BY 123 Exam 1 (Ch 1-7)

Carbon's most frequent bonding partners (major organic components)

H, O, N

centrosomes

"microtubule organizing center" with a pair of centrioles and 9 triplets of microtubules for each centriole microtubules grow out of this near the nucleus

methyl group

(-CH3), methylated compound -affects gene expression and sex hormone shape

carboxyl group

(-COOH), carboxlyic acid or organic acids -acts as an acid

amino group

(-NH2), amine -acts as a base

hydroxyl group

(-OH), alcohols -polar due to O, forms H bonds with water

phosphate group

(-OPO3(-2)), organic phosphate -contributes negative energy from electrons, which gives it reactivity with water -ATP

sulfhydryl group

(-SH), thiol -two properties, SH groups can react and create a "cross-link" that stabilizes structure

carbonyl group

(C--O), ketone or aldehyde -sugars with ketone are ketoses, sugars with aldehydes are aldoses

How do carbon atoms form diverse molecules by bonding to four other atoms?

-4 valence electrons allows 4 covalent bonds to form, which allows for large structural diversity -variation in carbon structure (including isomers)

cortex and how they relate to microfilaments

the outer cytoplasmic layer of a cell -the network of microfilaments that gives the cell shape support create a semisolid gel consistency here

Evolution

the process of change that is the key to biodiversity

What happens after the rough ER synthesizes a secretory protein?

the protein is kept separate from the free proteins and are packaged into region called the "transport ER", which then transports into transport vesicles that go to the Golgi

heat

thermal energy in transfer from one body of matter to another

What are the pores in the nuclear envelope's biggest function?

transport of proteins and RNA and the large complexes of macromolecules

What does the combination of a glycerol and 3 fatty acids bring?

triglycerides bound together by ester linkages

Stanley Miller's experiment

O2 was not in the atmosphere, meaning that anaerobic metabolism was formed by bacteria as a result of a lack of oxygen

Are trans fats saturated or unsaturated?

They can be both; found in hydrogenated oils, they lead to a rapid build-up of plaque and atherosclerosis

Pyrimidines

Thymine, Cytosine, Uracil -one six member ring of carbon

nucleolus

a nonmembranous region (dark spots in the nucleus) that synthesizes rRNA to make ribosomes and RNA

feedback regulation

a process is regulated by its input or output

fat

a type of lipid made up of glycerol and fatty acids whose main purpose is energy storage from converted polysaccharides

Which action would produce a carbonyl group? a) the replacement of the -OH of a carboxyl group with hydrogen b) the addition of a thiol to a hydroxyl c) the addition of a hydroxyl group to a phosphate d) the replacement of the nitrogen of an amine with oxygen

a; carbonyl group is (C--O)

specific heat and how it relates to water

amount of heat that must be absorbed or lost for 1 g of the substance to change its temperature by 1 degree water has a high specific heat, making it a good thermal stabilizer b/c of its resistance to change temperature (oceans)

matter

anything that has mass and takes up space

Organic chemistry is defined as a) the study of compounds made only by living cells b) the study of carbon compounds c) the study of natural (as opposed to synthetic) compounds d) the study of hydrocarbons

b

endosymbiont theory

b/c mitochondria and chloroplasts exhibit features similar to bacteria: 1) bound by 2 membranes unlike the single membrane organelles 2) contain ribosomes and circule DNA 3) autonomous within the cell, reproducing on its own

Which chemical group is most likely to be responsible for an organic molecule behaving as a base? a) hydroxyl b) carbonyl c) amino d) phosphate

b; amino NOT hydroxyl

microtubules

biggest component of cytoskeleton; hollow tubes maintenance of cell shape (compression-resisting) cell motility chromosome movements in cell division organelle movements

Quaternary structure of a protein

bonding of multiple polypeptide subunits

What's the difference between bound and free ribosomes?

