bio exam 3

All energy come from protons of ______.

Light

What is the formula for photosynthesis?

6H2O + 6CO2+ sunlight --> C6H12O6 + 6O2

Photosynthesis is the most important ___________ process.

Endergonic

The formula for photosynthesis moves from ____________ reactants to _____________ products.

Inorganic to Organic

What do both the product and reactants of photosynthesis have?

H20 or water

Define Chloroplasts:

Photosynthetic organelle; Thylakoid contain light-absorbing pigments.

Chlorophyll molecules are in which part of the chloroplasts?

Thylakoid membranes

Photosynthesis happens within what parts of the chloroplast?

Stroma, Thylakoid, and Thylakoid space

Define stroma:

liquid surrounding thylakoids

What is the first step of photosynthesis?

Energy is extracted from protons of light (apart of light reactions)

When light is absorbed, an electron

boosted to a higher energy level/ gets excited

During the light reactions what is split?

Water is split and O2 is released

Excited electrons produce (products of light reactions)

ATP and NADPH

The second step of photosynthesis is the

Calvin Cycle

Top of Form

\Bottom of Form

The calvin cycle takes Co2 from the at and does what?

Attaches it to an orgainc molecule (carbon fixation)

Define carbon fixation:

The capture of CO2 into an organic molecule 

(Rubisco = enzyme that is critical for carbon fixation in plants) makes inorganic carbon into organic carbon

Define rubisco:

an enzyme that catalyzes the fixation of carbon dioxide in the Calvin cycle

What are the products of the Calvin Cycle?

G3P, ADP, Pi, NAD+, and sugar

2G3Ps =

1 sugar molecule

What is the Calvin cycle dependent on and why?

The Calvin cycle depends on energy from light reactions because it cannot convert light into energy.

The energy used to produce ATP in the light reactions of photosynthesis comes from...

The movement of H+ throughout a membrane

Define photophosphorylation:

The production of ATP by chemiosmosis during the light reactions of photosynthesis

Define chemiosmosis:

the movement of ions across a semipermeable membrane, down their electrochemical gradient

Light can be absorbed by _________.

Photopigments

Chlorophyll can absorb all wavelengths of light except _______.

Green

Green light is _______.

reflected

Pigments are located in a protein complex called the....

Photosystem

The photosystem can be found where?

Embedded in the thylakoid membrane

Define Chlorophyll a:

Primary pigment that converts light energy to chemical energy

Chlorophyll b and carotenoids are ___________ pigments.

Accessory

Chlorophyll b has a higher ________ than Chlorophyll a.

Wavelength

The only light-dependent step (and first step) in the photosystem is what?

The transfer of light energy to pigment molecules

an energy transfer causes the "special pair" of chlorophyll a molecules to become ________.

Excited

A transfer of electrons (in the photosystem) occurs between __________ to _________.

chlorophyll a to Primary electron acceptor

How do electrons enter the photosystem?

the splitting of water/ H20

What has to be replaced during this process? If not what will happen?

Electrons must be replaced with the primary pair if not the process will stop.

The primary acceptor reduces electrons by moving electrons threw a...

electron transport chain

The moving of electrons threw an ETC creates a _________ _________.

Proton (H+) gradient

What is made during photosystem 2?

ATP

How many photosystems are there?

2, photosystem I and photosystem II

Which photosystem comes first?

Photosystem II

What are the products at the end of photosystem 1?

NADPH

ATP and NADPH from the photosystems move to the....

Calvin cycle

The Calvin cycle reduces CO2 using ______ and high energy _________ from NADPH. (fixing carbon)

ATP, electrons

1st phase of the Calvin cycle:

Carbon fixation

What happens during carbon fixation?

- Inorganic CO2 is converted to an organic compound.
- Three molecules of CO2 combine with RuBP, and RuBisCO catalyzes a reaction between CO2 and RuBP
- which forms a six-carbon compound that is immediately converted into two three-carbon compounds called 3PG

2nd stage of the Calvin cycle:

Reduction

What happens during reduction?

6ATP invested to make 6 ADP 1,3-bisphosphoglycerate
6NADH converts them to six G3P
one of these is removed

3rd stage of the Calvin cycle:

regeneration of RuBP

Regeneration of RuBP

G3P is used to regenerate RuBP

The Calvin cycle requires what to produce 1 molecule of G3P?

9 ATP, 6 NADPH, 3 CO2

When a leaf gets hot what happens?

Water leaves threw stomata

When the stomata closes what happens?

