Cell Bio Exam 2

Entropy

thermodynamic quantity that measures the degree of disorder in a system

Living systems maintain order that is trending towards ______

disorder

Enzymes

proteins that catalyze chemical reactions

Metabolism 

the sum of the chemical reactions that take place in the cells of a living organism 

Catabolism

set of reactions that molecules are broken down

Anabolism

set of reactions that molecules are synthesized (built)

Second law of thermodynamics

• disorder can ONLY INCREASE 

• systems change spontaneously

• systems change in ways that increase entropy 

First law of thermodynamics 

energy cannot be created or destroyed, but it can be converted to another form 

Kinetic energy + heat energy

potential energy

Activated carriers

small molecule that stores energy or chemical groups in a form that can be transferred to many different metabolic reactions

Carbon Fixation

the process by which inorganic carbon is converted to organic compounds.

Cells obtain energy by the ______ of organic molecules 

oxidation (loss of electrons)

Cellular respiration

the complex stepwise process by which food molecules are broken down

Oxidation-reduction reactions

chemical reactions involving the transfer of electrons where one substance loses an electron and one substance gains an electron

Is photosynthesis oxidation or reduction?

reduction 

In the reactions involving electron transfer, what gets overall oxidized?

Activated carriers

Chemical reactions proceed in the direction that causes loss of ______

free energy

Free energy

energy that can be used to do work

Activation energy

the energy that must be acquired by a molecule to undergo chemical reaction

Substrate

a molecule on which an enzyme acts to catalyze a reaction

Enzymes can direct molecules along _______

Specific pathways

A reaction is favorable when …

the products have lower free energy than the reactants

Equilibrium

state in which the forward and reverse rats of a chemical reaction are equal so that no net chemical change occurs

Cells rarely allow reactions to reach ____ and are constantly fighting against it

equilibrium=death 

Standard free energy change

the free energy change measured at a defined concentration, temperature, and pressure

Enzyme catalyzed reactions depend on rapid _______

molecular collisions

Diffusion

process by which molecules and small particles move from one location to another by random thermally driven motion

_____ interactions allow enzymes to bind to specific molecules

noncovalent

_____ are responsible for all reversible interactions in the cell and folding of macromolecules 

noncovalent

Affinity constant 

equilibrium constant of binding, larger the constant= more tight binding

The formation of an activated carrier is a _____ reaction

uphill, which means it must be paired to a downhill reaction 

Coupled reaction

linked pair of chemical reactions in which free energy released by one reactions serves to drive the other reaction

______ is the most widely used activated carrier

ATP (uphill reaction)

Transfer of a phosphate is a _____ reaction 

phosphorylation 

What drives the synthesis of many macromolecules by powering the reaction of the subunit attaching to the growing polymer

ATP

____ is the activated carrier of phosphate groups

ATP

NADH and NADPH are activated carriers of _____

electrons 

NADH/NAD+ will come back in ______

cellular respiration

NADPH/NADP+ will come back in ______

photosynthesis

NADH is mostly _____ reactions 

catabolic 

NADPH is mostly _____ reactions

anabolic

Activated carrier that donates the carbon atoms in its readily transferable acetyl group to many metabolic reactions, including the citric acid cycle and fatty acid biosynthesis 

acetyl CoA

A large carrier is easily recognizable by ________

enzymes

Condensation means….

making

Hydrolysis means…

breaking

Proteins

macromolecules built from amino acids that provide cells with their shape and structure and perform most of their functions

Each individual amino acid in a protein is connected to the next via a _______

covalent bond

Peptide bond

covalent chemical bond between the carbonyl group of one amino acid and the amino group of a second amino acid

Polypeptide

linear polymer composed of multiple amino acids

Polypeptide backbone

repeating sequence of the atoms -N-C-C- that form the core of a protein molecule to which the amino acid side chains are attached

Polypeptide chains have _______

directionality (do not read the same forward and backward)