bound ribosomes are found in the ER or nuclear envelope (usually make proteins made to be packaged, shipped for membrane integration, or secreted) while the free ribosomes are in the cytosol (typically makes proteins found in the cytosol) -they are, however, structurally identical and can alternate between the two roles

monomer

building blocks of macromolecules (form polymers)

Which of the following hydrocarbons has a double bond in its carbon skeleton? a) C3H8 b) C2H6 c) C2H4 d) C2H2

c; carbon-carbon double bond, two more valence electrons per each carbon

macromolecules

carbohydrates, lipids, proteins, nucleic acids

phagocytosis

carried out by lysosomes where they fuse with food vacuoles and engulf the nutrient products within for food autophagy is also a thing where damaged cells are engulfed

plasmodesmata

cell junction in plant cells that connect plant cells and allowing cytosol to pass in between this makes plant cell connections continuous water and small solutes and maybe some proteins and RNA molecules can pass through

extracellular components

cell wall, extracellular matrix

What is an example of a structural polysaccharide?

cellulose; the most abundant compound on Earth!!!!; differs from starch based on its glycosidic linkage chitin in arthropods and fungi; exoskeleton (beta ring like cellulose except with a nitrogen)

vacuoles and plants

central vacuole: in mature plant cells, sap solution with inorganic ions are held here and hold a large role in plant growth certain vacuoles carry out enzymatic hydrolysis pigments organic compound storage

functional groups

chemical groups directly responsible for reactions -differing in shape and size

The protein and DNA complexes making up a chromosome is known as

chromatin

plastids

closely related plant organelles (chloroplasts, amyloplasts, chromoplast)

cholesterol

common steroid component of animal cell membranes

ribosomes

complexes made of rRNA and proteins that combine to make proteins from RNA -cells with high rates of protein synthesis will have more ribosomes (pancreas creating enzymes)

element

components of matter that can't be reduced by other substances

centrioles

composed of 9 sets of triplet microtubules

nucleus

contain the genes of a eukaryotic (nuclear envelope

hormonal proteins

coordination of organism's activities -i.e. insulin

glycosidic linkage

covalent bond between two monosaccharides formed by dehydration synthesis

dehydration synthesis

covalent bond forms through the loss of a water molecule -one group provides a hydroxyl group -the other group provides a H+

hydrolysis

covalent bond is broken through the addition of water -hydrogen attaches to one group -hydroxyl group attaches to other group

gap junctions

create cytoplasmic channels between cells allowing ions, sugars, amino acids, and small molecules to pass (similar to the plasmodesmata)

peptide bond

dehydration synthesis reactions between the amine group of one amino acid (N-terminus) and the carboxyl group of another (C-terminus)

DNA v. RNA

deoxyribose in DNA, ribose in RNA DNA directs RNA, which directs protein synth (known as gene expression)

cis-trans isomers

differ in atoms' arrangements AROUND a double bond due to the inflexibility of double bonds -cis: X element on the same side -trans: X element on opposite sides

Structural isomers

differ in the arrangement of covalent atoms (branched differently)

gene

discrete component of inheritance composed of nucleic acids

chromosomes

discrete units of DNA in genes

Shape of covalently (single) bonded carbons

double (or more) tetrahedron

nuclear envelope

double membrane encases the nucleus and separates in from the cytoplasm -its pores line the entire envelope consisting of lamina

trace elements

elements required for life only in small quantities

life requires the transfer and transformation of ___ and ___

energy and matter

kinetic energy

energy of motion

denaturation

environmental effect leads to the protein losing its shape and thus its functionality -most commonly happens when transferred from an aqueous solution to a nonpolar solvent, changing the orientation of the hydrophobic and hydrophillic regions

systems biology

exploration of a biological system by analyzing the interactions between the parts

pseudopodia

extensions of microfilaments to move a cell forward

Shape of covalently (double) bonded carbons

flat plane

membranes are not rigidly in place and are ___

fluid; the interactions between the amphipathic regions leads the membrane to constantly move (sometimes flip completely)

scanning electron microscope

focus a beam of electrons onto the surface of a specimen (3D appearance)

transmission electron microscopes

focus a beam of electrons through a specimen

form fits what

form fits function!!!!!!!!!