O2 builds up inside the leaves and CO2 cannot enter the leaves

Define photorespiration:

Rubisco fixes O2 instead of CO2

Process of Photorespiration

1) Stomata close to save water, but the plant runs out of CO₂ to make G3P.
2) The Rubisco enzymes then add O₂ to the Calvin cycle instead of CO₂
3) The unstable product quickly breaks down to CO₂

C4 plants:

plants that have adapted their photosynthetic process to more efficiently handle hot and dry conditions

C3 plants:

Fix CO2 to a 3 carbon molecule

CAM plants:

plants close their stomata during the day, collect CO2 at night, and store the CO2 in the form of acids until it is needed during the day for photosynthesis

The diffrence between C4 palnrs and C3 plants

C4 is the first product in plants, producing 4C instead of 3C

C3, C4, and CAM plants all aim to do what?

Minimize photorespiration

A plant without light can still live if....

The plant stored energy in the form of sugar or starch and derive energy from the stored molecules

G3P is used in...

Production of sucrose, cellulose, glucose, cell walls in growing plants, and starch

Where does the Calvin cycle photosynthesis occur?

stroma

Define autotroph:

An organism that makes its own food

Define heterotroph:

An organism that cannot make its own
food; a consumer

Metabolic pathways are typically redox processes. In photosynthesis, what molecule is oxidized and what molecule is reduced?

Water is oxidized and carbon dioxide is reduced

Define cell communication:

the process through which cells can detect and respond to signals in their environment

All cells respond to _________ in their environment.

Changes

steps of cell signaling

reception, transduction, response

What happens during reception?

A signaling molecule binds to a receptor

What happens during Transduction?

Signal pathway, Molecules change shape

What happens during response?

the cellular response is activated

What a cell does depends on what?

which combination of signals it receives

What are the four responses we discussed?

cells survive, divide, differentiate, and die

Which cell signaling response leads to cancer?

Division

Differentiating is when a cell does what?

Takes on adult characteristics and carries out normal cell functions

Define central dogma

transcription and translation, by which the information in genes flows into proteins: DNA → RNA → protein.

Gene Expression:

Production of the protein of a particular gene

Transcription and translation are both...

Gene expressions

Transcription requires proteins called what? What do these proteins do?

Transcription factors they regulate transcription

a cellular response may be the production of a...

particular protein

What does a growth factor do?

stimulates the growth and division of cells

what is a ligand?

A molecule that binds specifically to a receptor site of another molecule. A small moleculeHo that specifically binds to a larger molecule.

Heart muscle ligand:

decreased rate and force of contraction (Response contraction)

Salivary glad cell ligand:

saliva is secreted

Responses to ligands may be _______ in different cells.

diffrent

What are the two types of signaling molecules?

hydrophilic, hydrophobic

Hydrophobic molecules can....

Diffuse threw the membrane

Cell- surface receptors are _________ molecules.

Hydrophilic

Intracellular receptors are ________ molecules.

Hydrophobic

local signaling two main types:

Paracrine and synaptic signalling

paracrine signaling:

secreting cell diffuse locally and trigger a response in neighboring target cells (indirect)

synaptic signaling:

a nerve cell releases neurotransmitter molecules into a synapse, stimulating the target cell (direct)

long distance signaling

endocrine signaling - hormonal

endocrine signaling

secreted molecules diffuse into the bloodstream and trigger responses in target cells anywhere in the body

Hormones can be _________ or ___________.

proteins or steroids

What are the four kinds of receptors?

Ligand-gated ion channels, G protein-coupled receptors, Receptor tyrosine kinases, Intracellular receptors

Ligand-gated ion channels

membrane ion channels operated by the binding of specific molecules to channel proteins

G Protein-coupled receptors

A special class of membrane receptors with an associated GTP binding protein

What are the three G protein subunits:

Alfa, Beta, Gama

receptor tyrosine kinases

membrane receptors that attach phosphates to tyrosines creating a dimer

What is a dimer?

two monomers bonded together

intracellular receptors

receptors located inside the cell rather than on its cell membrane

What is GTP?

Guanosine Triphosphate is similar to ATP and is used by some plant cells. can be used to make n ATP or to directly power work in the cell

Receptor tyrosine kinases are involved in

Gene expression (cancer)

Steps of Receptor tyrosine kinases

1) 2 receptors, 2)ligand binds- receptors dimerize, 3)Autophosphorylation (phosphorylate each other), 4)receptors activate relay proteins

intracellular receptors process

Receptors in the cytoplasm (not embedded into the plasma membrane), Bind w molecule and move into nucleus and binds w DNA

A receptor with a bound signal is a _________ ___________.

