BI108 Quiz 1

What does the null hypothesis imply? How do you reject it?

There is no relationship between variables and no significant difference between groups. To reject it, find the p-value, and if it's <0.05 H0 can be rejected

What does the alternate hypothesis imply?

There is a relationship between variables and there is a significant difference between groups

What is pH and how do you calculate it?

How acidic/basic a solution is, and it is calculated by -log[H+]

What is an acid?

A molecule that releases a proton when it dissolves

What is a base?

A molecule that acquires a proton/releases OH- when it dissolves

How do Van der Waals forces form?

As electrons move, their density may be temporarily asymmetrical, making fluctuating dipoles and allowing interactions (relatively weak)

What are macromolecules?

Polymers of smaller molecules (monomers) joined by covalent bonds

What kind of reaction is the formation of polymers?

Condensation reaction (releases water)

What elements form carbohydrates and in what ratio?

(CH20)n, where n is some factor to multiply by

What are the building blocks of carbohydrates?

Monosaccharides: 5-6 carbon sugars linked together

Carbohydrates: What is the structure of monosaccharides?

- a chain of carbons

- a carbonyl group

- several -OH hydroxyl groups

Carbohydrates: How do monosaccharides differ from each other?

- length of carbon chains

- orientation of carbonyl and hydroxyl groups

Carbohydrates: What are the different variations of monosaccharides?

disaccharides: 2 monosaccharides

trisaccharides: 3 monosaccharides

oligosaccharides: 3-20 monosaccharides

polysaccharides: 100s-1000s monosaccharides

Carbohydrates: What is a glycan?

many monosaccharides linked together

Carbohydrates: What is a glycosidic linkage?

a covalent bond between monosaccharides (specifically C-O-C)

Carbohydrates: What are the different orientations and examples of glycosidic linkages?

alpha: bent/branched networks, easier to break

- ex: starch (storage of glucose in plants), glycogen (storage of glucose in animals)

beta: linear fibers/sheets, harder to break because of hydrogen bonding

- ex: cellulose (structural components in plants), chitin (structural component in shells)

Carbohydrates: Forming glycosidic linkages occurs through which type of reaction?

Condensation

What are the main functions of carbohydrates?

1. energy storage and processing

2. structural support

3. identification of cells and cell parts

What makes lipids unique?

They are insoluble in water (hydrophobic) because they are comprised of C-C and C-H bonds that are nonpolar because they have similar electronegativity

Lipids: What are the 2 types of hydrocarbon chains?

Saturated: no double bonds, held together more tightly because they are straight, solid at room temperature (ex: animal fats)

Unsaturated: 1+ double bonds, bent shape, liquid at room temperature (ex: plant oils)

Lipids: What is the structure and function of fats?

Structure: 3 fatty acids with carboxyl groups interact with the hydroxyl group of one glycerol (3-carbon molecule) to form an ester bond.

Function: energy processing and storage

Lipids: What is the structure of steroids?

Carbon atoms arranged in 4 fused-rings, vary in R-groups attached to core structure

Lipids: What is the structure of phospholipids?

- 2 long hydrophobic tails

- a hydrophilic head with a phosphate group and a polar group (1+ charges or partial charges)

Lipids: How do phospholipids vary from each other?

Each has a different polar group and hydrocarbon tails that vary in length and/or saturation

What is an amphipathic lipid?

A lipid which has one region which is hydrophobic and one region which is hydrophilic.

Lipids: How do vesicles form?

They form spontaneously (without energy) because phospholipids are more stable that way based on:

- hydrophobic interactions of hydrocarbon tails

- hydrogen bonding between water and hydrophilic heads.

Functional groups: Hydroxyl

Polar

Functional groups: Methyl

Nonpolar

Functional groups: Carbonyl

Polar

Functional groups: Sulfhydryl

Polar

Functional groups: Carboxyl

Charged, ionizes to release H+ (acidic)

Functional groups: Amino

Charged, accepts H+ to form NH3 (basic)

Functional groups: Phosphate

Charged, ionizes to release H+ (acidic)

What are the building blocks of nucleic acids?

