cells

5.) What happens when you double the diameter of a cell?

SA increases 4x and volume increases 8x (Cell size is limited because of a surface area-to-volume ratio)

6.) How do cells increase surface area?

With the usage of extensions or folds (Allows for greater diffusion and movement of cargo)

7.) What is resolution?

Minimum distance two points can be apart to be distinguished as separate (100 micrometers in humans)

8.) Name the types of microscopes:

Light microscopes: use magnifying lens with visible light (200 nanometers apart)

Electron microscopes: uses beams of electrons (Resolve structures 0.2 nanometers apart)

9.) What are similarities between prokaryotes and eukaryotes?

Nucleoid of nucleus

Cytoplasm (Matrix with cytosol and organelles)

Ribosomes (Synthesize proteins)

Plasma membrane (Phospholipid bilayer)

10.) Name some characteristics of prokaryotic cells:

Simplest organisms (Lack a membrane-bound nucleus)

Cell wall outside the plasma membrane (Have ribosomes)

Two domains: archaea and bacteria

11.) What is the function of the bacterial cell wall?

Protects the cell, maintains shape, and prevents desiccation (Composed of peptidoglycan)

12.) How to antibiotics work?

Target weaknesses within the cell wall of bacterium (Archaea lack peptidoglycan)

13.) What is a eukaryote?

Characterized by endomembrane system, and the presence of membrane-bound organelles

14.) What is the function of the nucleus?

Repository of genetic information and production of rRNA + ribosomal subunits (Nucleolus)

15.) Define the parts of the nuclear envelope:

Two phospholipid bilayers (Reinforced by lamins)

Nuclear pore complex: regulates passage of molecules in and out

16.) How is DNA organized in eukaryotes?

It's divided into multiple linear chromosomes (Chromatic is a combination of DNA and protein)

17.) What is the nucleoplasm?

The liquid within the nucleus (Comparable to the cytoplasm within the plasma membrane)

18.) Breakdown the different parts of cell fractionation:

500 g (Leaves nuclei)

20,000 g (Mitochondria or chloroplasts)

150,000 g (Ribosomes, proteins, nucleic acids)

19.) Name some different characteristics of ribosomes:

Composed of a large and small subunit (Formed in nucleolus)

Freely suspended in cytosol or membrane-bound (Rough ER)

May remain in cytosol, enter nucleus, or become parts of other structures

Site of protein synthesis (Arrange amino acids into primary structure)

20.) What is the endomembrane system?

A series of cytoplasmic membranes that divides the cell into sections with different functions

21.) What is the endoplasmic reticulum?

Reticulum of membranous channels & cisternae that enclose spaces called ER lumen (Rough & smooth)

22.) What is the function of rough ER?

Folds proteins into final form & makes chemical modifications (ER lumen) before packaging into vesicles

23.) What is the function of smooth ER?

Synthesizes lipids that become a part of cell membranes (Convert toxins within the confines of the liver)

24.) What is the Golgi apparatus?

Network of Golgi bodies with cis, medial, & trans compartments (Packages materials, protein folding)

25.) Describe the process of Golgi complex function:

a.) Proteins from the rough ER enter on the cis face (Delivered by transport vesicles)

b.) Modified proteins exit on the trans face (Transported in secretory vesicles)

c.) Exocytosis: membrane of vesicle fuses with membrane and releases contents extracellularly

26.) What is endocytosis?

Plasma membrane forms pocket and pinches off into the cytoplasm (Transported by endocytic vesicles)

27.) Where to endocytic vesicles travel?

Golgi complex and lysosomes

28.) Describe lysosome structure and function:

a.) Membrane-bound digestive vesicles with an acidic pH

b.) Arise from the Golgi apparatus (Destroys cells and foreign material)

c.) Enzymes catalyze the breakdown of macromolecules

29.) What are the different kinds of lysosomal processes?

Autophagy (Self-destruction), phagocytosis (Insoluble material), and pinocytosis (Soluble material)

30.) What are peroxisomes?

Vesicles that contain enzymes involved with oxidation of fatty acids (Hydrogen peroxide by-product)

31.) Name the steps in the secretory pathway:

a.) Proteins made by ER ribosomes enter lumenal space and undergo modification

b.) Transport vesicles bud off from the ER membrane and transport cargo to the Golgi complex

c.) Chemical modification completed in the Golgi complex (Packaged in secretory vesicles)

d.) Vesicles fuse with the plasma membrane and are released by exocytosis

e.) Endocytic vesicles encounter lysosomes and are enzymatically degraded (Form at membrane)

32.) Describe mitochondria (Contain two membranes):

Powerhouse of the cell that produces ATP through oxidative phosphorylation (Maternally inherited)

33.) What are chloroplasts?

Contain chlorophyll for photosynthesis and stacks of thylakoids called grana (Two membranes)

34.) Name some important functions of central vacuoles:

a.) Tonoplast: membrane that surrounds the vacuole and regulates its overall pressure

b.) Store sugars, salts, pigments, waste products, proteins, and much more

c.) Contains molecules that provide chemical defenses against pathogens

35.) What is the cytoskeleton?

Filamentous structure that is extremely dynamic (Maintains cell shape, transports cargo, connects cells)

36.) What is the function of actin?

Involved with muscle contraction, crawling, or pinching (About 7 nanometers in diameter)

37.) Describe intermediate filaments:

Mechanical strength of the cell (Tissue specific and provides structural support, 8-10 nm diameter)

38.) How are microtubules constructed?

Dynamic structure consisting of tubulin dimers arranged with a + (Growth) and - (Removal) end

39.) Where do microtubules originate from?

Radiate outward from the centrosome (Anchor many organelles in their positions)

40.) How do microtubules transport vesicles?

Utilize ATP hydrolysis to move kinesins or dyneins along another microtubule (Connected to vesicle)

41.) Describe microtubule role in cell division:

Separate and move chromosomes, or complete move the eukaryotic cells themselves

42.) What are centrosomes (Centrioles are found in triplets)?

Microtubule-organizing center found in animal cells and protists (Not found in plants or fungi)

43.) What is the arrangement of microtubules in flagella?

Have a 9 + 2 arrangement that moves in an s-motion (Not related to prokaryotic flagella)

45.) Where do flagella and cilia come from?

Arise from the centrioles (Remains as the basal body within the innermost part of the structure)

46.) Describe the different components of cell walls:

a.) Primary cell wall: soft and flexible (Made of cellulose)

b.) Secondary cell wall: additional cellulose between PCW and membrane (Lignin reinforces it)

c.) Middle lamella: holds adjacent walls together with polysaccharides (Pectin)

d.) Plasmodesmata: connects the cytosols of adjacent plant cells (Allows particle movement)

47.) What surface proteins are used for cell identity?

MHC proteins determine recognition of self and non-self (Glycolipids are the most tissue-specific)