Transcription factor

What are the two important factors of transduction?

2nd messenger systems and protein phosphorylation/dephosphorylation

The 1st second messenger is a ________.

cAMP

What are the characteristics of a cAMP?

Small, non-protein, diffuse in the cytosol, first discovered

cAMP does what?

carries message throughout the cell

Ca++ is a second messenger and its function is what?

Maintain low levels of cytosol

A calcium pump...

secretes calcium from the rest of the cell

where is HIgh Ca++ found?

Outside the cell, inside mitochondria, in the ER

High calcium in the cytosol is a _______. This causes biological effects.

signal

IP3 is a 2nd messenger. What is its function?

One of the products of PIP2 cleavage in the Ca++/phosphoinositide signal pathway.
Moves to the cytoplasm to trigger Ca++ release from an intracellular gated channel -> triggers cellular response

Protein phosphorylation acts as a

molecular switch

Phosphatase does what?

removes phosphate

Kinase does what?

adds phosphate

Phosphorylated proteins =

protein with a phosphate attached

When a protein is phosphorylated...

switch is turned on and can catalyze reactions

When a protein is de-phosphorylated...

switch is turned off not reactions occur

define phosphorylation cascade:

A series of enzyme-catalyzed phosphorylation reactions is commonly used in signal transduction pathways to amplify and convey a signal inward from the plasma membrane.

what are the two main things phosphorylation cascade does?

1) amplifys response, 2) more sites for regulation

Transduction pathways interact =

better communication

PP=

Protein phosphatase

signal amplification

Enzyme cascades amp the cell's response to a signal. At each step in the cascade, the number of activated products is much greater than the prev step

what is apoptosis?

A pathway that signals cell death, certain cells die during development

receptor tyrosine kinases have

enzymatic functions

Protein kinase:

Transfers phosphate groups from ATP to other molecules

How does adenylyl cyclase help transmit signals within a cell?

It converts ATP to cAMP which broadcasts the signal to the rest of the cell.

After a signaling molecule binds to a G protein-coupled receptor, what activates the associated G protein?

GTP displaces GDP on the G protein

Top of Form

Bottom of Form

A G protein is active when...

GTP is bound to it

Why does testosterone not affect all cells in the body?

only certain cells have cytoplasmic receptors for testosterone

Kinases are useful for cellular transduction because..

They amplify the original signal

Respiration=

Chemical signal is detected

cell division in prokaryotes

binary fission

what happens in binary fission

the chromosome replicates (beginning at the origin of replication), and the two daughter chromosomes actively move apart

phases of cell cycle

1.        Interphase (G1, S, G2)
2. Mitosis (PMAT)
3. Cytokinesis (cell division)

what happens in interphase G1, S, G2

organelles replicate, proteins synthesized, cell grows

what happens in S phase

DNA replicates

what happens in M phase

mitosis and cytokinesis

what is mitosis

division of the nucleus

what is cytokinesis

division of the cytoplasm

where does the cell spend the longest amount of time

S phase (10-12 hours)

how many chromosomes do human somatic cells have

46 (23 pairs)

how many chromosomes do gametes (sperm & eggs) have

23

diploid

(2n) two sets of chromosomes from each parent

haploid

(1n) one set of chromosomes (egg and sperm)

sex chromosomes

X and Y chromosomes.

autosomes

Any chromosome that is not a sex chromosome (22 pairs)

homologs

Matching Chromosomes that are similar but not identical

sister chromatids

identical dna sequenced copy of a chromosome

where are sister chromatids attached

by cohesion proteins at the centromere

kineteochore

special protein complex at the centromere

chromatid

one long coiled dan molecule

homologous chromosomes

2 chromosomes with 2 sister chromatids/ 2 DNA molecules

prophase

what happens in prophase

Chromosomes condense
Nuclear membrane disintegrates
Centrioles move to opposite poles
Spindle apparatus formed by microtubules

metaphase

what happens in metaphase

Chromosomes line up in the middle of the cell

anaphase

what happens in anaphase

Centromeres split
microtubules contract
chromosomes pulled apart to opposite poles.

telophase

what happens in telophase

Nuclear membrane reforms
Chromosomes decondense

cytokinesis

what happens in cytokinesis

cytoplasm divides

spindle

microtubule structure required for chromosome alignment, segregation and separation

actin

myosin fibers form a ring around the plasma membrane

cleavage furrow

contractile ring of microfilaments in animal cells

cytokinesis in plant cells

cell plat forms from vesicles and divides the cytoplasm to form a new wall

cyclin dependent kinases (Cdks)