Nucleotides

Nucleic Acids: what are nucleotides made of?

A phosphate group, a 5-carbon sugar, and a nitrogenous base

Nucleic Acids: How do nucleotide connect?

They join through covalent bonds between the phosphate group of one and the sugar of another, called phosphodiester bonds

Nucleic Acids: How is the polarity of nucleotides descirbed?

Using 5’ to 3’ polarity, additional ones are added to the 3’ end.

Nucleic Acids: Describe the primary structure of DNA

It is the series of nucleotides consisting of the 4 bases (A, C, T, G) written in the 5’ to 3’ direction. They are connected along the sugar-phosphate backbone so the nitrogenous bases stick out

Nucleic Acids: Describe the RNA primary structure

It is similar to DNA in 5’ to 3’ polarity and the sugar-phosphate backbone, but Thymine is replaced by Uracil and it is single-stranded

Nucleic Acids: Describe the DNA secondary structure

Forms a double helix, but only if strands line up antiparellel, each G has an opposing C, and each A has an opposing T

Nucleic Acids: What is a purine?

A nitrogenous base that has 2 rings (A and G)

Nucleic Acids: What is a prymidine?

A nitrogenous base that has one ring (T and C)

Nucleic Acids: Describe the RNA secondary structure

Generally single stranded, but some form double helices when A-U and G-C hydrogen bond, forming a stem and loop structure

Nucleic Acids: Describe RNA teritiary structure

Multiple stem and loop structures twist and fold into a 3D shape

Nucleic Acids: What is a gene?

Instructions of nucleotides to make proteins

Proteins: Name the 6 functions of proteins

1. Catalysis: making reactions happen

2. Transporting materials

3. Movement

4. Cell structure

5. Defense

6. Signaling and communication

Proteins: Describe the structure of amino acids

• amino group: NH2

• Carboxyl group: COOH

• R-group: what makes each one unique

Proteins: How to R-groups in amino acids vary?

• they can be fully charged, partially charged, or not charged

• They can be hydrophobic (clumping together) or hydrophilic (faces surrounding aqueous environment)

Proteins: Describe the primary structure of proteins

Amino acids linked with peptide bonds creating a polar peptide-bonded backbone with relatively flexible bonds

Proteins: Describe the secondary structure of a protein

Either fold into:

1. Alpha helix where R-groups stick out and are free to interact

2. Beta-pleated sheet wheee N-H and C=O groups stick out free to interact

Proteins: Describe the tertiary structure of a protein

Proteins fold again including secondary structures with 4 possible interactions:

1. Hydrogen bonds between partial charges of N-H and C=O groups in backbone and/or R-groups

2. Ionic bonds between full charges on R-groups

3. Covalent bonds (disulfide bridges) between S atoms in R-groups

4. Hydrophobic interactions between hydrophobic regions of R-groups (more stable that way)

Proteins: How is function ensured when the tertiary structure is forming?

Chaperone proteins ensure folding lines up for interactions

Proteins: What is denaturation?

The unfolding of proteins

Proteins: Describe the quaternary structure of proteins

Folded subunits stick together with similar interactions in tertiary

What are peripheral proteins?

Membrane proteins that are on the exterior or interior of the bilayer. They interact with water so they are polar and charged.

What are transmembrane proteins?

Membrane proteins that span the width of the bilayer, making the two ends that interact with water polar/charged and the middle that doesn’t nonpolar (amphipathic)

What determines the permeability of a membrane?

1. Length of hydrocarbon tails → longer tails = more hydrophobic

2. Saturation of hydrocarbon tails → saturated = more hydrophobic

3. Cholesterol presence → bulky rings cause packing, so makes it more hydrophobic

What determines if a molecule can pass through the membrane vs bump into it?

1. Nature of the molecule (smaller and uncharged molecules go through)

2. Structure of the membrane (less hydrophobic = more permeable)

What is entropy?

The tendency for systems to tend toward a state of randomness or disorder

What is osmosis and when does it occur?