basal body

forms the base of a cilia or flagellum, very similar to centriole with 9 triplet microtubules

other functions of a protein

gene regulation and sensory input

What proteins are spherical and what proteins are long fibers?

globular and fibrous; form fits function and can be replicated if similar enough

fibronectin

glycoprotein in the ECM that binds to an integrin protein in the plasma membrane

Extracellular matrix (ECM)

glycoproteins (like collagen) and carbon-including molecules exist outside the cell membrane

surface tension

happens as a result of the cohesion between water molecules, giving the substance more structure in an ordered arrangement

surface area to volume ratio

having a high ratio allows for a greater number of specialized functions to occur (which is beneficial to the cell) -microvilli do this without increasing the volume -this is why there are many small cells instead of several large ones

cohesion

hydrogen bonds linking water molecules to one another

adhesion

hydrogen bonds linking water molecules to other substances

lipids

hydrophobic chains made of mostly hydrocarbons -fats, phospholipids, steroids

What bond is weaker, hydrophobic or covalent bonds?

hydrophobic interactions

nucleoid

in a prokaryote, the region where DNA is concentrated

intermediate filaments

in between microtubule and microfilament sizes; only found in some animal cells maintenance of cell shape (tension bearing) anchorage of nucleus and certain other organelles formation of nuclear lamina tend to be more stationary than microtubules or microfilaments

cytoplasm

in both prokaryotes and eukaryotes -euk: space between the nucleus and plasma membrane

chloroplasts

in plant cells, photosynthetic components derive energy from the sun; are mobile and their shape is changeable

cell wall

in plants, exist outside of the plasma membrane in order to provide structural integrity, prevent excessive water uptake,

Endomembrane system

includes the nuclear envelope, ER, Golgi, lysosomes, vesicles/vacuoles, plasma membrane

desmosomes

intermediate filaments form a solid bond between the cells in strong sheets, with keratin proteins anchoring the desmosomes in the cytoplasm

vacuoles

large vesicles of the ER or Golgi -food vacuoles -contractile vacuoles in freshwater eukaryotes -several functions in plants that lead to a smaller cytosol

primary structure of a protein

linear chain of amino acids it dictates the secondary and tertiary bc of the backbone and side chains

Only macromolecule to not be a polymer?

lipid boys

steroids

lipid characterized by 4 carbon ring structure

reductionism

looking at biology by studying individual parts

enzymes

lower activation energy, thus speeding up reactions (hydrolytic or synthetic) acting as catalysts

Proteins

macromolecules consisting of amino acids bound together by peptide bounds in order to form polypeptides -unique 3D shape -many functions

polymer

made of many covalently bonded monomers

plasma membrane

made of phospholipids; selectively permeable membrane that allows oxygen, nutrients and wastes to enter/leave

temperature

measure of energy that represents the average kinetic energy

fluid mosaic model

membrane is a mosaic of fluid bilayer in phospholipids

endoplasmic reticulum

membrane network in the cytoplasm made of cisternae and an internal compartment of the ER lumen that is separate from the cytosol Active role in synthesis of membranes, metabolism and synthetic activities

lysosomes

membranous sacs of hydrolytic enzymes that digest macromolecules -typically works better in a low pH (does nothing to the neutral cytosol until too many lysosomes break) -digests proteins, fats, polysaccharides, and nucleic acids

microvilli are a common type of

microfilament

cilia

microtubule controlled signal receiving (nonmotile) can either be motile or nonmotile based on function