A protein kinase that is active only when attached to a particular cyclin.

cyclin

bind to Cdks and regulate their ability to phosphorylate target proteins

Cdk/cyclin complexes

give the 'go ahead' signal at checkpoints to continue cycle

G1 checkpoint influenced by

growth factors, nutrients, cell size, DNA damage

G2 checkpoint influenced by

cell size, DNA damage, DNA replication

M checkpoint influenced by

chromosome attachments to the spindle

growth factor

signaling molecule that promotes cell division

when cells get to a certain density, what happens

they stop dividing

In which of the following chromosomal entities are an individual's traits specified?

Genes

Nucleotides contain a sugar, a phosphate, and a nitrogenous _____.

base

Which of these are used in RNA?

Adenine
Uracil
Guanine
Cytosine

Adjacent nucleotides in the same DNA strand are held together by covalent bonds known as _____ bonds.

phosphodiester

We have an expert-written solution to this problem!

Chargaff's rule indicates that the amount of A in a sample is equal to the amount of _______ and the amount of C in a sample is equal to the amount of ______.

T, G

Genes, which contain trait specifying information, are located on ______.

chromosomes

DNA's phosphodiester _____ is composed of alternating sugars and phosphates.

backbone, spine, or back-bone

Select all of the following that are components of a nucleotide.

Phosphate group
Sugar
Nitrogenous base

The level of DNA structure that resembles a spiral staircase is the ______.

double helix

Indicate the 4 nitrogenous bases used in DNA.

Thymine
Adenine
Cytosine
Guanine

In DNA, consecutive nucleotides are linked via _______bonds, which are made between the 5' phosphate of one nucleotide and the 3' _______ group of another nucleotide.

phosphodiester, OH

The DNA structure proposed by Watson and Crick involves ______.

two grooves (major and minor)
a sugar phosphate backbone
a helical structure
a double stranded structure
Each DNA molecule is composed of two strands that run antiparallel.
Each DNA molecule is composed of 2 phosphodiester strands.

The DNA backbone is composed of ______.

phosphate groups
sugars

The interaction of two strands of DNA via hydrogen bonds results in a structure called the ______.

double helix

How many hydrogen bonds are formed between adenine and thymine in the double DNA helix?

2

A segment of DNA has the sequence 5'-ATGCCC-3'. The complementary sequence would be Blank______.

5'-GGGCAT-3'
Reason:
Recall that the two molecules of DNA in a double helix must be anti-parallel. If you put the two strands in this answer together so that the bases complement each other, they will be running parallel to each other, not anti-parallel.

Which of the following bonds, while individually weak, are numerous enough to hold the two strands of a double-stranded DNA molecule tightly together?

hydrogen

DNA's phosphodiester i____ s composed of alternating sugars and phosphates.

backbone

In a DNA double helix, two hydrogen bonds form between ______.

adenine and thymine

In a DNA double helix, three hydrogen bonds form between ______.

cytosine and guanine

DNA replication that leads to the production of double helices with one parental strand and one newly synthesized strand is consistent with Blank______.

semiconservative replication

what is required for DNA replication?

Polymerase
Template
Nucleotides

During semiconservative DNA replication, ______.

one of the strands in each new double helix comes from the original molecule, and one is newly synthesized

During DNA synthesis, each nucleotide used as a building block provides the __________ for its own incorporation into the new strand as its two terminal ______ are cleaved.

energy, phosphates

What are the three phases in DNA replication?

Termination
Elongation
Initiation

Of the following list, which 3 items are required for DNA replication?

Template
Nucleotides
Polymerase

Which enzyme covalently links nucleotides together?

DNA polymerase

Repeating sugar and phosphate units in a single DNA strand make up the Blank______.

phosphodiester backbone

During the synthesis of the new DNA molecule, where are the new nucleotides added by DNA polymerase?

The 3' end of the growing strand

What provides the energy for the addition of nucleotides to a newly synthesized strand of DNA?