The diffusion of water across membranes, occurs when:

1. 2 solutions are separated by a lipid bilayer

2. solutions have different concentrations of dissolved ions/molecules

3. dissolved substances cannot move across the membrane, but water can

How is potential energy determined?

If a molecule has a high chance of moving (i.e. glucose at a high concentration wants to move to a lower concentration).

What is passive transport?

spontaneous movement of ions/molecules without the input of energy due to movement down the concentration gradient

What are the two proteins possible in facilitated diffusion?

Channels: transmembrane proteins that acts as tunnels to allow ions and other small molecules to pass

Carriers: proteins that allow molecules to bind and change shape (conformation) to move molcule

What are the properties of channel proteins?

Specificity: specific R-groups only admit 1 ion

Regulation: gated channels can open or close based on the presence/attachment of another molecules causing it to conform (i.e. ATP to chloride channel) or an electrical charge difference

Structure: interior of channel is hydrophilic due to polarity or charged R-groups

What are the properties of carrier proteins?

Specificity: specific R-groups only admit 1 ion

Regulation: controlled by the presence/attachment of another molecules causing it to conform

How do molecules bind to carrier proteins?

Molecules have kinetic energy where each one has an equal chance of hitting a binding site

What is exocytosis?

Active transport that allows larger molecules (i.e. waste) to leave the cell via vesicles

What is endocytosis?

Active transport that allows larger molecules to enter the cell via vesicles

What is active transport?

Movement of molecules up/against a concentration gradient (requires energy)

What are characteristics of Archaea?

• live in extreme habitats (i.e. hot springs, deep sea) that are frozen, lack oxygen, very acidic, or very basic

• unique hydrocarbon chains

• unique carbohydrates in their cell walls

What are characteristics of Bacteria?

• have cell walls and flagella

• mostly single-celled, bit sometimes multicellular

• most have a single circular chromosome (double helix)

What are characteristics of Eukaryotes?

• multicellular or single-celled

• nucleus is studded with pores that regulate what enters/exits the nucleus

Organelles: Cell membrane

Composed of lipid bilayer and membrane proteins

Function: regulates molecules in and out of the cell

Organelles: Ribosomes

Complex of RNA and protein molecules

Function: amino acids are linked and proteins are created using mRNA instructions

Organelles: Cell wall

a stiff wall made of cellulose fibers

Function: prevents plant cells from moving and helps them survive in harsh conditions

Organelles: flagella

long-thin projections

Function: propel the cell. through water

Organelles: nucleus

contains genetic material (usually chromosomes)

Function: DNA replication and gene expression

Organelles: nuclear envelope

2 membranes around the nucleus

Function: regulates trafficking of molecules (RNAs, proteins) via nuclear pore complexes

Organelles: mitochondria

surrounded by 2 membranes, inner one forms tubes and sacs

Function: site of cellular respiration and ATP production

Organelles: Vacuole

more prominent in plant cells

Function: stores key molecules, waste, and provides/regulates turgor pressure

Organelles: Choloroplasts

2 membranes, has stacks (vesicles)

Function: capture sunlight and convert to bonds in photosynthesis

Organelles: Endoplasmic Reticulum

forms a network of tubules and sacs near the nuclear envelope

Rough ER: areas with ribosomes for proteins to enter and be modified, folded, and transported

Smooth ER: no ribosomes, chemically modifies small molecules

Organelles: Golgi Apparatus

located near ER in a sequence of stacks close together

Function: receives proteins from the ER to package and store them

Organelles: Cytokeleton

dynamic network of long fibers (actin filaments, intermediate filaments, microtubules)

Function: movement and support

Organelles: Extracellular matrix

proteins and carbs

Function: protection and support in animal cells

What organelles are specific to plant cells?

• cell wall

• vacuoles are more prominent in plant cells

• chloroplasts

What organelles are specific to animal cells?

Extracellular matrix

What is the endomembrane system?

The process of creating and transporting lipids and proteins:

ER → Golgi → vesicles → membrane

Why do organelles have a high surface-area-to-volume ratio?

Small volume = more likely for molecules to collide to interact

High surface area = more space for processes