BIO Exam 1: Chapters 1-5

How do we know what information to trust?

information is built on results and data

Since scientific progress is a team effort, how is consensus built?

thought collegial criticism and skepticism

advances occur through a rigorous testing of ideas to see if the results are the same

self-correcting progress (slow and diligent)

What are the five shared practices in which problems are identified in theories and experiments, allowing the pursuit of necessary corrections?

1. Independent replication- using methods section of experiments to replicate

2. Randomizes controlled trials- comparing results between experimental and control groups to assess effects (control group is a gold standard: removes bias and placebo)

3. Blinded analysis- remove identifying info from data (ie. age, sex)

4. Statistical validation- see how likely a result is by chance or experimentation

5. Peer review- high quality info through expert validation

What yields sound scientific models, and what do these models allow?

continual generation and critique of scientific progress

Models must accommodate all of the data. What if it doesn’t?

revision or tossed and start with another that aligns better with the data

What is a cell?

The basic unit from which a living organism is made; an aqueous solution of chemicals, enclosed by a membrane, that has an ability to self-replicate.

unit of life

How can cells vary?

appearance and function

What are some characteristics of living cells?

1. all have similar basic chemistry

2. self-replicating collections of catalysts

3. evolved from same ancestral cell

What do genes provide instructions for?

form, function, and behavior of cells and organisms

What is the life process of a cell?

self replicating autocatalytic process

What are the steps from nucleotides to catalytic activity?

nucleotides, DNA and RNA, sequence formation, amino acids to protein, catalytic activity

How do we learn about cells?

light microscopes- surface of cell

fluorescence microscopes- different parts of the cell

electron microscopes-

• Transmission- detailed internal structures of cell

• Scanning- outside structures of cells

What is a fluorescence microscope?

Instrument used to visualize a specimen that has been labeled with a fluorescent dye; samples are illuminated with a wavelength of light that excites the dye, causing it to fluoresce.

What is an electron microscope?

Instrument that passes a beam of electrons through the specimen to reveal and magnify the structures of very small objects, such as organelles and large molecules.

What is the most clear microscopy below 200 micrometers?

superresolution fluorescent microscopy allows microtubules to be visualized with high precision and detail

What are the three major divisions in the tree of life?

Bacteria, Archaea, Eukarya

What are the characteristics of bacteria?

• prokaryotic (no nucleus)

• peptidoglycan cell wall

• unbranched fatty acid membrane

• distinct rRNA

What are the characteristics of archaea?

• extremophiles

• prokaryotic (no nucleus)

• no peptidoglycan cell wall

• branched fatty acid membrane

• distinct rRNA

What are the characteristics of eukaryotes?

• eukaryotic (with nucleus)

• no peptidoglycan in cell wall

• unbranched fatty acid membrane

• distinct rRNA

What is peptidoglycan?

polymer of sugars and amino acids that makes up bacteria cell wall

How does penicillin kill bacteria?

disrupting polymerization of peptidoglycan cell wall

How did organelles evolve?

A eukaryotic asgard common ancestor engulfed a bacterium through endosymbiosis to produce an early eukaryote with mitochondria

Organelles evolved through a process called endosymbiosis, where early eukaryotic cells likely engulfed prokaryotic cells that eventually became integral to their function, such as mitochondria and chloroplasts.

What is Asgard?

A proposed superphylum of Archaea that includes organisms believed to be closely related to the ancestors of eukaryotes and responsible for complex cellular structures.
missing link in evolutionary history of eukaryotes, most similar to ancestral cell behavior

What are the cellular parts of Asgard?

archeon cell body & protrusions as well as ectosymbionts (such as bacteria)

What is the evidence behind the endosymbiosis theory?

ribosomal RNA of mitochondria and chloroplasts is most similar to rRNA of bacteria

What are the three types of bacteria?

1. spherical cells (ie. streptococcus)

2. rod-shaped cells (ie. e coli, salmonella)

3. spiral cells (ie. treponema, spirochetes)

What is an example of a simple photosynthetic bacterium?

anabaena (cyanobacteria)- blue-green algae

What are the parts of a bacteria?

simplistic internal structure

cellular processes take place altogether, contained by a cell wall

cell wall, plasma membrane, outer membrane, ribosomes in cytosol, DNA clumps, outer flagellum

What is the nucleus?