High energy bonds in the nucleotides used to synthesize the strand

All DNA polymerases require a short strand of DNA or RNA, called a _______, to begin their synthesis.

primer

The enzyme DNA __________ covalently links nucleotides to synthesize new DNA strands together during DNA replication.

polymerase

DNA replication in E. coli ends at a site called the

terminus

When the double stranded DNA helix is unwound, two single strands of DNA are formed. These strands have to be stabilized because their hydrophobic bases are exposed to water. The proteins that stabilize the two single strands are called Blank______.

single-strand binding proteins

Direction of DNA replication

5' to 3'

In contrast to DNA polymerases, RNA polymerases Blank______.

do not require primers to begin synthesis

The term _____ refers to the increased twisting of two DNA strands around each other which leads to torsional strain.

supercoiling

In E. coli, oriC is the site at which replication Blank______.

begins

The enzyme ______ uses ATP to unwind the DNA template.

helicase

During DNA replication, torsional strain in the DNA molecule is relieved by a topoisomerase called DNA

gyrase

The topological state of DNA refers to Blank______.

how the DNA coils

During DNA replication, the _______ strand is synthesized continuously while the ______ strand is synthesized as small fragments that are connected to each other to form a continuous strand.

leading, lagging

Short fragments of DNA synthesized on the lagging strand of DNA during replication are called Blank______.

Okazaki fragments

The partial opening of a DNA helix to form two single strands is called Blank______.

the replication fork

Match these enzymes involved in DNA replication with their function.
Helicase Gyrase Primase Polymerase

Helicase- Unwinds the double helix
Gyrase- Relieves coiling in DNA strands ahead of the replication fork
Primase- Makes a 10-12 bp complementary primer, rna primer
DNA Polymerase- Attaches a nucleotide to the 3' end of the DNA strand
Ligase- joins 2 strands together

What class of enzymes relieve torsional strain in DNA strands ahead of the replication fork?

Topoisomerases

Match the leading and lagging strands with the features of DNA synthesis.
leading, lagging strand

leading strand-Synthesized continuously, Requires a single primer
lagging strand- Synthesized in small fragments that are later connected, Requires multiple primers

The enzyme DNA ______ synthesizes the RNA primers required by DNA polymerases during replication.

primase

The ability of a DNA polymerase to remain attached to its template is called the polymerase's

processivity

Which subunit of DNA polymerase III forms the sliding clamp?

The β subunit

Which DNA polymerase removes and replaces RNA primer segments in the synthesis of the lagging stand because it has 5' to 3' exonuclease activity.

I

DNA primase Blank______.

makes a primer about 10 -20 nucleotides in length.
makes a primer of RNA complementary to the DNA.

In a bacterium, where does termination of replication occur, relative to the origin?

The termination site is opposite to the origin

The DNA polymerase III enzyme of E. coli contains a subunit called the β subunit, which dramatically increases the enzyme's ______.

processivity

Why do eukaryotic cells have multiple origins of replication?

To ensure timely replication of multiple, relatively large chromosomes

The sliding clamp of a DNA polymerase Blank______.

holds the polymerase to the DNA template

steps of lagging strand synthesis in the correct order (start at the top):

synthesize primers using primase
synthesize dna
replace rna primers with dna
seal nicks in dna

In prokaryotes, the two daughter molecules (each a double strand) produced at the end of replication are intertwined, similar to two links in a chain. What is the name of the enzyme that unlinks the two daughter DNA molecules?

Gyrase

On this strand, the removal of the last primer leaves a gap that cannot be primed at the ends of the chromosome.

lagging

Which of the following are short repeats of DNA on the ends of eukaryotic chromosomes?

Telomeres

The enzyme _______, contains a small internal piece of RNA, which is used as a template to extend the end of a linear DNA

telomerase

The problems in replicating the ends of linear chromosomes are caused by Blank______.

the directionality of polymerases
the need for a primer

Telomerase uses what as a template?

A short internal RNA

Because they must be able to continue to divide, the level of telomerase stays high in Blank______, despite their age.

lymphocytes

If normal fibroblast cells are grown in cell culture and the enzyme telomerase is introduced in them, Blank______.

the cells show an increased lifespan

Agents that cause mutation are known as Blank______.

mutagens

The amount of the enzyme________ declines within cells as they age, resulting in a gradual shortening of the ends of chromosomes.

telomerase

DNA repair mechanisms have likely evolved because Blank______.

there is no way for cells to avoid exposure to mutagens

Damage caused by UV light leading to thymine dimers is corrected during photorepair by the enzyme Blank______.

photolyase

Cancer cells typically contain Blank______.

higher levels of telomerase than normal, non-cancer cells

Which of the following facilitates the reversal of damage to our hereditary material before a permanent mutation can occur?

DNA repair systems

What is a thymine dimer?

A site where two adjacent thymine bases become covalently cross-linked to each other

The enzyme _____ can repair UV damage by binding to a thymine dimer and cleaving it, therefore restoring two thymines. To repair DNA, the enzyme uses energy from ______ light.

photolyase, visible