Enantiomers

mirror images of one another -ibuprofen and albuterol

amphipathic

molecule has both a hydrophilic and hydrophobic region phospholipids have the hydrophilic phosphate head and hydrophobic nonpolar fatty acid tails

amino acid

monomers of proteins

flagella

motility structure in some animals extending from the plasma membrane

dyneins

motor proteins that use ATP to "walk" up a microtubule

contractile and motor proteins

movement -i.e. cilia and flagella

cytoskeleton

network of fibers extending throughout the cytoplasm, organizing its structure and anchoring many of the organelles main roles involve support and structure, but through the use of motor proteins, also motility and manipulation of the plasma membrane consists of microfilaments, intermediate filaments and microtubules

peroxisomes

removes H+ from the environment and transfers them to O2 to make hydrogen peroxide that is converted to water

receptor proteins

response of cell to chemical stimuli -i.e. receptors built into nerve cells

rough er

ribosomes on outer surface; continuous with the nuclear envelope synthesis of proteins like glycoproteins; polypeptide chain pumped into the ER lumen through a pore complex where it folds into its functional shape also makes phospholipids makes membranes by combining phospholipids and membrane proteins

Difference between saturated and unsaturated fats

saturated fats have SINGLE bonds between the carbons, so the hydrogens can saturate the fatty acids easily; the unsaturated have DOUBLE bonds, so there's less hydrogen to saturate

Most animal fats are

saturated, which is why they can pack more closely together without the double bond kink

biology

scientific study of life

glycoproteins

secretory proteins with carbohydrates covalently bonded; typically seen in the plasma membrane

enzymatic proteins

selective acceleration of chemical reactions -i.e. digestive enzymes used to catalyze hydrolysis reactions

plasma membranes are ___ permeable

selectively

cytosol

semifluid, jelly-like substance which subcellular components are suspended from

mitochondria

site of cellular respiration to synthesize ATP from energy

microfilament

smallest cytoskeleton component; thin, solid rods made from the globular protein actin maintenance of cell shape (tension) changes in cell shape muscle contraction cytoplasmic streaming cell motility cell division (cleavage furrow formation)

atom

smallest unit of matter that retains the property of an element

Does starch or cellulose have the alpha ring structure? What does this structure affect?

starch 3D shape (starch is helical while cellulose tends to be straight); cellulose is never branched

storage proteins

storage of amino acids -i.e. casein in milk, ovalbumin in egg whites

Isomers

structural variation in compounds with the same chemical formula, thus leading to various properties

genomics

study of a whole set of genes of a species

proteomics and a proteome

study of sets of proteins and their properties; the entire set of proteins in a cell

compound

substance that has 2 or more elements combined in a fixed ratio

sickle cell disease

substitution of valine instead of glutamic acid (primary structure) that leads to to "collapsed" secondary and tertiary structures, which affects quaternary structure of the polypeptide subunits and preventing oxygen to be effectively carried in hemoglobin

carbohydrates

sugars and starches -simplest being monosaccharides, then disaccharides, and then polysaccharides -made of carbonyl (C--O) and multiple hydroxyl (-OH) groups that are either aldoses or ketoses based on the location of the the carbonyl group -form rings in aqueous solutions

structural proteins

support -i.e. keratin

cell fractionation

takes cells apart and separates the organelles and subcellular structures from one another (centrifuge)

Shape of covalently bonded carbon to other molecules

tetrahedron

secondary structure of a protein

the alpha helices (fibrous proteins usually) and beta pleated sheets (globular proteins usually)

What separates a functional protein and a polypeptide?

the alternative structures (twisting and folding)

Refraction

the bending of light to magnify an image

What's the reason that humans can't ingest cellulose?

the beta structure of cellulose can't be hydrolyzed by the enzymes in the animal digestive tract this is why it's so important for bacteria to exist b/c they can hydrolyze it

What is the cis face of the Golgi and how is it different from the trans face?