• contains DNA genome

• site of transcription and DNA replication

• double membrane

• nuclear pores

information sent to the cell; (double membrane as evidence for endosymbiosis)

“city hall”

What is the mitochondria?

• site of citric acid cycle and cellular respiration

“power plant”

What are endosomes?

• carry endocytosed material

• deliver to Golgi

• or mature into lysosomes

“postal system”

What are peroxisomes?

• degrade toxins

• oxidation reactors

“trash trucks”

What are lysosomes?

• degrade macromolecules

• acidified lumen

• develop from endosomes

“recycling center”

What is the endoplasmic reticulum?

• membrane synthesis

• protein folding

• protein modifications

two types:

smooth: no ribosomes

rough: ribosomes on surface

“construction site”

What is the Golgi apparatus?

• protein modifications

• protein sorting and distribution

• receives and distributes vesicles

“manufacturing plant”

What is the cytosol?

• site of translation (at ribosomes)

• site of glycolysis

component of cytoplasm

What are three distinct features of plant cells?

• cell wall

• chloroplasts

• large central vacuole

What is the chloroplast of plant cells?

• site of photosynthesis

• carries own genome

“solar panels”

What is the cell wall of plant cells?

• made of cellulose

• structural support

What is the vacuole of plant cells?

• fluid-filled organelle

• structural support

What is the cytoskeleton?

• responsible for directed cell movements

• provides structural support, but not sturdy

  • in constant motion; made of tubules/ filaments

What are the three types of things that make up cytoskeleton?

1. actin filaments

2. intermediate filaments

3. microtubules

How many atoms are cells made of?

relatively few types of atoms

What determines how atoms interact?

outermost electrons

How do covalent bonds form?

sharing of electrons

How are electrons in covalent bonds distributed?

often shared unequally

What bonds are strong enough to survive inner cellular conditions?

Covalent bonds

How do ionic bonds form?

gain and loss of electrons

What is important about inert gases?

They have a full outer shell of electrons, making them stable and unreactive (ie. helium, neon, argon)

What is the electrostatic effect?

The attraction or repulsion between charged particles, influencing the behavior of ions and molecules in various chemical reactions.

ie. ionic bonds transfer electrons constantly

What occurs when there is an unequal share of electrons in a covalent bond?

polar covalent bond forms

What are hydrogen bonds?

Weak attractions between polar molecules that result from the electrostatic interaction between the hydrogen atom of one molecule and an electronegative atom (like oxygen or nitrogen) in another molecule. They play a crucial role in stabilizing structures like DNA and proteins.

(In hydrogen bonding) What is known as the atom with the hydrogen bond?

donor atom

(In hydrogen bonding) What is known as the atom with the nitrogen or oxygen that bonds?

acceptor atom

How do molecules of water join together?

transiently in a hydrogen-bonded lattice formation

What happens when two atoms connected by a covalent bond exert different attractions for the electrons of the bond?

This results in a polar covalent bond, where electrons are not shared equally, creating a partial positive charge on one atom and a partial negative charge on the other.

What property of water is responsible for high surface tension, specific heat capacity, and heat of vaporization?

Water's cohesive nature due to hydrogen bonding.

What are hydrophilic molecules?

substances that dissolve readily in water

ions and polar molecules that attract water molecules through electrical charge effect

What are hydrophobic molecules?

substances that do not dissolve in water, typically nonpolar molecules that repel water due to lack of attraction

ie. hydrocarbons

Explain why the hydrogen bonds formed in water between two peptide bonds are relatively weak.

they are transient, forming and breaking quickly due to the dynamic nature of water molecules and their interactions.

What are Van Der Waals attractions?

non polar molecules very close together synchronize charge fluctuations creating weak attractive forces

not strong enough to be bonds

between molecules

What is the additive effect of many small Van Der Waals interactions?

It results in a significant overall attraction between molecules, contributing to the stability and structure of larger biological macromolecules.

What kind of compounds form a cell?

carbon compounds

What are the four major families of small organic molecules that cells contain?

Amino acids, nucleotides, sugars, and fatty acids.

What are sugars?

energy sources and subunits of polysaccharides and oligosaccharides

What are fatty acid chains?

components of cell membranes; subunits of fats and membrane lipids

What are amino acids?

subunits of protein

What are nucleotides?

subunits of nucleic acids that create DNA and RNA

What is the general formula of monosaccharides, and what are their components?