Side chain of an amino acid is ____ involved in forming peptide bonds

NOT

What allows proteins to fold? 

polypeptide bonds are planer but allow some rotation between amino acids 

The shapes the backbone can make are limited by _________ between the side chains

weak interactions

Polypeptide backbone can _______ bond with itself

hydrogen

Amino acid side chains can hydrogen bond with …..

each other and the polypeptide backbone

Amino acid side chains may group together due to ….

hydrophobic interactions 

Proteins fold into the conformation of _____ energy

lowest

Denature

the process of a protein unfolding

Renature 

the process of a protein re-folding after having been unfolded, happens SPONTANEOUSLY 

Protein folding is assisted by ____

chaperones

a-helix

single polypeptide chain twists around itself to form a cylinder, stabilized by hydrogen bonds

b sheet 

neighboring regions of the polypeptide chain associate side by side with each other through hydrogen bonding 

Prions

misfolded proteins that are infectious because they convert properly folded proteins into the misfolded form

Primary structure 

the amino acid sequence of a protein 

Secondary structure

regular local folding pattern of a peptide chain (a helices and b sheets)

Tertiary structure

complete 3D structure of fully folded polypeptide 

Protein families 

group of protein that share a similar amino acid sequence 

The binding site is a region that interacts with another molecules through sets of ______ bonds

noncovalent 

Fibrous shape

a protein with a elongates rod-like shape

Extracellular matrix

gel-like exterior of a cell made of proteins and polysaccharides

Crosslinks

covalent stabilizing connections that strengthen proteins. like disulfide bonds (2 cysteines)

Extracellular proteins are often stabilized by______ cross linkage

covalent 

Ligand

small molecules that binds to a specific site on a macromolecule

Antibodies

proteins produces by B lymphocytes in response to invading a organism. binds to antigen

Immunoprecipitation

purify a specific protein from a complex mixture by using an antibody that binds to that protein

Lysozyme

• severs polysaccharide chains in bacteria cell walls

• illustrate how enzymes work

Feedback inhibition= negative regulation

metabolic control in which the end product of a chain of enzymatic reactions reduces the activity of an enzyme early in the pathway

Allosteric regulation

binding of a regulator to the site other than the active site to alter the function of an enzyme usually by inducing a conformation change

Phosphorylation can control protein activity by

causing conformational change by adding a phosphate group covalently to the side chains

Chromatography

uses a resin to separate proteins based on size, charge, or affinity

Electrophoresis 

uses an electrical field to separate molecules based on size 

A DNA molecule consists of two complementary stands of ____

nucleotides (covalently linked vis phosphodiester bonds)

Base pair

two complementary nucleotides held together by HYDROGEN BONDS, perpendicular to axis

Which is stronger, A&T or C&G?

C & G because they have 3 bonds 

Replication happens in _______ (what phase?)

interphase

Nucleolus

where ribosomal DNA is transcribed into ribosomal RNA and subunits are assembled

What 2 classes of proteins are involved in packing chromosomes?

Histones and nonhistones

What complex is formed by DNA and histones/nonhistone?

chromatin

Histones 

proteins that DNA wraps around to form nucleosomes 

Cohesin

specific protein complex that organizes interphase chromosomes into loops

Condensins

SMC complex proteins that compact chromosomes during nuclear division

Chromatin 

remodeling complexes- enzymes that use ATP to alter the arrangement of nucleosomes 

Methyl groups, phosphate groups, or acetyl groups can be added covalently to _____ altering how tightly DNA is packaged

histones

Heterochromatin

highly condensed region of interphase chromosome

Euchromatin 

main state in which chromatin exists in interphase cell 

DNA polymerase

enzyme that catalyzes the synthesis of DNA molecule from a DNA template using deoxyribonucleoside triphosphate precursors

Which way does DNA polymerase synthesize?

5’ to 3’

Which way does polymerase read?

3’ to 5’

Primase

RNA polymerase that uses DNA as a template to produce a short RNA fragment that serves as a primer for DNA synthesis