the cis face receives ER products and the trans face ships the transport vesicles. products of the ER are typically editing between the cis and trans faces

nuclear matrix

the fibrous structures consisting of the inside of the nucleus

thermal energy

the measure of kinetic energy within the movement of atoms; in part relating to volume

resolution

the measure of the clarity of the image

diseases associated with misfolded proteins

Alzheimer's, Parkinson's, mad cow

atomic nucleus

protons and neutrons at the center

3 subatomic particles

protons, neutrons, electrons

transport proteins

provides transport for substances -i.e. hemoglobin and oxygen

Purines

Adenine and Guanine -a six member ring of carbon bound to a 5 member ring

magnification

ratio of an object's image size to its real size

What factors affect protein structure?

-interactions between the amino acids, folding, the interactions btw those the different foldings, and the subunits (structures) -environmental factors (pH, salt concentration, temperature, etc.) that affect bonding

characteristics of a prokaryote

-no nucleus -DNA in nucleoid (no histone proteins) -no membrane-bound organelles -cytoplasm bound by plasma membrane

What are the structural components of a amino acid?

1) amino group 2) carboxyl group 3) R (functional) group 4) alpha carbon in the middle

Biological organization

1) biosphere 2) ecosystems 3) communities 4) populations 5) organisms 6) organs and organ systems 7) tissues 8) cells 9) organelles 10) molecules

structure of mitochondria

1) first double membrane 2) intermembrane space 3) cisternae of the inner membrane (increases surface area) 4) second (inner) membrane 5) mitochondrial matrix (enzymes, mitochondrial DNA, ribosomes)

properties of life

1) order 2) evolutionary adaptation 3) regulation 4) energy processing 5) growth and development 6) response to the environment 7) reproduction

Components of DNA

1) phosphate group (one or more) 2) 5 carbon sugar 3) nitrogenous base (tend to take up H+ in solution)

structure of a phospholipid

1) phosphate group (phillic) 2) glycerol (phillic) 3) fatty acid tail with the unsaturated hydrocarbon chain (phobic)

Describe the reinforcement process of a cell wall in plant cells

1) primary cell wall is formed in young plant cells 2) sticky w/ pectin, middle lamella layer is placed in between primary walls 3) Secondary cell wall can form btw plasma membrane and primary wall, or a hardening agent is incorporated

4 emergent properties of water

1) solvent of life 2) cohesion of water molecules 3) temperature control 4) floating of ice on water

structures of chloroplasts

1) thylakoids, granum, stroma 2) intermembrane space 3) thylakoid space

Glucose monomers in starch are joined by what linkages? What about amylose and complex starches?

1-4 (number 1 carbon to number 4); no branching; 1-6

4 ways carbon skeletons can vary

1. length 2. branching 3. position of double bond 4. presence of rings

essential elements make up ___%; 96% of those elements being __________

20-25%; C, H, O, N

What direction is DNA read on a complimentary strand?

3' to 5' carbon on the sugar; aka running ANTIPARALLEL

How many monomers contribute to the diversity of life

40-50; arranged in various ways leads to infinite possibilities in monomers that form polymers of macromolecules

What percent of dry mass do proteins have?

50%

Why are unsaturated fats liquid?

Cis double bonds lead to there being a kink in the hydrocarbon chain that prevents the fat molecules from packing close together

characteristics of a eukaryote

DNA in nucleus membrane-bound organelles cytoplasm in the nucleus and in between usually larger

True or false: RNA cannot exist as a single strand

F

Inductive versus deductive reasoning

Inductive: small to big (specific observations lead to a generalization) Deductive reasoning: big to small (generalizations to ideas about a specific idea used to hypothesize)

Things both prokaryotes and eukaryotes have

Plasma membrane Cytosol Chromosomes Ribosomes

Difference between estragen and testosterone

Similar carbon ring structures, only differ in the groups attached to the carbon skeleton (functional groups) -different methyl group

How do you make a 1 M solution of glucose when the atomic mass is 180 g?