(CH2O)n, where n is usually 3 to 6

have 2+ hydroxyl groups + aldehyde group (aldoses) or a ketone group (ketoses)

How does a ring form in monosaccharides?

In aqueous solution, the aldehyde or ketone group of a sugar molecule tends to react with a hydroxyl group of the same molecule, closing the molecule into a ring

How does a disaccharide form?

the carbon that carries the aldehyde or the ketone can react with any hydroxyl group on a second sugar molecule to form a disaccharide

What are the three common disaccharides?

1. maltose (2 glucose)

2. lactose (glucose + galactose)

3. sucrose (glucose + fructose)

What are oligosaccharides and polysaccharides?

large linear and branched molecules made from simple repeating sugar subunits

short chains: oligosaccharides

long chains: polysaccharides (ie. glycogen)

What is the process of condensation between molecules?

two molecules (monosaccharides) combine to form a larger molecule (ie. disaccharide), releasing a small water

What is the process of hydrolysis between molecules?

larger molecules (disaccharides) are broken down into smaller ones (monosaccharides) through the addition of water

What are the components of fatty acids?

hydrophilic carboxylic acid head (polar)

hydrophobic hydrocarbon tail (non polar)

What are unsaturated fatty acids?

1+ double bonds between carbon atoms; typically liquid at room temperature (ie. olive oil)

What are saturated fatty acids?

no double bonds between carbon atoms; typically solid at room temperature (ie. butter)

How is energy stored in the cell?

fatty acids are an energy reserve through an ester linkage to glycerol to form triacylglycerols

What is amphipathic?

molecules- both hydrophilic (water loving) and hydrophobic (water fearing)

What is an example of an amphipathic molecule?

phospholipids, like those in cell membranes (polar head and non polar tail)

What is a micelle?

A spherical aggregation of amphipathic molecules in aqueous solution, where the hydrophilic heads face outward and the hydrophobic tails are sequestered inward.

What are the basis of cell membranes?

phospholipids and glycolipids, which form self-sealing lipid bilayers that create a barrier for cellular compartments.

What are the parts of amino acids?

• central carbon atom (alpha),

• an amino group,

• a carboxyl group,

• a hydrogen atom, and

• a variable R group (side chain from CH₃) that determines the specific properties of each amino acid.

How are amino acids combined?

Amino acids are combined through peptide bonds, which form via a dehydration reaction between the carboxyl group of one amino acid and the amino group of another. (n-terminus and c-terminus)

What is the process in which amino acids can be linked to form proteins?

condensation

What is the significance of the side chains of amino acids?

determine the unique characteristics and functions of each amino acid, influencing protein structure and function.

wide variation of side chains means wide variety of properties and shapes

What make up bases?

Nitrogen-containing compounds, including purines and pyrimidines.

What are pyrimidines?

A class of nitrogenous bases with a single-ring structure, including cytosine, thymine, and uracil, that are essential components of nucleic acids.

What are purines?

A class of nitrogenous bases with a double-ring structure, including adenine and guanine, that play a critical role in DNA and RNA.

What component does RNA have that DNA does not?

RNA contains uracil instead of thymine.

What makes up a nucleotide?

A nucleotide is composed of a nitrogenous base, a five-carbon sugar (ribose in RNA or deoxyribose in DNA), and one or more phosphate groups.

What are the two kinds of pentose used in sugars?

The two kinds of pentose sugars are ribose and deoxyribose, which are essential components of RNA and DNA respectively.

What are the components of a nucleoside?

base + sugar

What are the components of a nucleotide?

base + sugar + phosphate

How are nucleic acid polymers joined together during condensation?

Nucleic acid polymers are joined together by forming phosphodiester bonds between the 5' phosphate group of one nucleotide and the 3' hydroxyl group of the sugar of another nucleotide during a condensation reaction.

What are the three functions of nucleotides?

1. as nucleoside di- and triphosphate, they carry chemical energy in their easily hydrolyzed phosphoanhydride bonds (ie. ATP)

2. they combine with other groups to form coenzymes (ie. coenzyme A CoA)

3. they are used as small intracellular signaling molecules in the cell (ie. cyclic AMP)

When combining P and ADP, where is energy inputted?

input of energy from sunlight or food; water as product

When disassembling ATP, where does the energy go?

released energy (in phosphoanhydride bonds) available for intracellular work and for chemical synthesis

What is unique to each macromolecule?

specific sequence of subunits