Since you're finding the number of moles per 1 liter, it's just the amount of g in a mole of glucose; dissolve 180 g in 0.8 L of solution and then add enough water to fill it to the 1 L mark

smooth er

no ribosomes on outer surface synthesis of lipids (oils, steroids like sex hormones, phospholipids) detox drug and poisons by adding a hydroxyl group (barbiturates decrease the smooth ER function --> habituation) store Ca+ in the lumen

Hydrocarbons

nonpolar organic molecules with only carbon and hydrogen atoms -fat molecules

structures of a plant cell

nucleus (nuclear envelope, nucleolus, chromatin), ER (smooth and rough), mitochondria, vacuole, ribosomes, CHLOROPLASTS, Golgi, peroxisome, PLASMODESMATA, CELL WALL, cytoskeleton (microfilaments, microtubules)

structures of an animal cell

nucleus (nucleolus, nuclear envelope, chromatin), ER (smooth and rough), cytoplasm, Golgi apparatus, peroxisomes, mitochondria, plasma membrane, cytoskeleton (microfilaments, INTERMEDIATE FILAMENTS, microtubules), microvilli, FLAGELLUM, centrosome, lysosome, ribosomes

know basic science terms

ok

tertiary structure of a protein

overall shape of the polypeptide dictated by the secondary folding -held together by misleading hydrophobic interactions (caused by the interaction of nonpolar substances in the absence of water) -held loosely by London dispersion forces and the polar bonds by the side groups

glycerol

part of fat; an alcohol with 3 carbons that all form hydroxyl groups

fatty acid

part of fat; long strings of hydrocarbons featuring a functional group at the end (the acid)

What are the repeating sequences of polypeptides (excluding functional groups)? What are the the functional groups referred to?

peptide backbone; side chains

cytoplasmic streaming

plant cells: actin-myosin interactions lead to the circular flow of cytoplasm

What are storage polysaccharides used for typically?

plants in the form of starch stored in granules that are in plastids through dehydration synthesis that can be broken into glucose through hydrolysis when needed; animals in the form of glycogen stored in liver and muscle cells

tight junctions

plasma membranes of two different cells packed together very tightly and bound by specific proteins this creates an effective barrier to prevent extracellular leakage

nucleic acids

polymers of nucleotides (polynucleotides); polydiester bonds lead to helical shape

polypeptide

polymers of proteins bound together by peptide bonds

emergent properties

properties that a complex system or community has but an individual does not --> requires a specific level of organization in order to function

defensive proteins

protection against disease -i.e. antibodies

nuclear lamina

protein filaments that hold the shape of the nucleus together

myosin

protein in thicker filaments that interact with actin filaments in order to contract a muscle

chaperonins

protein molecules that help proteins fold properly

proteoglycans

protein/carb complex that form a collagen fiber network -complex bound together by noncovalent bonds

Most structurally sophisticated molecules?

proteins b/c of its unique 3D shape

integrin

proteins that span between the ECM and the cytoskeleton; they can transmit signals and integrate changes

phospholipids

type of lipid that are the major component of cell membranes -only differs from a triglyceride by having 2 fatty acids attached to the glycerol; the other hydroxyl group in the glycerol is bound by a negative phosphate group -fatty acid tails are hydrophobic while the glycerol head (with the phosphate group) is hydrophillic

calories

unit of heat

dalton (amu)

used for atoms and subatomic particles

contrast

visible differences in brightness between parts of the sample

light microscope

visible light is passed through a specimen and then through glass lenses

Golgi apparatus

warehouse of sorting, shipping, receiving, and some macromolecule manufacturing (like polysaccharides) of ER product -secretion into transport vesicles -composed of membranous sacs (cisternae)

Methods to study protein form and function

x-ray crystallography (but it's hard for them to form crystals) nuclear magnetic resonance (NMR) spectroscopy (which doesn't require crystallization) bioinformatics